Exposing Coverage Data to the Semantic Web within the MELODIES project: Challenges and Solutions

NASA Astrophysics Data System (ADS)

Riechert, Maik; Blower, Jon; Griffiths, Guy

2016-04-01

Coverage data, typically big in data volume, assigns values to a given set of spatiotemporal positions, together with metadata on how to interpret those values. Existing storage formats like netCDF, HDF and GeoTIFF all have various restrictions that prevent them from being preferred formats for use over the web, especially the semantic web. Factors that are relevant here are the processing complexity, the semantic richness of the metadata, and the ability to request partial information, such as a subset or just the appropriate metadata. Making coverage data available within web browsers opens the door to new ways for working with such data, including new types of visualization and on-the-fly processing. As part of the European project MELODIES (http://melodiesproject.eu) we look into the challenges of exposing such coverage data in an interoperable and web-friendly way, and propose solutions using a host of emerging technologies like JSON-LD, the DCAT and GeoDCAT-AP ontologies, the CoverageJSON format, and new approaches to REST APIs for coverage data. We developed the CoverageJSON format within the MELODIES project as an additional way to expose coverage data to the web, next to having simple rendered images available using standards like OGC's WMS. CoverageJSON partially incorporates JSON-LD but does not encode individual data values as semantic resources, making use of the technology in a practical manner. The development also focused on it being a potential output format for OGC WCS. We will demonstrate how existing netCDF data can be exposed as CoverageJSON resources on the web together with a REST API that allows users to explore the data and run operations such as spatiotemporal subsetting. We will show various use cases from the MELODIES project, including reclassification of a Land Cover dataset client-side within the browser with the ability for the user to influence the reclassification result by making use of the above technologies.

Data Publishing and Sharing Via the THREDDS Data Repository

NASA Astrophysics Data System (ADS)

Wilson, A.; Caron, J.; Davis, E.; Baltzer, T.

2007-12-01

The terms "Team Science" and "Networked Science" have been coined to describe a virtual organization of researchers tied via some intellectual challenge, but often located in different organizations and locations. A critical component to these endeavors is publishing and sharing of content, including scientific data. Imagine pointing your web browser to a web page that interactively lets you upload data and metadata to a repository residing on a remote server, which can then be accessed by others in a secure fasion via the web. While any content can be added to this repository, it is designed particularly for storing and sharing scientific data and metadata. Server support includes uploading of data files that can subsequently be subsetted, aggregrated, and served in NetCDF or other scientific data formats. Metadata can be associated with the data and interactively edited. The THREDDS Data Repository (TDR) is a server that provides client initiated, on demand, location transparent storage for data of any type that can then be served by the THREDDS Data Server (TDS). The TDR provides functionality to: * securely store and "own" data files and associated metadata * upload files via HTTP and gridftp * upload a collection of data as single file * modify and restructure repository contents * incorporate metadata provided by the user * generate additional metadata programmatically * edit individual metadata elements The TDR can exist separately from a TDS, serving content via HTTP. Also, it can work in conjunction with the TDS, which includes functionality to provide: * access to data in a variety of formats via -- OPeNDAP -- OGC Web Coverage Service (for gridded datasets) -- bulk HTTP file transfer * a NetCDF view of datasets in NetCDF, OPeNDAP, HDF-5, GRIB, and NEXRAD formats * serving of very large volume datasets, such as NEXRAD radar * aggregation into virtual datasets * subsetting via OPeNDAP and NetCDF Subsetting services This talk will discuss TDR/TDS capabilities as well as how users can install this software to create their own repositories.

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

PubMed

Hancock, David; Wilson, Michael; Velarde, Giles; Morrison, Norman; Hayes, Andrew; Hulme, Helen; Wood, A Joseph; Nashar, Karim; Kell, Douglas B; Brass, Andy

2005-11-03

maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

Assessing Metadata Quality of a Federally Sponsored Health Data Repository.

PubMed

Marc, David T; Beattie, James; Herasevich, Vitaly; Gatewood, Laël; Zhang, Rui

2016-01-01

The U.S. Federal Government developed HealthData.gov to disseminate healthcare datasets to the public. Metadata is provided for each datasets and is the sole source of information to find and retrieve data. This study employed automated quality assessments of the HealthData.gov metadata published from 2012 to 2014 to measure completeness, accuracy, and consistency of applying standards. The results demonstrated that metadata published in earlier years had lower completeness, accuracy, and consistency. Also, metadata that underwent modifications following their original creation were of higher quality. HealthData.gov did not uniformly apply Dublin Core Metadata Initiative to the metadata, which is a widely accepted metadata standard. These findings suggested that the HealthData.gov metadata suffered from quality issues, particularly related to information that wasn't frequently updated. The results supported the need for policies to standardize metadata and contributed to the development of automated measures of metadata quality.

Assessing Metadata Quality of a Federally Sponsored Health Data Repository

PubMed Central

Marc, David T.; Beattie, James; Herasevich, Vitaly; Gatewood, Laël; Zhang, Rui

2016-01-01

The U.S. Federal Government developed HealthData.gov to disseminate healthcare datasets to the public. Metadata is provided for each datasets and is the sole source of information to find and retrieve data. This study employed automated quality assessments of the HealthData.gov metadata published from 2012 to 2014 to measure completeness, accuracy, and consistency of applying standards. The results demonstrated that metadata published in earlier years had lower completeness, accuracy, and consistency. Also, metadata that underwent modifications following their original creation were of higher quality. HealthData.gov did not uniformly apply Dublin Core Metadata Initiative to the metadata, which is a widely accepted metadata standard. These findings suggested that the HealthData.gov metadata suffered from quality issues, particularly related to information that wasn’t frequently updated. The results supported the need for policies to standardize metadata and contributed to the development of automated measures of metadata quality. PMID:28269883

Archive of Boomer and Chirp Seismic Reflection Data Collected During USGS Cruise 01RCE02, Southern Louisiana, April and May 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.

2003-01-01

In April and May of 2001, the U.S. Geological Survey conducted a geophysical study of the Mississippi River Delta, Atchafalaya River Delta, and Shell Island Pass in southern Louisiana. This study was part of a larger USGS River Contaminant Evaluation (RCE) Project. This disc serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, shotpoint navigation maps, observers' logbooks, GIS information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a filtered and gained digital GIF-formatted image of each seismic profile is provided. For your convenience, a list of acronyms and abbreviations frequently used in this report has also been provided. This DVD (Digital Versatile Disc) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information by using a web browser (i.e. Netscape or Internet Explorer). To access the information contained on this disc, open the file 'index.htm' located at the top level of the disc using your web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the internet is available while viewing the DVD. The archived boomer and chirp seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes. Examples of SU processing scripts are provided in the boom.tar and chirp.tar files located in the SU subfolder of the SOFTWARE folder located at the top level of this DVD. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zilhman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, shotpoint navigation maps, logbooks, and formal metadata may be viewed with your web browser.

Introducing a Web API for Dataset Submission into a NASA Earth Science Data Center

NASA Astrophysics Data System (ADS)

Moroni, D. F.; Quach, N.; Francis-Curley, W.

2016-12-01

As the landscape of data becomes increasingly more diverse in the domain of Earth Science, the challenges of managing and preserving data become more onerous and complex, particularly for data centers on fixed budgets and limited staff. Many solutions already exist to ease the cost burden for the downstream component of the data lifecycle, yet most archive centers are still racing to keep up with the influx of new data that still needs to find a quasi-permanent resting place. For instance, having well-defined metadata that is consistent across the entire data landscape provides for well-managed and preserved datasets throughout the latter end of the data lifecycle. Translators between different metadata dialects are already in operational use, and facilitate keeping older datasets relevant in today's world of rapidly evolving metadata standards. However, very little is done to address the first phase of the lifecycle, which deals with the entry of both data and the corresponding metadata into a system that is traditionally opaque and closed off to external data producers, thus resulting in a significant bottleneck to the dataset submission process. The ATRAC system was the NOAA NCEI's answer to this previously obfuscated barrier to scientists wishing to find a home for their climate data records, providing a web-based entry point to submit timely and accurate metadata and information about a very specific dataset. A couple of NASA's Distributed Active Archive Centers (DAACs) have implemented their own versions of a web-based dataset and metadata submission form including the ASDC and the ORNL DAAC. The Physical Oceanography DAAC is the most recent in the list of NASA-operated DAACs who have begun to offer their own web-based dataset and metadata submission services to data producers. What makes the PO.DAAC dataset and metadata submission service stand out from these pre-existing services is the option of utilizing both a web browser GUI and a RESTful API to facilitate rapid and efficient updating of dataset metadata records by external data producers. Here we present this new service and demonstrate the variety of ways in which a multitude of Earth Science datasets may be submitted in a manner that significantly reduces the time in ensuring that new, vital data reaches the public domain.

Enhanced Management of and Access to Hurricane Sandy Ocean and Coastal Mapping Data

NASA Astrophysics Data System (ADS)

Eakins, B.; Neufeld, D.; Varner, J. D.; McLean, S. J.

2014-12-01

NOAA's National Geophysical Data Center (NGDC) has significantly improved the discovery and delivery of its geophysical data holdings, initially targeting ocean and coastal mapping (OCM) data in the U.S. coastal region impacted by Hurricane Sandy in 2012. We have developed a browser-based, interactive interface that permits users to refine their initial map-driven data-type choices prior to bulk download (e.g., by selecting individual surveys), including the ability to choose ancillary files, such as reports or derived products. Initial OCM data types now available in a U.S. East Coast map viewer, as well as underlying web services, include: NOS hydrographic soundings and multibeam sonar bathymetry. Future releases will include trackline geophysics, airborne topographic and bathymetric-topographic lidar, bottom sample descriptions, and digital elevation models.This effort also includes working collaboratively with other NOAA offices and partners to develop automated methods to receive and verify data, stage data for archive, and notify data providers when ingest and archive are completed. We have also developed improved metadata tools to parse XML and auto-populate OCM data catalogs, support the web-based creation and editing of ISO-compliant metadata records, and register metadata in appropriate data portals. This effort supports a variety of NOAA mission requirements, from safe navigation to coastal flood forecasting and habitat characterization.

CruiseViewer: SIOExplorer Graphical Interface to Metadata and Archives.

NASA Astrophysics Data System (ADS)

Sutton, D. W.; Helly, J. J.; Miller, S. P.; Chase, A.; Clark, D.

2002-12-01

We are introducing "CruiseViewer" as a prototype graphical interface for the SIOExplorer digital library project, part of the overall NSF National Science Digital Library (NSDL) effort. When complete, CruiseViewer will provide access to nearly 800 cruises, as well as 100 years of documents and images from the archives of the Scripps Institution of Oceanography (SIO). The project emphasizes data object accessibility, a rich metadata format, efficient uploading methods and interoperability with other digital libraries. The primary function of CruiseViewer is to provide a human interface to the metadata database and to storage systems filled with archival data. The system schema is based on the concept of an "arbitrary digital object" (ADO). Arbitrary in that if the object can be stored on a computer system then SIOExplore can manage it. Common examples are a multibeam swath bathymetry file, a .pdf cruise report, or a tar file containing all the processing scripts used on a cruise. We require a metadata file for every ADO in an ascii "metadata interchange format" (MIF), which has proven to be highly useful for operability and extensibility. Bulk ADO storage is managed using the Storage Resource Broker, SRB, data handling middleware developed at the San Diego Supercomputer Center that centralizes management and access to distributed storage devices. MIF metadata are harvested from several sources and housed in a relational (Oracle) database. For CruiseViewer, cgi scripts resident on an Apache server are the primary communication and service request handling tools. Along with the CruiseViewer java application, users can query, access and download objects via a separate method that operates through standard web browsers, http://sioexplorer.ucsd.edu. Both provide the functionability to query and view object metadata, and select and download ADOs. For the CruiseViewer application Java 2D is used to add a geo-referencing feature that allows users to select basemap images and have vector shapes representing query results mapped over the basemap in the image panel. The two methods together address a wide range of user access needs and will allow for widespread use of SIOExplorer.

Archive of digital boomer seismic reflection data collected during USGS cruises 94GFP01, 95GFP01, 96GFP01, 97GFP01, and 98GFP02 in Lakes Pontchartrain, Borgne, and Maurepas, Louisiana, 1994-1998

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Williams, S. Jeffress; Flocks, James G.; Penland, Shea; Wiese, Dana S.

2003-01-01

The U.S. Geological Survey, in cooperation with the University of New Orleans, the Lake Pontchartrain Basin Foundation, the National Oceanic and Atmospheric Administration, the Coalition to Restore Coastal Louisiana, the U.S. Army Corps of Engineers, the Environmental Protection Agency, and the University of Georgia, conducted five geophysical surveys of Lakes Pontchartrain, Borgne, and Maurepas in Louisiana from 1994 to 1998. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, observers' logbooks, GIS information, and formal FGDC metadata. In addition, a filtered and gained digital GIF image of each seismic profile is provided. Refer to the Acronyms page for expansion of acronyms and abbreviations used in this report. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y headers (Zihlman, 1992) are also provided. Processed profile images, trackline maps, navigation files, and formal metadata may be viewed with a web browser, and scanned handwritten logbooks may be viewed with Adobe Reader. To access the information contained on these discs, open the file 'index.htm' located at the top level of the discs using a web browser. This report also contains hyperlinks to USGS collaborators and other agencies. These links are only accessible if access to the Internet is available while viewing these documents.

Lightweight Advertising and Scalable Discovery of Services, Datasets, and Events Using Feedcasts

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Ramachandran, R.; Movva, S.

2010-12-01

Broadcast feeds (Atom or RSS) are a mechanism for advertising the existence of new data objects on the web, with metadata and links to further information. Users then subscribe to the feed to receive updates. This concept has already been used to advertise the new granules of science data as they are produced (datacasting), with browse images and metadata, and to advertise bundles of web services (service casting). Structured metadata is introduced into the XML feed format by embedding new XML tags (in defined namespaces), using typed links, and reusing built-in Atom feed elements. This “infocasting” concept can be extended to include many other science artifacts, including data collections, workflow documents, topical geophysical events (hurricanes, forest fires, etc.), natural hazard warnings, and short articles describing a new science result. The common theme is that each infocast contains machine-readable, structured metadata describing the object and enabling further manipulation. For example, service casts contain type links pointing to the service interface description (e.g., WSDL for SOAP services), service endpoint, and human-readable documentation. Our Infocasting project has three main goals: (1) define and evangelize micro-formats (metadata standards) so that providers can easily advertise their web services, datasets, and topical geophysical events by adding structured information to broadcast feeds; (2) develop authoring tools so that anyone can easily author such service advertisements, data casts, and event descriptions; and (3) provide a one-stop, Google-like search box in the browser that allows discovery of service, data and event casts visible on the web, and services & data registered in the GEOSS repository and other NASA repositories (GCMD & ECHO). To demonstrate the event casting idea, a series of micro-articles—with accompanying event casts containing links to relevant datasets, web services, and science analysis workflows--will be authored for several kinds of geophysical events, such as hurricanes, smoke plume events, tsunamis, etc. The talk will describe our progress so far, and some of the issues with leveraging existing metadata standards to define lightweight micro-formats.

Oceans 2.0: a Data Management Infrastructure as a Platform

NASA Astrophysics Data System (ADS)

Pirenne, B.; Guillemot, E.

2012-04-01

Oceans 2.0: a Data Management Infrastructure as a Platform Benoît Pirenne, Associate Director, IT, NEPTUNE Canada Eric Guillemot, Manager, Software Development, NEPTUNE Canada The Data Management and Archiving System (DMAS) serving the needs of a number of undersea observing networks such as VENUS and NEPTUNE Canada was conceived from the beginning as a Service-Oriented Infrastructure. Its core functional elements (data acquisition, transport, archiving, retrieval and processing) can interact with the outside world using Web Services. Those Web Services can be exploited by a variety of higher level applications. Over the years, DMAS has developed Oceans 2.0: an environment where these techniques are implemented. The environment thereby becomes a platform in that it allows for easy addition of new and advanced features that build upon the tools at the core of the system. The applications that have been developed include: data search and retrieval, including options such as data product generation, data decimation or averaging, etc. dynamic infrastructure description (search all observatory metadata) and visualization data visualization, including dynamic scalar data plots, integrated fast video segment search and viewing Building upon these basic applications are new concepts, coming from the Web 2.0 world that DMAS has added: They allow people equipped only with a web browser to collaborate and contribute their findings or work results to the wider community. Examples include: addition of metadata tags to any part of the infrastructure or to any data item (annotations) ability to edit and execute, share and distribute Matlab code on-line, from a simple web browser, with specific calls within the code to access data ability to interactively and graphically build pipeline processing jobs that can be executed on the cloud web-based, interactive instrument control tools that allow users to truly share the use of the instruments and communicate with each other and last but not least: a public tool in the form of a game, that crowd-sources the inventory of the underwater video archive content, thereby adding tremendous amounts of metadata Beyond those tools that represent the functionality presently available to users, a number of the Web Services dedicated to data access are being exposed for anyone to use. This allows not only for ad hoc data access by individuals who need non-interactive access, but will foster the development of new applications in a variety of areas.

A Model for the Creation of Human-Generated Metadata within Communities

ERIC Educational Resources Information Center

Brasher, Andrew; McAndrew, Patrick

2005-01-01

This paper considers situations for which detailed metadata descriptions of learning resources are necessary, and focuses on human generation of such metadata. It describes a model which facilitates human production of good quality metadata by the development and use of structured vocabularies. Using examples, this model is applied to single and…

South Platte Data Browser

EPA Science Inventory

The common goal among the developers of the South Platte River Basin Data Browser is to improve decision-making relative to environmental management through the development of applied research. The focus of the research has been to design an integrated system of landscape metri...

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

PubMed

Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, Avi

2015-09-15

Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills. Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO. GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/. avi.maayan@mssm.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multi-facetted Metadata - Describing datasets with different metadata schemas at the same time

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Klump, Jens; Bertelmann, Roland

2013-04-01

Inspired by the wish to re-use research data a lot of work is done to bring data systems of the earth sciences together. Discovery metadata is disseminated to data portals to allow building of customized indexes of catalogued dataset items. Data that were once acquired in the context of a scientific project are open for reappraisal and can now be used by scientists that were not part of the original research team. To make data re-use easier, measurement methods and measurement parameters must be documented in an application metadata schema and described in a written publication. Linking datasets to publications - as DataCite [1] does - requires again a specific metadata schema and every new use context of the measured data may require yet another metadata schema sharing only a subset of information with the meta information already present. To cope with the problem of metadata schema diversity in our common data repository at GFZ Potsdam we established a solution to store file-based research data and describe these with an arbitrary number of metadata schemas. Core component of the data repository is an eSciDoc infrastructure that provides versioned container objects, called eSciDoc [2] "items". The eSciDoc content model allows assigning files to "items" and adding any number of metadata records to these "items". The eSciDoc items can be submitted, revised, and finally published, which makes the data and metadata available through the internet worldwide. GFZ Potsdam uses eSciDoc to support its scientific publishing workflow, including mechanisms for data review in peer review processes by providing temporary web links for external reviewers that do not have credentials to access the data. Based on the eSciDoc API, panMetaDocs [3] provides a web portal for data management in research projects. PanMetaDocs, which is based on panMetaWorks [4], is a PHP based web application that allows to describe data with any XML-based schema. It uses the eSciDoc infrastructures REST-interface to store versioned dataset files and metadata in a XML-format. The software is able to administrate more than one eSciDoc metadata record per item and thus allows the description of a dataset according to its context. The metadata fields can be filled with static or dynamic content to reduce the number of fields that require manual entries to a minimum and, at the same time, make use of contextual information available in a project setting. Access rights can be adjusted to set visibility of datasets to the required degree of openness. Metadata from separate instances of panMetaDocs can be syndicated to portals through RSS and OAI-PMH interfaces. The application architecture presented here allows storing file-based datasets and describe these datasets with any number of metadata schemas, depending on the intended use case. Data and metadata are stored in the same entity (eSciDoc items) and are managed by a software tool through the eSciDoc REST interface - in this case the application is panMetaDocs. Other software may re-use the produced items and modify the appropriate metadata records by accessing the web API of the eSciDoc data infrastructure. For presentation of the datasets in a web browser we are not bound to panMetaDocs. This is done by stylesheet transformation of the eSciDoc-item. [1] http://www.datacite.org [2] http://www.escidoc.org , eSciDoc, FIZ Karlruhe, Germany [3] http://panmetadocs.sf.net , panMetaDocs, GFZ Potsdam, Germany [4] http://metaworks.pangaea.de , panMetaWorks, Dr. R. Huber, MARUM, Univ. Bremen, Germany

openBEB: open biological experiment browser for correlative measurements

PubMed Central

2014-01-01

Background New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput approaches. The measurement of several correlative physical properties would further improve data consistency. Accordingly, a considerable quantity of data must be acquired, correlated, catalogued and stored in a database for subsequent analysis. Results We have developed openBEB (open Biological Experiment Browser), a software framework for data acquisition, coordination, annotation and synchronization with database solutions such as openBIS. OpenBEB consists of two main parts: A core program and a plug-in manager. Whereas the data-type independent core of openBEB maintains a local container of raw-data and metadata and provides annotation and data management tools, all data-specific tasks are performed by plug-ins. The open architecture of openBEB enables the fast integration of plug-ins, e.g., for data acquisition or visualization. A macro-interpreter allows the automation and coordination of the different modules. An update and deployment mechanism keeps the core program, the plug-ins and the metadata definition files in sync with a central repository. Conclusions The versatility, the simple deployment and update mechanism, and the scalability in terms of module integration offered by openBEB make this software interesting for a large scientific community. OpenBEB targets three types of researcher, ideally working closely together: (i) Engineers and scientists developing new methods and instruments, e.g., for systems-biology, (ii) scientists performing biological experiments, (iii) theoreticians and mathematicians analyzing data. The design of openBEB enables the rapid development of plug-ins, which will inherently benefit from the “house keeping” abilities of the core program. We report the use of openBEB to combine live cell microscopy, microfluidic control and visual proteomics. In this example, measurements from diverse complementary techniques are combined and correlated. PMID:24666611

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

Archive of digital Boomer seismic reflection data collected during USGS Cruises 94CCT01 and 95CCT01, eastern Texas and western Louisiana, 1994 and 1995

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Flocks, James G.; Morton, Robert A.; Wiese, Dana S.

2004-01-01

In June of 1994 and August and September of 1995, the U.S. Geological Survey, in cooperation with the University of Texas Bureau of Economic Geology, conducted geophysical surveys of the Sabine and Calcasieu Lake areas and the Gulf of Mexico offshore eastern Texas and western Louisiana. This report serves as an archive of unprocessed digital boomer seismic reflection data, trackline maps, navigation files, observers' logbooks, GIS information, and formal FGDC metadata. In addition, a filtered and gained GIF image of each seismic profile is provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and others, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y files (Zihlman, 1992) are also provided. Processed profile images, trackline maps, navigation files, and formal metadata may be viewed with a web browser. Scanned handwritten logbooks and Field Activity Collection System (FACS) logs may be viewed with Adobe Reader.

Archive of digital Boomer and Chirp seismic reflection data collected during USGS Cruises 01RCE05 and 02RCE01 in the Lower Atchafalaya River, Mississippi River Delta, and offshore southeastern Louisiana, October 23-30, 2001, and August 18-19, 2002

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Flocks, James G.; Ferina, Nicholas F.; Wiese, Dana S.

2004-01-01

In October of 2001 and August of 2002, the U.S. Geological Survey conducted geophysical surveys of the Lower Atchafalaya River, the Mississippi River Delta, Barataria Bay, and the Gulf of Mexico south of East Timbalier Island, Louisiana. This report serves as an archive of unprocessed digital marine seismic reflection data, trackline maps, navigation files, observers' logbooks, GIS information, and formal FGDC metadata. In addition, a filtered and gained GIF image of each seismic profile is provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry and othes, 1975) and may be downloaded and processed with commercial or public domain software such as Seismic Unix (SU). Examples of SU processing scripts and in-house (USGS) software for viewing SEG-Y files (Zihlman, 1992) are also provided. Processed profile images, trackline maps, navigation files, and formal metadata may be viewed with a web browser. Scanned handwritten logbooks and Field Activity Collection System (FACS) logs may be viewed with Adobe Reader.

Archive of Boomer Seismic Reflection Data Collected During USGS Cruises 01SCC01 and 01SCC02, Timbalier Bay and Offshore East Timbalier Island, Louisiana, June-August, 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Kindinger, Jack G.; Wiese, Dana S.

2003-01-01

In June, July, and August of 2001, the U.S. Geological Survey (USGS), in cooperation with the University of New Orleans (UNO), the U.S. Army Corps of Engineers, and the Louisiana Department of Natural Resources, conducted a shallow geophysical and sediment core survey of Timbalier Bay and the Gulf of Mexico offshore East Timbalier Island, Louisiana. This report serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, trackline navigation maps, observers' logbooks, Geographic Information Systems (GIS) information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a filtered and gained digital Graphics Interchange Format (GIF) image of each seismic profile is provided. Please see Kulp and others (2002), Flocks and others (2003), and Kulp and others (in prep.) for further information about the sediment cores collected and the geophysical results. For convenience, a list of acronyms and abbreviations frequently used in this report is also included. This Digital Versatile Disc (DVD) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information using a web browser (i.e. Netscape, Internet Explorer). To access the information contained on this disc, open the file 'index.htm' located at the top level of the disc using a web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the Internet is available while viewing this DVD. The archived boomer seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes/index.html. Examples of SU processing scripts are provided in the BOOM.tar file located in the SU subfolder of the SOFTWARE folder located at the top level of this disc. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zihlman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, trackline navigation maps, logbooks, and formal metadata may be viewed with a web browser.

Archive of Chirp Seismic Reflection Data Collected During USGS Cruises 01SCC01 and 01SCC02, Timbalier Bay and Offshore East Timbalier Island, Louisiana, June 30 - July 9 and August 1 - 12, 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.; Kindinger, Jack G.

2003-01-01

In June, July, and August of 2001, the U.S. Geological Survey (USGS), in cooperation with the University of New Orleans, the U.S. Army Corps of Engineers, and the Louisiana Department of Natural Resources, conducted a shallow geophysical and sediment core survey of Timbalier Bay and the Gulf of Mexico offshore East Timbalier Island, Louisiana. This report serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, trackline navigation maps, observers' logbooks, Geographic Information Systems (GIS) information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a gained digital Graphics Interchange Format (GIF) image of each seismic profile is provided. Please see Kulp and others (2002), Flocks and others (2003), and Kulp and others (in prep.) for further information about the sediment cores collected and the geophysical results. For convenience, a list of acronyms and abbreviations frequently used in this report is also included. This Digital Versatile Disc (DVD) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information using a web browser (i.e. Netscape, Internet Explorer). To access the information contained on these discs, open the file 'index.htm' located at the top level of each disc using a web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the internet is available while viewing these DVDs. The archived chirp seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes/index.html. Examples of SU processing scripts are provided in the CHIRP.tar file located in the SU subfolder of the SOFTWARE folder located at the top level of each disc. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zihlman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, trackline navigation maps, logbooks, and formal metadata may be viewed with a web browser.

A Metadata Management Framework for Collaborative Review of Science Data Products

NASA Astrophysics Data System (ADS)

Hart, A. F.; Cinquini, L.; Mattmann, C. A.; Thompson, D. R.; Wagstaff, K.; Zimdars, P. A.; Jones, D. L.; Lazio, J.; Preston, R. A.

2012-12-01

Data volumes generated by modern scientific instruments often preclude archiving the complete observational record. To compensate, science teams have developed a variety of "triage" techniques for identifying data of potential scientific interest and marking it for prioritized processing or permanent storage. This may involve multiple stages of filtering with both automated and manual components operating at different timescales. A promising approach exploits a fast, fully automated first stage followed by a more reliable offline manual review of candidate events. This hybrid approach permits a 24-hour rapid real-time response while also preserving the high accuracy of manual review. To support this type of second-level validation effort, we have developed a metadata-driven framework for the collaborative review of candidate data products. The framework consists of a metadata processing pipeline and a browser-based user interface that together provide a configurable mechanism for reviewing data products via the web, and capturing the full stack of associated metadata in a robust, searchable archive. Our system heavily leverages software from the Apache Object Oriented Data Technology (OODT) project, an open source data integration framework that facilitates the construction of scalable data systems and places a heavy emphasis on the utilization of metadata to coordinate processing activities. OODT provides a suite of core data management components for file management and metadata cataloging that form the foundation for this effort. The system has been deployed at JPL in support of the V-FASTR experiment [1], a software-based radio transient detection experiment that operates commensally at the Very Long Baseline Array (VLBA), and has a science team that is geographically distributed across several countries. Daily review of automatically flagged data is a shared responsibility for the team, and is essential to keep the project within its resource constraints. We describe the development of the platform using open source software, and discuss our experience deploying the system operationally. [1] R.B.Wayth,W.F.Brisken,A.T.Deller,W.A.Majid,D.R.Thompson, S. J. Tingay, and K. L. Wagstaff, "V-fastr: The vlba fast radio transients experiment," The Astrophysical Journal, vol. 735, no. 2, p. 97, 2011. Acknowledgement: This effort was supported by the Jet Propulsion Laboratory, managed by the California Institute of Technology under a contract with the National Aeronautics and Space Administration.

Integrating Ideas for International Data Collaborations Through The Committee on Earth Observation Satellites (CEOS) International Directory Network (IDN)

NASA Technical Reports Server (NTRS)

Olsen, Lola M.

2006-01-01

The capabilities of the International Directory Network's (IDN) version MD9.5, along with a new version of the metadata authoring tool, "docBUILDER", will be presented during the Technology and Services Subgroup session of the Working Group on Information Systems and Services (WGISS). Feedback provided through the international community has proven instrumental in positively influencing the direction of the IDN s development. The international community was instrumental in encouraging support for using the IS0 international character set that is now available through the directory. Supporting metadata descriptions in additional languages encourages extended use of the IDN. Temporal and spatial attributes often prove pivotal in the search for data. Prior to the new software release, the IDN s geospatial and temporal searches suffered from browser incompatibilities and often resulted in unreliable performance for users attempting to initiate a spatial search using a map based on aging Java applet technology. The IDN now offers an integrated Google map and date search that replaces that technology. In addition, one of the most defining characteristics in the search for data relates to the temporal and spatial resolution of the data. The ability to refine the search for data sets meeting defined resolution requirements is now possible. Data set authors are encouraged to indicate the precise resolution values for their data sets and subsequently bin these into one of the pre-selected resolution ranges. New metadata authoring tools have been well received. In response to requests for a standalone metadata authoring tool, a new shareable software package called "docBUILDER solo" will soon be released to the public. This tool permits researchers to document their data during experiments and observational periods in the field. interoperability has been enhanced through the use of the Open Archives Initiative s (OAI) Protocol for Metadata Harvesting (PMH). Harvesting of XML content through OAI-MPH has been successfully tested with several organizations. The protocol appears to be a prime candidate for sharing metadata throughout the international community. Data services for visualizing and analyzing data have become valuable assets in facilitating the use of data. Data providers are offering many of their data-related services through the directory. The IDN plans to develop a service-based architecture to further promote the use of web services. During the IDN Task Team session, ideas for further enhancements will be discussed.

Semantic Networks and Social Networks

ERIC Educational Resources Information Center

Downes, Stephen

2005-01-01

Purpose: To illustrate the need for social network metadata within semantic metadata. Design/methodology/approach: Surveys properties of social networks and the semantic web, suggests that social network analysis applies to semantic content, argues that semantic content is more searchable if social network metadata is merged with semantic web…

samiDB: A Prototype Data Archive for Big Science Exploration

NASA Astrophysics Data System (ADS)

Konstantopoulos, I. S.; Green, A. W.; Cortese, L.; Foster, C.; Scott, N.

2015-04-01

samiDB is an archive, database, and query engine to serve the spectra, spectral hypercubes, and high-level science products that make up the SAMI Galaxy Survey. Based on the versatile Hierarchical Data Format (HDF5), samiDB does not depend on relational database structures and hence lightens the setup and maintenance load imposed on science teams by metadata tables. The code, written in Python, covers the ingestion, querying, and exporting of data as well as the automatic setup of an HTML schema browser. samiDB serves as a maintenance-light data archive for Big Science and can be adopted and adapted by science teams that lack the means to hire professional archivists to set up the data back end for their projects.

PanMetaDocs - A tool for collecting and managing the long tail of "small science data"

NASA Astrophysics Data System (ADS)

Klump, J.; Ulbricht, D.

2011-12-01

In the early days of thinking about cyberinfrastructure the focus was on "big science data". Today, the challenge is not anymore to store several terabytes of data, but to manage data objects in a way that facilitates their re-use. Key to re-use by a user as a data consumer is proper documentation of the data. Also, data consumers need discovery metadata to find the data they need and they need descriptive metadata to be able to use the data they retrieved. Thus, data documentation faces the challenge to extensively and completely describe these objects, hold the items easily accessible at a sustainable cost level. However, data curation and documentation do not rank high in the everyday work of a scientist as a data producer. Data producers are often frustrated by being asked to provide metadata on their data over and over again, information that seemed very obvious from the context of their work. A challenge to data archives is the wide variety of metadata schemata in use, which creates a number of maintenance and design challenges of its own. PanMetaDocs addresses these issues by allowing an uploaded files to be described by more than one metadata object. PanMetaDocs, which was developed from PanMetaWorks, is a PHP based web application that allow to describe data with any xml-based metadata schema. Its user interface is browser based and was developed to collect metadata and data in collaborative scientific projects situated at one or more institutions. The metadata fields can be filled with static or dynamic content to reduce the number of fields that require manual entries to a minimum and make use of contextual information in a project setting. In the development of PanMetaDocs the business logic of panMetaWorks is reused, except for the authentication and data management functions of PanMetaWorks, which are delegated to the eSciDoc framework. The eSciDoc repository framework is designed as a service oriented architecture that can be controlled through a REST interface to create version controlled items with metadata records in XML format. PanMetaDocs utilizes the eSciDoc items model to add multiple metadata records that describe uploaded files in different metadata schemata. While datasets are collected and described, shared to collaborate with other scientists and finally published, data objects are transferred from a shared data curation domain into a persistent data curation domain. Through an RSS interface for recent datasets PanMetaWorks allows project members to be informed about data uploaded by other project members. The implementation of the OAI-PMH interface can be used to syndicate data catalogs to research data portals, such as the panFMP data portal framework. Once data objects are uploaded to the eSciDoc infrastructure it is possible to drop the software instance that was used for collecting the data, while the compiled data and metadata are accessible for other authorized applications through the institution's eSciDoc middleware. This approach of "expendable data curation tools" allows for a significant reduction in costs for software maintenance as expensive data capture applications do not need to be maintained indefinitely to ensure long term access to the stored data.

DASMiner: discovering and integrating data from DAS sources

PubMed Central

2009-01-01

Background DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources. Results We developed DASMiner, a Matlab toolkit for querying DAS data sources that enables creation of integrated biological models using the information available in DAS-compliant repositories. DASMiner is composed by a browser application and an API that work together to facilitate gathering of data from different DAS sources, which can be used for creating enriched datasets from multiple sources. The browser is used to formulate queries and navigate data contained in DAS sources. Users can execute queries against these sources in an intuitive fashion, without the need of knowing the specific DAS syntax for the particular source. Using the source's metadata provided by the DAS Registry, the browser's layout adapts to expose only the set of commands and coordinate systems supported by the specific source. For this reason, the browser can interrogate any DAS source, independently of the type of data being served. The API component of DASMiner may be used for programmatic access of DAS sources by programs in Matlab. Once the desired data is found during navigation, the query is exported in the format of an API call to be used within any Matlab application. We illustrate the use of DASMiner by creating integrative models of histone modification maps and protein-protein interaction networks. These enriched datasets were built by retrieving and integrating distributed genomic and proteomic DAS sources using the API. Conclusion The support of the DAS protocol allows that hundreds of molecular biology databases to be treated as a federated, online collection of resources. DASMiner enables full exploration of these resources, and can be used to deploy applications and create integrated views of biological systems using the information deposited in DAS repositories. PMID:19919683

Natural Language Processing in aid of FlyBase curators

PubMed Central

Karamanis, Nikiforos; Seal, Ruth; Lewin, Ian; McQuilton, Peter; Vlachos, Andreas; Gasperin, Caroline; Drysdale, Rachel; Briscoe, Ted

2008-01-01

Background Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. Conclusion We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully. PMID:18410678

The rendering context for stereoscopic 3D web

NASA Astrophysics Data System (ADS)

Chen, Qinshui; Wang, Wenmin; Wang, Ronggang

2014-03-01

3D technologies on the Web has been studied for many years, but they are basically monoscopic 3D. With the stereoscopic technology gradually maturing, we are researching to integrate the binocular 3D technology into the Web, creating a stereoscopic 3D browser that will provide users with a brand new experience of human-computer interaction. In this paper, we propose a novel approach to apply stereoscopy technologies to the CSS3 3D Transforms. Under our model, each element can create or participate in a stereoscopic 3D rendering context, in which 3D Transforms such as scaling, translation and rotation, can be applied and be perceived in a truly 3D space. We first discuss the underlying principles of stereoscopy. After that we discuss how these principles can be applied to the Web. A stereoscopic 3D browser with backward compatibility is also created for demonstration purposes. We take advantage of the open-source WebKit project, integrating the 3D display ability into the rendering engine of the web browser. For each 3D web page, our 3D browser will create two slightly different images, each representing the left-eye view and right-eye view, both to be combined on the 3D display to generate the illusion of depth. And as the result turns out, elements can be manipulated in a truly 3D space.

Evaluating and Evolving Metadata in Multiple Dialects

NASA Astrophysics Data System (ADS)

Kozimor, J.; Habermann, T.; Powers, L. A.; Gordon, S.

2016-12-01

Despite many long-term homogenization efforts, communities continue to develop focused metadata standards along with related recommendations and (typically) XML representations (aka dialects) for sharing metadata content. Different representations easily become obstacles to sharing information because each representation generally requires a set of tools and skills that are designed, built, and maintained specifically for that representation. In contrast, community recommendations are generally described, at least initially, at a more conceptual level and are more easily shared. For example, most communities agree that dataset titles should be included in metadata records although they write the titles in different ways. This situation has led to the development of metadata repositories that can ingest and output metadata in multiple dialects. As an operational example, the NASA Common Metadata Repository (CMR) includes three different metadata dialects (DIF, ECHO, and ISO 19115-2). These systems raise a new question for metadata providers: if I have a choice of metadata dialects, which should I use and how do I make that decision? We have developed a collection of metadata evaluation tools that can be used to evaluate metadata records in many dialects for completeness with respect to recommendations from many organizations and communities. We have applied these tools to over 8000 collection and granule metadata records in four different dialects. This large collection of identical content in multiple dialects enables us to address questions about metadata and dialect evolution and to answer those questions quantitatively. We will describe those tools and results from evaluating the NASA CMR metadata collection.

Dynamic reusable workflows for ocean science

USGS Publications Warehouse

Signell, Richard; Fernandez, Filipe; Wilcox, Kyle

2016-01-01

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now possible to create catalog-driven workflows that automate — end-to-end — data search, analysis and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill-assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enters the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic notebooks across the geoscience domains.

Provenance through Time

NASA Astrophysics Data System (ADS)

Chandler, C. L.; Groman, R. C.; Shepherd, A.; Allison, M. D.; Kinkade, D.; Rauch, S.; Wiebe, P. H.; Glover, D. M.

2014-12-01

The ability to reproduce scientific results is a cornerstone of the scientific method, and access to the data upon which the results are based is essential to reproducibility. Access to the data alone is not enough though, and research communities have recognized the importance of metadata (data documentation) to enable discovery and data access, and facilitate interpretation and accurate reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was first funded in late 2006 by the National Science Foundation (NSF) Division of Ocean Sciences (OCE) Biology and Chemistry Sections to help ensure that data generated during NSF OCE funded research would be preserved and available for future use. The BCO-DMO was formed by combining the formerly independent data management offices of two marine research programs: the United States Joint Global Ocean Flux Study (US JGOFS) and the US GLOBal Ocean ECosystems Dynamics (US GLOBEC) program. Since the US JGOFS and US GLOBEC programs were both active (1990s) there have been significant changes in all aspects of the research data life cycle, and the staff at BCO-DMO has modified the way in which we manage data contributed to the office. The supporting documentation that describes each dataset was originally displayed as a human-readable text file retrievable via a Web browser. BCO-DMO still offers that form because our primary audience is marine researchers using Web browser clients; however we are seeing an increased demand to support machine client access. Metadata records from the BCO-DMO data system are now extracted and published out in a variety of formats. The system supports ISO 19115, FGDC, GCMD DIF, schema.org Dataset extension, formal publication with a DOI, and RDF with semantic markup including PROV-O, FOAF and more. In the 1990s, data documentation helped researchers locate data of interest and understand the provenance sufficiently to determine fitness for purpose. Today, providing data documentation in a machine interpretable form enables researchers to make more effective use of machine clients to discover and access data. This presentation will describe the challenges associated with and benefits realized from layering modern Semantic Web technologies on top of a legacy data system. http://bco-dmo.org/

The VIMS Data Explorer: A tool for locating and visualizing hyperspectral data

NASA Astrophysics Data System (ADS)

Pasek, V. D.; Lytle, D. M.; Brown, R. H.

2016-12-01

Since successfully entering Saturn's orbit during Summer 2004 there have been over 300,000 hyperspectral data cubes returned from the visible and infrared mapping spectrometer (VIMS) instrument onboard the Cassini spacecraft. The VIMS Science Investigation is a multidisciplinary effort that uses these hyperspectral data to study a variety of scientific problems, including surface characterizations of the icy satellites and atmospheric analyses of Titan and Saturn. Such investigations may need to identify thousands of exemplary data cubes for analysis and can span many years in scope. Here we describe the VIMS data explorer (VDE) application, currently employed by the VIMS Investigation to search for and visualize data. The VDE application facilitates real-time inspection of the entire VIMS hyperspectral dataset, the construction of in situ maps, and markers to save and recall work. The application relies on two databases to provide comprehensive search capabilities. The first database contains metadata for every cube. These metadata searches are used to identify records based on parameters such as target, observation name, or date taken; they fall short in utility for some investigations. The cube metadata contains no target geometry information. Through the introduction of a post-calibration pixel database, the VDE tool enables users to greatly expand their searching capabilities. Users can select favorable cubes for further processing into 2-D and 3-D interactive maps, aiding in the data interpretation and selection process. The VDE application enables efficient search, visualization, and access to VIMS hyperspectral data. It is simple to use, requiring nothing more than a browser for access. Hyperspectral bands can be individually selected or combined to create real-time color images, a technique commonly employed by hyperspectral researchers to highlight compositional differences.

36 CFR 1220.18 - What definitions apply to the regulations in Subchapter B?

Code of Federal Regulations, 2014 CFR

2014-07-01

... under the Federal Records Act. The term includes both record content and associated metadata that the... dissemination of information in accordance with defined procedures, whether automated or manual. Metadata...

36 CFR 1220.18 - What definitions apply to the regulations in Subchapter B?

Code of Federal Regulations, 2012 CFR

2012-07-01

... under the Federal Records Act. The term includes both record content and associated metadata that the... dissemination of information in accordance with defined procedures, whether automated or manual. Metadata...

36 CFR § 1220.18 - What definitions apply to the regulations in Subchapter B?

Code of Federal Regulations, 2013 CFR

2013-07-01

... content and associated metadata that the agency determines is required to meet agency business needs..., whether automated or manual. Metadata consists of preserved contextual information describing the history...

ISO, FGDC, DIF and Dublin Core - Making Sense of Metadata Standards for Earth Science Data

NASA Astrophysics Data System (ADS)

Jones, P. R.; Ritchey, N. A.; Peng, G.; Toner, V. A.; Brown, H.

2014-12-01

Metadata standards provide common definitions of metadata fields for information exchange across user communities. Despite the broad adoption of metadata standards for Earth science data, there are still heterogeneous and incompatible representations of information due to differences between the many standards in use and how each standard is applied. Federal agencies are required to manage and publish metadata in different metadata standards and formats for various data catalogs. In 2014, the NOAA National Climatic data Center (NCDC) managed metadata for its scientific datasets in ISO 19115-2 in XML, GCMD Directory Interchange Format (DIF) in XML, DataCite Schema in XML, Dublin Core in XML, and Data Catalog Vocabulary (DCAT) in JSON, with more standards and profiles of standards planned. Of these standards, the ISO 19115-series metadata is the most complete and feature-rich, and for this reason it is used by NCDC as the source for the other metadata standards. We will discuss the capabilities of metadata standards and how these standards are being implemented to document datasets. Successful implementations include developing translations and displays using XSLTs, creating links to related data and resources, documenting dataset lineage, and establishing best practices. Benefits, gaps, and challenges will be highlighted with suggestions for improved approaches to metadata storage and maintenance.

Interpreting the ASTM 'content standard for digital geospatial metadata'

USGS Publications Warehouse

Nebert, Douglas D.

1996-01-01

ASTM and the Federal Geographic Data Committee have developed a content standard for spatial metadata to facilitate documentation, discovery, and retrieval of digital spatial data using vendor-independent terminology. Spatial metadata elements are identifiable quality and content characteristics of a data set that can be tied to a geographic location or area. Several Office of Management and Budget Circulars and initiatives have been issued that specify improved cataloguing of and accessibility to federal data holdings. An Executive Order further requires the use of the metadata content standard to document digital spatial data sets. Collection and reporting of spatial metadata for field investigations performed for the federal government is an anticipated requirement. This paper provides an overview of the draft spatial metadata content standard and a description of how the standard could be applied to investigations collecting spatially-referenced field data.

ASDC Collaborations and Processes to Ensure Quality Metadata and Consistent Data Availability

NASA Astrophysics Data System (ADS)

Trapasso, T. J.

2017-12-01

With the introduction of new tools, faster computing, and less expensive storage, increased volumes of data are expected to be managed with existing or fewer resources. Metadata management is becoming a heightened challenge from the increase in data volume, resulting in more metadata records needed to be curated for each product. To address metadata availability and completeness, NASA ESDIS has taken significant strides with the creation of the United Metadata Model (UMM) and Common Metadata Repository (CMR). These UMM helps address hurdles experienced by the increasing number of metadata dialects and the CMR provides a primary repository for metadata so that required metadata fields can be served through a growing number of tools and services. However, metadata quality remains an issue as metadata is not always inherent to the end-user. In response to these challenges, the NASA Atmospheric Science Data Center (ASDC) created the Collaboratory for quAlity Metadata Preservation (CAMP) and defined the Product Lifecycle Process (PLP) to work congruently. CAMP is unique in that it provides science team members a UI to directly supply metadata that is complete, compliant, and accurate for their data products. This replaces back-and-forth communication that often results in misinterpreted metadata. Upon review by ASDC staff, metadata is submitted to CMR for broader distribution through Earthdata. Further, approval of science team metadata in CAMP automatically triggers the ASDC PLP workflow to ensure appropriate services are applied throughout the product lifecycle. This presentation will review the design elements of CAMP and PLP as well as demonstrate interfaces to each. It will show the benefits that CAMP and PLP provide to the ASDC that could potentially benefit additional NASA Earth Science Data and Information System (ESDIS) Distributed Active Archive Centers (DAACs).

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

PubMed

Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

2006-01-01

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

Creating Access Points to Instrument-Based Atmospheric Data: Perspectives from the ARM Metadata Manager

NASA Astrophysics Data System (ADS)

Troyan, D.

2016-12-01

The Atmospheric Radiation Measurement (ARM) program has been collecting data from instruments in diverse climate regions for nearly twenty-five years. These data are made available to all interested parties at no cost via specially designed tools found on the ARM website (www.arm.gov). Metadata is created and applied to the various datastreams to facilitate information retrieval using the ARM website, the ARM Data Discovery Tool, and data quality reporting tools. Over the last year, the Metadata Manager - a relatively new position within the ARM program - created two documents that summarize the state of ARM metadata processes: ARM Metadata Workflow, and ARM Metadata Standards. These documents serve as guides to the creation and management of ARM metadata. With many of ARM's data functions spread around the Department of Energy national laboratory complex and with many of the original architects of the metadata structure no longer working for ARM, there is increased importance on using these documents to resolve issues from data flow bottlenecks and inaccurate metadata to improving data discovery and organizing web pages. This presentation will provide some examples from the workflow and standards documents. The examples will illustrate the complexity of the ARM metadata processes and the efficiency by which the metadata team works towards achieving the goal of providing access to data collected under the auspices of the ARM program.

Establishment of Kawasaki disease database based on metadata standard.

PubMed

Park, Yu Rang; Kim, Jae-Jung; Yoon, Young Jo; Yoon, Young-Kwang; Koo, Ha Yeong; Hong, Young Mi; Jang, Gi Young; Shin, Soo-Yong; Lee, Jong-Keuk

2016-07-01

Kawasaki disease (KD) is a rare disease that occurs predominantly in infants and young children. To identify KD susceptibility genes and to develop a diagnostic test, a specific therapy, or prevention method, collecting KD patients' clinical and genomic data is one of the major issues. For this purpose, Kawasaki Disease Database (KDD) was developed based on the efforts of Korean Kawasaki Disease Genetics Consortium (KKDGC). KDD is a collection of 1292 clinical data and genomic samples of 1283 patients from 13 KKDGC-participating hospitals. Each sample contains the relevant clinical data, genomic DNA and plasma samples isolated from patients' blood, omics data and KD-associated genotype data. Clinical data was collected and saved using the common data elements based on the ISO/IEC 11179 metadata standard. Two genome-wide association study data of total 482 samples and whole exome sequencing data of 12 samples were also collected. In addition, KDD includes the rare cases of KD (16 cases with family history, 46 cases with recurrence, 119 cases with intravenous immunoglobulin non-responsiveness, and 52 cases with coronary artery aneurysm). As the first public database for KD, KDD can significantly facilitate KD studies. All data in KDD can be searchable and downloadable. KDD was implemented in PHP, MySQL and Apache, with all major browsers supported.Database URL: http://www.kawasakidisease.kr. © The Author(s) 2016. Published by Oxford University Press.

ESDORA: A Data Archive Infrastructure Using Digital Object Model and Open Source Frameworks

NASA Astrophysics Data System (ADS)

Shrestha, Biva; Pan, Jerry; Green, Jim; Palanisamy, Giriprakash; Wei, Yaxing; Lenhardt, W.; Cook, R. Bob; Wilson, B. E.; Leggott, M.

2011-12-01

There are an array of challenges associated with preserving, managing, and using contemporary scientific data. Large volume, multiple formats and data services, and the lack of a coherent mechanism for metadata/data management are some of the common issues across data centers. It is often difficult to preserve the data history and lineage information, along with other descriptive metadata, hindering the true science value for the archived data products. In this project, we use digital object abstraction architecture as the information/knowledge framework to address these challenges. We have used the following open-source frameworks: Fedora-Commons Repository, Drupal Content Management System, Islandora (Drupal Module) and Apache Solr Search Engine. The system is an active archive infrastructure for Earth Science data resources, which include ingestion, archiving, distribution, and discovery functionalities. We use an ingestion workflow to ingest the data and metadata, where many different aspects of data descriptions (including structured and non-structured metadata) are reviewed. The data and metadata are published after reviewing multiple times. They are staged during the reviewing phase. Each digital object is encoded in XML for long-term preservation of the content and relations among the digital items. The software architecture provides a flexible, modularized framework for adding pluggable user-oriented functionality. Solr is used to enable word search as well as faceted search. A home grown spatial search module is plugged in to allow user to make a spatial selection in a map view. A RDF semantic store within the Fedora-Commons Repository is used for storing information on data lineage, dissemination services, and text-based metadata. We use the semantic notion "isViewerFor" to register internally or externally referenced URLs, which are rendered within the same web browser when possible. With appropriate mapping of content into digital objects, many different data descriptions, including structured metadata, data history, auditing trails, are captured and coupled with the data content. The semantic store provides a foundation for possible further utilizations, including provide full-fledged Earth Science ontology for data interpretation or lineage tracking. Datasets from the NASA-sponsored Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) as well as from the Synthesis Thematic Data Center (MAST-DC) are used in a testing deployment with the system. The testing deployment allows us to validate the features and values described here for the integrated system, which will be presented here. Overall, we believe that the integrated system is valid, reusable data archive software that provides digital stewardship for Earth Sciences data content, now and in the future. References: [1] Devarakonda, Ranjeet, and Harold Shanafield. "Drupal: Collaborative framework for science research." Collaboration Technologies and Systems (CTS), 2011 International Conference on. IEEE, 2011. [2] Devarakonda, Ranjeet, et al. "Semantic search integration to climate data." Collaboration Technologies and Systems (CTS), 2014 International Conference on. IEEE, 2014.

A metadata template for ocean acidification data

NASA Astrophysics Data System (ADS)

Jiang, L.

2014-12-01

Metadata is structured information that describes, explains, and locates an information resource (e.g., data). It is often coarsely described as data about data, and documents information such as what was measured, by whom, when, where, and how it was sampled, analyzed, with what instruments. Metadata is inherent to ensure the survivability and accessibility of the data into the future. With the rapid expansion of biological response ocean acidification (OA) studies, the lack of a common metadata template to document such type of data has become a significant gap for ocean acidification data management efforts. In this paper, we present a metadata template that can be applied to a broad spectrum of OA studies, including those studying the biological responses of organisms on ocean acidification. The "variable metadata section", which includes the variable name, observation type, whether the variable is a manipulation condition or response variable, and the biological subject on which the variable is studied, forms the core of this metadata template. Additional metadata elements, such as principal investigators, temporal and spatial coverage, platforms for the sampling, data citation are essential components to complete the template. We explain the structure of the template, and define many metadata elements that may be unfamiliar to researchers. For that reason, this paper can serve as a user's manual for the template.

The NOAO NVO Portal

NASA Astrophysics Data System (ADS)

Miller, C. J.; Gasson, D.; Fuentes, E.

2007-10-01

The NOAO NVO Portal is a web application for one-stop discovery, analysis, and access to VO-compliant imaging data and services. The current release allows for GUI-based discovery of nearly a half million images from archives such as the NOAO Science Archive, the Hubble Space Telescope WFPC2 and ACS instruments, XMM-Newton, Chandra, and ESO's INT Wide-Field Survey, among others. The NOAO Portal allows users to view image metadata, footprint wire-frames, FITS image previews, and provides one-click access to science quality imaging data throughout the entire sky via the Firefox web browser (i.e., no applet or code to download). Users can stage images from multiple archives at the NOAO NVO Portal for quick and easy bulk downloads. The NOAO NVO Portal also provides simplified and direct access to VO analysis services, such as the WESIX catalog generation service. We highlight the features of the NOAO NVO Portal (http://nvo.noao.edu).

Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer

PubMed Central

Gutman, David A.; Dunn, William D.; Cobb, Jake; Stoner, Richard M.; Kalpathy-Cramer, Jayashree; Erickson, Bradley

2014-01-01

Advances in web technologies now allow direct visualization of imaging data sets without necessitating the download of large file sets or the installation of software. This allows centralization of file storage and facilitates image review and analysis. XNATView is a light framework recently developed in our lab to visualize DICOM images stored in The Extensible Neuroimaging Archive Toolkit (XNAT). It consists of a PyXNAT-based framework to wrap around the REST application programming interface (API) and query the data in XNAT. XNATView was developed to simplify quality assurance, help organize imaging data, and facilitate data sharing for intra- and inter-laboratory collaborations. Its zero-footprint design allows the user to connect to XNAT from a web browser, navigate through projects, experiments, and subjects, and view DICOM images with accompanying metadata all within a single viewing instance. PMID:24904399

Dynamic federations: storage aggregation using open tools and protocols

NASA Astrophysics Data System (ADS)

Furano, Fabrizio; Brito da Rocha, Ricardo; Devresse, Adrien; Keeble, Oliver; Álvarez Ayllón, Alejandro; Fuhrmann, Patrick

2012-12-01

A number of storage elements now offer standard protocol interfaces like NFS 4.1/pNFS and WebDAV, for access to their data repositories, in line with the standardization effort of the European Middleware Initiative (EMI). Also the LCG FileCatalogue (LFC) can offer such features. Here we report on work that seeks to exploit the federation potential of these protocols and build a system that offers a unique view of the storage and metadata ensemble and the possibility of integration of other compatible resources such as those from cloud providers. The challenge, here undertaken by the providers of dCache and DPM, and pragmatically open to other Grid and Cloud storage solutions, is to build such a system while being able to accommodate name translations from existing catalogues (e.g. LFCs), experiment-based metadata catalogues, or stateless algorithmic name translations, also known as “trivial file catalogues”. Such so-called storage federations of standard protocols-based storage elements give a unique view of their content, thus promoting simplicity in accessing the data they contain and offering new possibilities for resilience and data placement strategies. The goal is to consider HTTP and NFS4.1-based storage elements and metadata catalogues and make them able to cooperate through an architecture that properly feeds the redirection mechanisms that they are based upon, thus giving the functionalities of a “loosely coupled” storage federation. One of the key requirements is to use standard clients (provided by OS'es or open source distributions, e.g. Web browsers) to access an already aggregated system; this approach is quite different from aggregating the repositories at the client side through some wrapper API, like for instance GFAL, or by developing new custom clients. Other technical challenges that will determine the success of this initiative include performance, latency and scalability, and the ability to create worldwide storage federations that are able to redirect clients to repositories that they can efficiently access, for instance trying to choose the endpoints that are closer or applying other criteria. We believe that the features of a loosely coupled federation of open-protocols-based storage elements will open many possibilities of evolving the current computing models without disrupting them, and, at the same time, will be able to operate with the existing infrastructures, follow their evolution path and add storage centers that can be acquired as a third-party service.

Do Community Recommendations Improve Metadata?

NASA Astrophysics Data System (ADS)

Gordon, S.; Habermann, T.; Jones, M. B.; Leinfelder, B.; Mecum, B.; Powers, L. A.; Slaughter, P.

2016-12-01

Complete documentation of scientific data is the surest way to facilitate discovery and reuse. What is complete metadata? There are many metadata recommendations from communities like the OGC, FGDC, NASA, and LTER, that can provide data documentation guidance for discovery, access, use and understanding. Often, the recommendations that communities develop are for a particular metadata dialect. Two examples of this are the LTER Completeness recommendation for EML and the FGDC Data Discovery recommendation for CSDGM. Can community adoption of a recommendation ensure that what is included in the metadata is understandable to the scientific community and beyond? By applying quantitative analysis to different LTER and USGS metadata collections in DataOne and ScienceBase, we show that community recommendations can improve the completeness of collections over time. Additionally, by comparing communities in DataOne that use the EML and CSDGM dialects, but have not adopted the recommendations to the communities that have, the positive effects of recommendation adoption on documentation completeness can be measured.

Metadata Sets for e-Government Resources: The Extended e-Government Metadata Schema (eGMS+)

NASA Astrophysics Data System (ADS)

Charalabidis, Yannis; Lampathaki, Fenareti; Askounis, Dimitris

In the dawn of the Semantic Web era, metadata appear as a key enabler that assists management of the e-Government resources related to the provision of personalized, efficient and proactive services oriented towards the real citizens’ needs. As different authorities typically use different terms to describe their resources and publish them in various e-Government Registries that may enhance the access to and delivery of governmental knowledge, but also need to communicate seamlessly at a national and pan-European level, the need for a unified e-Government metadata standard emerges. This paper presents the creation of an ontology-based extended metadata set for e-Government Resources that embraces services, documents, XML Schemas, code lists, public bodies and information systems. Such a metadata set formalizes the exchange of information between portals and registries and assists the service transformation and simplification efforts, while it can be further taken into consideration when applying Web 2.0 techniques in e-Government.

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

PubMed

Panahiazar, Maryam; Dumontier, Michel; Gevaert, Olivier

2017-08-01

A crucial and limiting factor in data reuse is the lack of accurate, structured, and complete descriptions of data, known as metadata. Towards improving the quantity and quality of metadata, we propose a novel metadata prediction framework to learn associations from existing metadata that can be used to predict metadata values. We evaluate our framework in the context of experimental metadata from the Gene Expression Omnibus (GEO). We applied four rule mining algorithms to the most common structured metadata elements (sample type, molecular type, platform, label type and organism) from over 1.3million GEO records. We examined the quality of well supported rules from each algorithm and visualized the dependencies among metadata elements. Finally, we evaluated the performance of the algorithms in terms of accuracy, precision, recall, and F-measure. We found that PART is the best algorithm outperforming Apriori, Predictive Apriori, and Decision Table. All algorithms perform significantly better in predicting class values than the majority vote classifier. We found that the performance of the algorithms is related to the dimensionality of the GEO elements. The average performance of all algorithm increases due of the decreasing of dimensionality of the unique values of these elements (2697 platforms, 537 organisms, 454 labels, 9 molecules, and 5 types). Our work suggests that experimental metadata such as present in GEO can be accurately predicted using rule mining algorithms. Our work has implications for both prospective and retrospective augmentation of metadata quality, which are geared towards making data easier to find and reuse. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Intelligent Discovery for Learning Objects Using Semantic Web Technologies

ERIC Educational Resources Information Center

Hsu, I-Ching

2012-01-01

The concept of learning objects has been applied in the e-learning field to promote the accessibility, reusability, and interoperability of learning content. Learning Object Metadata (LOM) was developed to achieve these goals by describing learning objects in order to provide meaningful metadata. Unfortunately, the conventional LOM lacks the…

A Shared Infrastructure for Federated Search Across Distributed Scientific Metadata Catalogs

NASA Astrophysics Data System (ADS)

Reed, S. A.; Truslove, I.; Billingsley, B. W.; Grauch, A.; Harper, D.; Kovarik, J.; Lopez, L.; Liu, M.; Brandt, M.

2013-12-01

The vast amount of science metadata can be overwhelming and highly complex. Comprehensive analysis and sharing of metadata is difficult since institutions often publish to their own repositories. There are many disjoint standards used for publishing scientific data, making it difficult to discover and share information from different sources. Services that publish metadata catalogs often have different protocols, formats, and semantics. The research community is limited by the exclusivity of separate metadata catalogs and thus it is desirable to have federated search interfaces capable of unified search queries across multiple sources. Aggregation of metadata catalogs also enables users to critique metadata more rigorously. With these motivations in mind, the National Snow and Ice Data Center (NSIDC) and Advanced Cooperative Arctic Data and Information Service (ACADIS) implemented two search interfaces for the community. Both the NSIDC Search and ACADIS Arctic Data Explorer (ADE) use a common infrastructure which keeps maintenance costs low. The search clients are designed to make OpenSearch requests against Solr, an Open Source search platform. Solr applies indexes to specific fields of the metadata which in this instance optimizes queries containing keywords, spatial bounds and temporal ranges. NSIDC metadata is reused by both search interfaces but the ADE also brokers additional sources. Users can quickly find relevant metadata with minimal effort and ultimately lowers costs for research. This presentation will highlight the reuse of data and code between NSIDC and ACADIS, discuss challenges and milestones for each project, and will identify creation and use of Open Source libraries.

A System for Automated Extraction of Metadata from Scanned Documents using Layout Recognition and String Pattern Search Models.

PubMed

Misra, Dharitri; Chen, Siyuan; Thoma, George R

2009-01-01

One of the most expensive aspects of archiving digital documents is the manual acquisition of context-sensitive metadata useful for the subsequent discovery of, and access to, the archived items. For certain types of textual documents, such as journal articles, pamphlets, official government records, etc., where the metadata is contained within the body of the documents, a cost effective method is to identify and extract the metadata in an automated way, applying machine learning and string pattern search techniques.At the U. S. National Library of Medicine (NLM) we have developed an automated metadata extraction (AME) system that employs layout classification and recognition models with a metadata pattern search model for a text corpus with structured or semi-structured information. A combination of Support Vector Machine and Hidden Markov Model is used to create the layout recognition models from a training set of the corpus, following which a rule-based metadata search model is used to extract the embedded metadata by analyzing the string patterns within and surrounding each field in the recognized layouts.In this paper, we describe the design of our AME system, with focus on the metadata search model. We present the extraction results for a historic collection from the Food and Drug Administration, and outline how the system may be adapted for similar collections. Finally, we discuss some ongoing enhancements to our AME system.

Physical Samples and Persistent Identifiers: The Implementation of the International Geo Sample Number (IGSN) Registration Service in CSIRO, Australia

NASA Astrophysics Data System (ADS)

Devaraju, Anusuriya; Klump, Jens; Tey, Victor; Fraser, Ryan

2016-04-01

Physical samples such as minerals, soil, rocks, water, air and plants are important observational units for understanding the complexity of our environment and its resources. They are usually collected and curated by different entities, e.g., individual researchers, laboratories, state agencies, or museums. Persistent identifiers may facilitate access to physical samples that are scattered across various repositories. They are essential to locate samples unambiguously and to share their associated metadata and data systematically across the Web. The International Geo Sample Number (IGSN) is a persistent, globally unique label for identifying physical samples. The IGSNs of physical samples are registered by end-users (e.g., individual researchers, data centers and projects) through allocating agents. Allocating agents are the institutions acting on behalf of the implementing organization (IGSN e.V.). The Commonwealth Scientific and Industrial Research Organisation CSIRO) is one of the allocating agents in Australia. To implement IGSN in our organisation, we developed a RESTful service and a metadata model. The web service enables a client to register sub-namespaces and multiple samples, and retrieve samples' metadata programmatically. The metadata model provides a framework in which different types of samples may be represented. It is generic and extensible, therefore it may be applied in the context of multi-disciplinary projects. The metadata model has been implemented as an XML schema and a PostgreSQL database. The schema is used to handle sample registrations requests and to disseminate their metadata, whereas the relational database is used to preserve the metadata records. The metadata schema leverages existing controlled vocabularies to minimize the scope for error and incorporates some simplifications to reduce complexity of the schema implementation. The solutions developed have been applied and tested in the context of two sample repositories in CSIRO, the Capricorn Distal Footprints project and the Rock Store.

Inheritance rules for Hierarchical Metadata Based on ISO 19115

NASA Astrophysics Data System (ADS)

Zabala, A.; Masó, J.; Pons, X.

2012-04-01

Mainly, ISO19115 has been used to describe metadata for datasets and services. Furthermore, ISO19115 standard (as well as the new draft ISO19115-1) includes a conceptual model that allows to describe metadata at different levels of granularity structured in hierarchical levels, both in aggregated resources such as particularly series, datasets, and also in more disaggregated resources such as types of entities (feature type), types of attributes (attribute type), entities (feature instances) and attributes (attribute instances). In theory, to apply a complete metadata structure to all hierarchical levels of metadata, from the whole series to an individual feature attributes, is possible, but to store all metadata at all levels is completely impractical. An inheritance mechanism is needed to store each metadata and quality information at the optimum hierarchical level and to allow an ease and efficient documentation of metadata in both an Earth observation scenario such as a multi-satellite mission multiband imagery, as well as in a complex vector topographical map that includes several feature types separated in layers (e.g. administrative limits, contour lines, edification polygons, road lines, etc). Moreover, and due to the traditional split of maps in tiles due to map handling at detailed scales or due to the satellite characteristics, each of the previous thematic layers (e.g. 1:5000 roads for a country) or band (Landsat-5 TM cover of the Earth) are tiled on several parts (sheets or scenes respectively). According to hierarchy in ISO 19115, the definition of general metadata can be supplemented by spatially specific metadata that, when required, either inherits or overrides the general case (G.1.3). Annex H of this standard states that only metadata exceptions are defined at lower levels, so it is not necessary to generate the full registry of metadata for each level but to link particular values to the general value that they inherit. Conceptually the metadata registry is complete for each metadata hierarchical level, but at the implementation level most of the metadata elements are not stored at both levels but only at more generic one. This communication defines a metadata system that covers 4 levels, describes which metadata has to support series-layer inheritance and in which way, and how hierarchical levels are defined and stored. Metadata elements are classified according to the type of inheritance between products, series, tiles and the datasets. It explains the metadata elements classification and exemplifies it using core metadata elements. The communication also presents a metadata viewer and edition tool that uses the described model to propagate metadata elements and to show to the user a complete set of metadata for each level in a transparent way. This tool is integrated in the MiraMon GIS software.

Open Access Metadata, Catalogers, and Vendors: The Future of Cataloging Records

ERIC Educational Resources Information Center

Flynn, Emily Alinder

2013-01-01

The open access (OA) movement is working to transform scholarly communication around the world, but this philosophy can also apply to metadata and cataloging records. While some notable, large academic libraries, such as Harvard University, the University of Michigan, and the University of Cambridge, released their cataloging records under OA…

Quantifying the web browser ecosystem

PubMed Central

Ferdman, Sela; Minkov, Einat; Gefen, David

2017-01-01

Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to “sneak in” through third party installations or to get “kicked out” by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality. Analyzing addon interactions at user level using the Personalized PageRank (PPR) random walk measure shows that the graph demonstrates ecological resilience. Adapting the PPR model to analyzing the browser ecosystem at the level of addon manufacturer, the study shows that some addon companies are in symbiosis and others clash with each other as shown by analyzing the behavior of 18 prominent addon manufacturers. Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market. PMID:28644833

{Semantic metadata application for information resources systematization in water spectroscopy} A.Fazliev (1), A.Privezentsev (1), J.Tennyson (2) (1) Institute of Atmospheric Optics SB RAS, Tomsk, Russia, (2) University College London, London, UK (faz@iao

NASA Astrophysics Data System (ADS)

Fazliev, A.

2009-04-01

The information and knowledge layers of information-computational system for water spectroscopy are described. Semantic metadata for all the tasks of domain information model that are the basis of the layers have been studied. The principle of semantic metadata determination and mechanisms of the usage during information systematization in molecular spectroscopy has been revealed. The software developed for the work with semantic metadata is described as well. Formation of domain model in the framework of Semantic Web is based on the use of explicit specification of its conceptualization or, in other words, its ontologies. Formation of conceptualization for molecular spectroscopy was described in Refs. 1, 2. In these works two chains of task are selected for zeroth approximation for knowledge domain description. These are direct tasks chain and inverse tasks chain. Solution schemes of these tasks defined approximation of data layer for knowledge domain conceptualization. Spectroscopy tasks solutions properties lead to a step-by-step extension of molecular spectroscopy conceptualization. Information layer of information system corresponds to this extension. An advantage of molecular spectroscopy model designed in a form of tasks chain is actualized in the fact that one can explicitly define data and metadata at each step of solution of these molecular spectroscopy chain tasks. Metadata structure (tasks solutions properties) in knowledge domain also has form of a chain in which input data and metadata of the previous task become metadata of the following tasks. The term metadata is used in its narrow sense: metadata are the properties of spectroscopy tasks solutions. Semantic metadata represented with the help of OWL 3 are formed automatically and they are individuals of classes (A-box). Unification of T-box and A-box is an ontology that can be processed with the help of inference engine. In this work we analyzed the formation of individuals of molecular spectroscopy applied ontologies as well as the software used for their creation by means of OWL DL language. The results of this work are presented in a form of an information layer and a knowledge layer in W@DIS information system 4. 1 FORMATION OF INDIVIDUALS OF WATER SPECTROSCOPY APPLIED ONTOLOGY Applied tasks ontology contains explicit description of input an output data of physical tasks solved in two chains of molecular spectroscopy tasks. Besides physical concepts, related to spectroscopy tasks solutions, an information source, which is a key concept of knowledge domain information model, is also used. Each solution of knowledge domain task is linked to the information source which contains a reference on published task solution, molecule and task solution properties. Each information source allows us to identify a certain knowledge domain task solution contained in the information system. Water spectroscopy applied ontology classes are formed on the basis of molecular spectroscopy concepts taxonomy. They are defined by constrains on properties of the selected conceptualization. Extension of applied ontology in W@DIS information system is actualized according to two scenarios. Individuals (ontology facts or axioms) formation is actualized during the task solution upload in the information system. Ontology user operation that implies molecular spectroscopy taxonomy and individuals is performed solely by the user. For this purpose Protege ontology editor was used. For the formation, processing and visualization of knowledge domain tasks individuals a software was designed and implemented. Method of individual formation determines the sequence of steps of created ontology individuals' generation. Tasks solutions properties (metadata) have qualitative and quantitative values. Qualitative metadata are regarded as metadata describing qualitative side of a task such as solution method or other information that can be explicitly specified by object properties of OWL DL language. Quantitative metadata are metadata that describe quantitative properties of task solution such as minimal and maximal data value or other information that can be explicitly obtained by programmed algorithmic operations. These metadata are related to DatatypeProperty properties of OWL specification language Quantitative metadata can be obtained automatically during data upload into information system. Since ObjectProperty values are objects, processing of qualitative metadata requires logical constraints. In case of the task solved in W@DIS ICS qualitative metadata can be formed automatically (for example in spectral functions calculation task). The used methods of translation of qualitative metadata into quantitative is characterized as roughened representation of knowledge in knowledge domain. The existence of two ways of data obtainment is a key moment in the formation of applied ontology of molecular spectroscopy task. experimental method (metadata for experimental data contain description of equipment, experiment conditions and so on) on the initial stage and inverse task solution on the following stages; calculation method (metadata for calculation data are closely related to the metadata used for the description of physical and mathematical models of molecular spectroscopy) 2 SOFTWARE FOR ONTOLOGY OPERATION Data collection in water spectroscopy information system is organized in a form of workflow that contains such operations as information source creation, entry of bibliographic data on publications, formation of uploaded data schema an so on. Metadata are generated in information source as well. Two methods are used for their formation: automatic metadata generation and manual metadata generation (performed by user). Software implementation of support of actions related to metadata formation is performed by META+ module. Functions of META+ module can be divided into two groups. The first groups contains the functions necessary to software developer while the second one the functions necessary to a user of the information system. META+ module functions necessary to the developer are: 1. creation of taxonomy (T-boxes) of applied ontology classes of knowledge domain tasks; 2. creation of instances of task classes; 3. creation of data schemes of tasks in a form of an XML-pattern and based on XML-syntax. XML-pattern is developed for instances generator and created according to certain rules imposed on software generator implementation. 4. implementation of metadata values calculation algorithms; 5. creation of a request interface and additional knowledge processing function for the solution of these task; 6. unification of the created functions and interfaces into one information system The following sequence is universal for the generation of task classes' individuals that form chains. Special interfaces for user operations management are designed for software developer in META+ module. There are means for qualitative metadata values updating during data reuploading to information source. The list of functions necessary to end user contains: - data sets visualization and editing, taking into account their metadata, e.g.: display of unique number of bands in transitions for a certain data source; - export of OWL/RDF models from information system to the environment in XML-syntax; - visualization of instances of classes of applied ontology tasks on molecular spectroscopy; - import of OWL/RDF models into the information system and their integration with domain vocabulary; - formation of additional knowledge of knowledge domain for the construction of ontological instances of task classes using GTML-formats and their processing; - formation of additional knowledge in knowledge domain for the construction of instances of task classes, using software algorithm for data sets processing; - function of semantic search implementation using an interface that formulates questions in a form of related triplets in order for getting an adequate answer. 3 STRUCTURE OF META+ MODULE META+ software module that provides the above functions contains the following components: - a knowledge base that stores semantic metadata and taxonomies of information system; - software libraries POWL and RAP 5 created by third-party developer and providing access to ontological storage; - function classes and libraries that form the core of the module and perform the tasks of formation, storage and visualization of classes instances; - configuration files and module patterns that allow one to adjust and organize operation of different functional blocks; META+ module also contains scripts and patterns implemented according to the rules of W@DIS information system development environment. - scripts for interaction with environment by means of the software core of information system. These scripts provide organizing web-oriented interactive communication; - patterns for the formation of functionality visualization realized by the scripts Software core of scientific information-computational system W@DIS is created with the help of MVC (Model - View - Controller) design pattern that allows us to separate logic of application from its representation. It realizes the interaction of three logical components, actualizing interactivity with the environment via Web and performing its preprocessing. Functions of «Controller» logical component are realized with the help of scripts designed according to the rules imposed by software core of the information system. Each script represents a definite object-oriented class with obligatory class method of script initiation called "start". Functions of actualization of domain application operation results representation (i.e. "View" component) are sets of HTML-patterns that allow one to visualize the results of domain applications operation with the help of additional constructions processed by software core of the system. Besides the interaction with the software core of the scientific information system this module also deals with configuration files of software core and its database. Such organization of work provides closer integration with software core and deeper and more adequate connection in operating system support. 4 CONCLUSION In this work the problems of semantic metadata creation in information system oriented on information representation in the area of molecular spectroscopy have been discussed. The described method of semantic metadata and functions formation as well as realization and structure of META+ module have been described. Architecture of META+ module is closely related to the existing software of "Molecular spectroscopy" scientific information system. Realization of the module is performed with the use of modern approaches to Web-oriented applications development. It uses the existing applied interfaces. The developed software allows us to: - perform automatic metadata annotation of calculated tasks solutions directly in the information system; - perform automatic annotation of metadata on the solution of tasks on task solution results uploading outside the information system forming an instance of the solved task on the basis of entry data; - use ontological instances of task solution for identification of data in information tasks of viewing, comparison and search solved by information system; - export applied tasks ontologies for the operation with them by external means; - solve the task of semantic search according to the pattern and using question-answer type interface. 5 ACKNOWLEDGEMENT The authors are grateful to RFBR for the financial support of development of distributed information system for molecular spectroscopy. REFERENCES A.D.Bykov, A.Z. Fazliev, N.N.Filippov, A.V. Kozodoev, A.I.Privezentsev, L.N.Sinitsa, M.V.Tonkov and M.Yu.Tretyakov, Distributed information system on atmospheric spectroscopy // Geophysical Research Abstracts, SRef-ID: 1607-7962/gra/EGU2007-A-01906, 2007, v. 9, p. 01906. A.I.Prevezentsev, A.Z. Fazliev Applied task ontology for molecular spectroscopy information resources systematization. The Proceedings of 9th Russian scientific conference "Electronic libraries: advanced methods and technologies, electronic collections" - RCDL'2007, Pereslavl Zalesskii, 2007, part.1, 2007, P.201-210. OWL Web Ontology Language Semantics and Abstract Syntax, W3C Recommendation 10 February 2004, http://www.w3.org/TR/2004/REC-owl-semantics-20040210/ W@DIS information system, http://wadis.saga.iao.ru RAP library, http://www4.wiwiss.fu-berlin.de/bizer/rdfapi/.

A System for Automated Extraction of Metadata from Scanned Documents using Layout Recognition and String Pattern Search Models

PubMed Central

Misra, Dharitri; Chen, Siyuan; Thoma, George R.

2010-01-01

One of the most expensive aspects of archiving digital documents is the manual acquisition of context-sensitive metadata useful for the subsequent discovery of, and access to, the archived items. For certain types of textual documents, such as journal articles, pamphlets, official government records, etc., where the metadata is contained within the body of the documents, a cost effective method is to identify and extract the metadata in an automated way, applying machine learning and string pattern search techniques. At the U. S. National Library of Medicine (NLM) we have developed an automated metadata extraction (AME) system that employs layout classification and recognition models with a metadata pattern search model for a text corpus with structured or semi-structured information. A combination of Support Vector Machine and Hidden Markov Model is used to create the layout recognition models from a training set of the corpus, following which a rule-based metadata search model is used to extract the embedded metadata by analyzing the string patterns within and surrounding each field in the recognized layouts. In this paper, we describe the design of our AME system, with focus on the metadata search model. We present the extraction results for a historic collection from the Food and Drug Administration, and outline how the system may be adapted for similar collections. Finally, we discuss some ongoing enhancements to our AME system. PMID:21179386

Exploring Large Scale Data Analysis and Visualization for ARM Data Discovery Using NoSQL Technologies

NASA Astrophysics Data System (ADS)

Krishna, B.; Gustafson, W. I., Jr.; Vogelmann, A. M.; Toto, T.; Devarakonda, R.; Palanisamy, G.

2016-12-01

This paper presents a new way of providing ARM data discovery through data analysis and visualization services. ARM stands for Atmospheric Radiation Measurement. This Program was created to study cloud formation processes and their influence on radiative transfer and also include additional measurements of aerosol and precipitation at various highly instrumented ground and mobile stations. The total volume of ARM data is roughly 900TB. The current search for ARM data is performed by using its metadata, such as the site name, instrument name, date, etc. NoSQL technologies were explored to improve the capabilities of data searching, not only by their metadata, but also by using the measurement values. Two technologies that are currently being implemented for testing are Apache Cassandra (noSQL database) and Apache Spark (noSQL based analytics framework). Both of these technologies were developed to work in a distributed environment and hence can handle large data for storing and analytics. D3.js is a JavaScript library that can generate interactive data visualizations in web browsers by making use of commonly used SVG, HTML5, and CSS standards. To test the performance of NoSQL for ARM data, we will be using ARM's popular measurements to locate the data based on its value. Recently noSQL technology has been applied to a pilot project called LASSO, which stands for LES ARM Symbiotic Simulation and Observation Workflow. LASSO will be packaging LES output and observations in "data bundles" and analyses will require the ability for users to analyze both observations and LES model output either individually or together across multiple time periods. The LASSO implementation strategy suggests that enormous data storage is required to store the above mentioned quantities. Thus noSQL was used to provide a powerful means to store portions of the data that provided users with search capabilities on each simulation's traits through a web application. Based on the user selection, plots are created dynamically along with ancillary information that enables the user to locate and download data that fulfilled their required traits.

Design and implementation of the NPOI database and website

NASA Astrophysics Data System (ADS)

Newman, K.; Jorgensen, A. M.; Landavazo, M.; Sun, B.; Hutter, D. J.; Armstrong, J. T.; Mozurkewich, David; Elias, N.; van Belle, G. T.; Schmitt, H. R.; Baines, E. K.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) has been recording astronomical observations for nearly two decades, at this point with hundreds of thousands of individual observations recorded to date for a total data volume of many terabytes. To make maximum use of the NPOI data it is necessary to organize them in an easily searchable manner and be able to extract essential diagnostic information from the data to allow users to quickly gauge data quality and suitability for a specific science investigation. This sets the motivation for creating a comprehensive database of observation metadata as well as, at least, reduced data products. The NPOI database is implemented in MySQL using standard database tools and interfaces. The use of standard database tools allows us to focus on top-level database and interface implementation and take advantage of standard features such as backup, remote access, mirroring, and complex queries which would otherwise be time-consuming to implement. A website was created in order to give scientists a user friendly interface for searching the database. It allows the user to select various metadata to search for and also allows them to decide how and what results are displayed. This streamlines the searches, making it easier and quicker for scientists to find the information they are looking for. The website has multiple browser and device support. In this paper we present the design of the NPOI database and website, and give examples of its use.

Toward Exposing Timing-Based Probing Attacks in Web Applications †

PubMed Central

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-01-01

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users’ browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach. PMID:28245610

Toward Exposing Timing-Based Probing Attacks in Web Applications.

PubMed

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-02-25

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users' browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach.

Progress and Plans in Support of the Polar Community

NASA Technical Reports Server (NTRS)

Olsen, Lola M.; Meaux, Melanie F.

2006-01-01

Feedback provided by the Antarctic community has proven instrumental in positively influencing the direction of the GCMD's development. For example, in response to requests for a stand alone metadata authoring tool, a new shareable software package called docBUILDER solo will be released to the public in March 2006. This tool permits researchers to document their data during experiments and observational periods in the field. The international polar community has also played a key role in encouraging support for the foreign language character set in the metadata display and tools (10% of the records in the AMD hold foreign characters). In the upcoming release, the full ISO character set, which also includes mathematical symbols, will be supported. Additional upgrades include the ability for users to search for data sets based on pre-selected temporal and spatial resolution ranges. Data providers are strongly encouraged to populate the resolution fields for their data sets, although these fields are not currently required. In prior versions, browser incompatibilities often resulted in unreliable performance for users attempting to initiate a spatial search using a map based on Java applet technology. The GCMD will offer an integrated Google map and date search, replacing the applet technology and enhancing the geospatial and temporal searches. It is estimated that 30% of the records in the AMD have direct access to data. A growing number of these records can be accessed through data service links. Related data services are therefore becoming valuable assets in facilitating the use and visualization of data. Users will gain the ability to refine services using the same options as those available for data set searches. Data providers are encouraged to describe available data-related services through the directory. Future plans include offering web services through a SOAP interface and extending semantic queries for the polar regions through the use of ontologies. The Open Archives Initiative's (OAI) Protocol for Metadata Harvesting (PMH) has been successfully tested with several organizations and appears to be a prime candidate for sharing metadata within the community. The GCMD anticipates contributing to the design of the data management system for the International Polar Year and to the ongoing efforts in the years to come. Further enhancements will be discussed at the meeting.

Principles of metadata organization at the ENCODE data coordination center

PubMed Central

Hong, Eurie L.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Malladi, Venkat S.; Strattan, J. Seth; Hitz, Benjamin C.; Gabdank, Idan; Narayanan, Aditi K.; Ho, Marcus; Lee, Brian T.; Rowe, Laurence D.; Dreszer, Timothy R.; Roe, Greg R.; Podduturi, Nikhil R.; Tanaka, Forrest; Hilton, Jason A.; Cherry, J. Michael

2016-01-01

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/). Database URL: www.encodeproject.org PMID:26980513

A novel metadata management model to capture consent for record linkage in longitudinal research studies.

PubMed

McMahon, Christiana; Denaxas, Spiros

2017-11-06

Informed consent is an important feature of longitudinal research studies as it enables the linking of the baseline participant information with administrative data. The lack of standardized models to capture consent elements can lead to substantial challenges. A structured approach to capturing consent-related metadata can address these. a) Explore the state-of-the-art for recording consent; b) Identify key elements of consent required for record linkage; and c) Create and evaluate a novel metadata management model to capture consent-related metadata. The main methodological components of our work were: a) a systematic literature review and qualitative analysis of consent forms; b) the development and evaluation of a novel metadata model. We qualitatively analyzed 61 manuscripts and 30 consent forms. We extracted data elements related to obtaining consent for linkage. We created a novel metadata management model for consent and evaluated it by comparison with the existing standards and by iteratively applying it to case studies. The developed model can facilitate the standardized recording of consent for linkage in longitudinal research studies and enable the linkage of external participant data. Furthermore, it can provide a structured way of recording consent-related metadata and facilitate the harmonization and streamlining of processes.

Dynamic federation of grid and cloud storage

NASA Astrophysics Data System (ADS)

Furano, Fabrizio; Keeble, Oliver; Field, Laurence

2016-09-01

The Dynamic Federations project ("Dynafed") enables the deployment of scalable, distributed storage systems composed of independent storage endpoints. While the Uniform Generic Redirector at the heart of the project is protocol-agnostic, we have focused our effort on HTTP-based protocols, including S3 and WebDAV. The system has been deployed on testbeds covering the majority of the ATLAS and LHCb data, and supports geography-aware replica selection. The work done exploits the federation potential of HTTP to build systems that offer uniform, scalable, catalogue-less access to the storage and metadata ensemble and the possibility of seamless integration of other compatible resources such as those from cloud providers. Dynafed can exploit the potential of the S3 delegation scheme, effectively federating on the fly any number of S3 buckets from different providers and applying a uniform authorization to them. This feature has been used to deploy in production the BOINC Data Bridge, which uses the Uniform Generic Redirector with S3 buckets to harmonize the BOINC authorization scheme with the Grid/X509. The Data Bridge has been deployed in production with good results. We believe that the features of a loosely coupled federation of open-protocolbased storage elements open many possibilities of smoothly evolving the current computing models and of supporting new scientific computing projects that rely on massive distribution of data and that would appreciate systems that can more easily be interfaced with commercial providers and can work natively with Web browsers and clients.

Handling Metadata in a Neurophysiology Laboratory

PubMed Central

Zehl, Lyuba; Jaillet, Florent; Stoewer, Adrian; Grewe, Jan; Sobolev, Andrey; Wachtler, Thomas; Brochier, Thomas G.; Riehle, Alexa; Denker, Michael; Grün, Sonja

2016-01-01

To date, non-reproducibility of neurophysiological research is a matter of intense discussion in the scientific community. A crucial component to enhance reproducibility is to comprehensively collect and store metadata, that is, all information about the experiment, the data, and the applied preprocessing steps on the data, such that they can be accessed and shared in a consistent and simple manner. However, the complexity of experiments, the highly specialized analysis workflows and a lack of knowledge on how to make use of supporting software tools often overburden researchers to perform such a detailed documentation. For this reason, the collected metadata are often incomplete, incomprehensible for outsiders or ambiguous. Based on our research experience in dealing with diverse datasets, we here provide conceptual and technical guidance to overcome the challenges associated with the collection, organization, and storage of metadata in a neurophysiology laboratory. Through the concrete example of managing the metadata of a complex experiment that yields multi-channel recordings from monkeys performing a behavioral motor task, we practically demonstrate the implementation of these approaches and solutions with the intention that they may be generalized to other projects. Moreover, we detail five use cases that demonstrate the resulting benefits of constructing a well-organized metadata collection when processing or analyzing the recorded data, in particular when these are shared between laboratories in a modern scientific collaboration. Finally, we suggest an adaptable workflow to accumulate, structure and store metadata from different sources using, by way of example, the odML metadata framework. PMID:27486397

Handling Metadata in a Neurophysiology Laboratory.

PubMed

Zehl, Lyuba; Jaillet, Florent; Stoewer, Adrian; Grewe, Jan; Sobolev, Andrey; Wachtler, Thomas; Brochier, Thomas G; Riehle, Alexa; Denker, Michael; Grün, Sonja

2016-01-01

To date, non-reproducibility of neurophysiological research is a matter of intense discussion in the scientific community. A crucial component to enhance reproducibility is to comprehensively collect and store metadata, that is, all information about the experiment, the data, and the applied preprocessing steps on the data, such that they can be accessed and shared in a consistent and simple manner. However, the complexity of experiments, the highly specialized analysis workflows and a lack of knowledge on how to make use of supporting software tools often overburden researchers to perform such a detailed documentation. For this reason, the collected metadata are often incomplete, incomprehensible for outsiders or ambiguous. Based on our research experience in dealing with diverse datasets, we here provide conceptual and technical guidance to overcome the challenges associated with the collection, organization, and storage of metadata in a neurophysiology laboratory. Through the concrete example of managing the metadata of a complex experiment that yields multi-channel recordings from monkeys performing a behavioral motor task, we practically demonstrate the implementation of these approaches and solutions with the intention that they may be generalized to other projects. Moreover, we detail five use cases that demonstrate the resulting benefits of constructing a well-organized metadata collection when processing or analyzing the recorded data, in particular when these are shared between laboratories in a modern scientific collaboration. Finally, we suggest an adaptable workflow to accumulate, structure and store metadata from different sources using, by way of example, the odML metadata framework.

Principles of metadata organization at the ENCODE data coordination center.

PubMed

Hong, Eurie L; Sloan, Cricket A; Chan, Esther T; Davidson, Jean M; Malladi, Venkat S; Strattan, J Seth; Hitz, Benjamin C; Gabdank, Idan; Narayanan, Aditi K; Ho, Marcus; Lee, Brian T; Rowe, Laurence D; Dreszer, Timothy R; Roe, Greg R; Podduturi, Nikhil R; Tanaka, Forrest; Hilton, Jason A; Cherry, J Michael

2016-01-01

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/). Database URL: www.encodeproject.org. © The Author(s) 2016. Published by Oxford University Press.

Automated metadata, provenance cataloging and navigable interfaces: ensuring the usefulness of extreme-scale data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schissel, David; Greenwald, Martin

The MPO (Metadata, Provenance, Ontology) Project successfully addressed the goal of improving the usefulness and traceability of scientific data by building a system that could capture and display all steps in the process of creating, analyzing and disseminating that data. Throughout history, scientists have generated handwritten logbooks to keep track of data, their hypotheses, assumptions, experimental setup, and computational processes as well as reflections on observations and issues encountered. Over the last several decades, with the growth of personal computers, handheld devices, and the World Wide Web, the handwritten logbook has begun to be replaced by electronic logbooks. This transitionmore » has brought increased capability such as supporting multi-media, hypertext, and fast searching. However, content creation and metadata (a set of data that describes and gives information about other data) capturing has for the most part remained a manual activity just as it was with handwritten logbooks. This has led to a fragmentation of data, processing, and annotation that has only accelerated as scientific workflows continue to increase in complexity. From a scientific perspective, it is very important to be able to understand the lineage of any piece of data: who, what, when, how, and why. This is typically referred to as data provenance. The fragmentation discussed previously often means that data provenance is lost. As scientific workflows move to powerful computers and become more complex, the ability to track all of the steps involved in creating a piece of data become even more difficult. It was the goal of the MPO (Metadata, Provenance, Ontology) Project to create a system (the MPO System) that allows for automatic provenance and metadata capturing in such a way to allow easy searching and browsing. This goal needed to be accomplished in a general way so that it may be used across a broad range of scientific domains, yet allow the addition of vocabulary (Ontology) that is domain specific as is required for intelligent searching and browsing in the scientific context. Through the creation and deployment of the MPO system, the goals of the project were achieved. An enhanced metadata, provenance, and ontology storage system was created. This was combined with innovative methodologies for navigating and exploring these data using a web browser for both experimental and simulation-based scientific research. In addition, a system to allow scientists to instrument their existing workflows for automatic metadata and provenance is part of the MPO system. In that way, a scientist can continue to use their existing methodology yet easily document their work. Workflows and data provenance can be displayed either graphically or in an electronic notebook format and support advanced search features including via ontology. The MPO system was successfully used in both Climate and Magnetic Fusion Energy Research. The software for the MPO system is located at https://github.com/MPO-Group/MPO and is open source distributed under the Revised BSD License. A demonstration site of the MPO system is open to the public and is available at https://mpo.psfc.mit.edu/. A Docker container release of the command line client is available for public download using the command docker pull jcwright/mpo-cli at https://hub.docker.com/r/jcwright/mpo-cli.« less

Building a high level sample processing and quality assessment model for biogeochemical measurements: a case study from the ocean acidification community

NASA Astrophysics Data System (ADS)

Thomas, R.; Connell, D.; Spears, T.; Leadbetter, A.; Burger, E. F.

2016-12-01

The scientific literature heavily features small-scale studies with the impact of the results extrapolated to regional/global importance. There are on-going initiatives (e.g. OA-ICC, GOA-ON, GEOTRACES, EMODNet Chemistry) aiming to assemble regional to global-scale datasets that are available for trend or meta-analyses. Assessing the quality and comparability of these data requires information about the processing chain from "sampling to spreadsheet". This provenance information needs to be captured and readily available to assess data fitness for purpose. The NOAA Ocean Acidification metadata template was designed in consultation with domain experts for this reason; the core carbonate chemistry variables have 23-37 metadata fields each and for scientists generating these datasets there could appear to be an ever increasing amount of metadata expected to accompany a dataset. While this provenance metadata should be considered essential by those generating or using the data, for those discovering data there is a sliding scale between what is considered discovery metadata (title, abstract, contacts, etc.) versus usage metadata (methodology, environmental setup, lineage, etc.), the split depending on the intended use of data. As part of the OA-ICC's activities, the metadata fields from the NOAA template relevant to the sample processing chain and QA criteria have been factored to develop profiles for, and extensions to, the OM-JSON encoding supported by the PROV ontology. While this work started focused on carbonate chemistry variable specific metadata, the factorization could be applied within the O&M model across other disciplines such as trace metals or contaminants. In a linked data world with a suitable high level model for sample processing and QA available, tools and support can be provided to link reproducible units of metadata (e.g. the standard protocol for a variable as adopted by a community) and simplify the provision of metadata and subsequent discovery.

TOPCAT -- Tool for OPerations on Catalogues And Tables

NASA Astrophysics Data System (ADS)

Taylor, Mark

TOPCAT is an interactive graphical viewer and editor for tabular data. It has been designed for use with astronomical tables such as object catalogues, but is not restricted to astronomical applications. It understands a number of different astronomically important formats, and more formats can be added. It is designed to cope well with large tables; a million rows by a hundred columns should not present a problem even with modest memory and CPU resources. It offers a variety of ways to view and analyse the data, including a browser for the cell data themselves, viewers for information about table and column metadata, tools for joining tables using flexible matching algorithms, and visualisation facilities including histograms, 2- and 3-dimensional scatter plots, and density maps. Using a powerful and extensible Java-based expression language new columns can be defined and row subsets selected for separate analysis. Selecting a row can be configured to trigger an action, for instance displaying an image of the catalogue object in an external viewer. Table data and metadata can be edited and the resulting modified table can be written out in a wide range of output formats. A number of options are provided for loading data from external sources, including Virtual Observatory (VO) services, thus providing a gateway to many remote archives of astronomical data. It can also interoperate with other desktop tools using the SAMP protocol. TOPCAT is written in pure Java and is available under the GNU General Public Licence. Its underlying table processing facilities are provided by STIL, the Starlink Tables Infrastructure Library.

Designing, Implementing, and Evaluating Secure Web Browsers

ERIC Educational Resources Information Center

Grier, Christopher L.

2009-01-01

Web browsers are plagued with vulnerabilities, providing hackers with easy access to computer systems using browser-based attacks. Efforts that retrofit existing browsers have had limited success since modern browsers are not designed to withstand attack. To enable more secure web browsing, we design and implement new web browsers from the ground…

A brief introduction to web-based genome browsers.

PubMed

Wang, Jun; Kong, Lei; Gao, Ge; Luo, Jingchu

2013-03-01

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

EMERALD: A Flexible Framework for Managing Seismic Data

NASA Astrophysics Data System (ADS)

West, J. D.; Fouch, M. J.; Arrowsmith, R.

2010-12-01

The seismological community is challenged by the vast quantity of new broadband seismic data provided by large-scale seismic arrays such as EarthScope’s USArray. While this bonanza of new data enables transformative scientific studies of the Earth’s interior, it also illuminates limitations in the methods used to prepare and preprocess those data. At a recent seismic data processing focus group workshop, many participants expressed the need for better systems to minimize the time and tedium spent on data preparation in order to increase the efficiency of scientific research. Another challenge related to data from all large-scale transportable seismic experiments is that there currently exists no system for discovering and tracking changes in station metadata. This critical information, such as station location, sensor orientation, instrument response, and clock timing data, may change over the life of an experiment and/or be subject to post-experiment correction. Yet nearly all researchers utilize metadata acquired with the downloaded data, even though subsequent metadata updates might alter or invalidate results produced with older metadata. A third long-standing issue for the seismic community is the lack of easily exchangeable seismic processing codes. This problem stems directly from the storage of seismic data as individual time series files, and the history of each researcher developing his or her preferred data file naming convention and directory organization. Because most processing codes rely on the underlying data organization structure, such codes are not easily exchanged between investigators. To address these issues, we are developing EMERALD (Explore, Manage, Edit, Reduce, & Analyze Large Datasets). The goal of the EMERALD project is to provide seismic researchers with a unified, user-friendly, extensible system for managing seismic event data, thereby increasing the efficiency of scientific enquiry. EMERALD stores seismic data and metadata in a state-of-the-art open source relational database (PostgreSQL), and can, on a timed basis or on demand, download the most recent metadata, compare it with previously acquired values, and alert the user to changes. The backend relational database is capable of easily storing and managing many millions of records. The extensible, plug-in architecture of the EMERALD system allows any researcher to contribute new visualization and processing methods written in any of 12 programming languages, and a central Internet-enabled repository for such methods provides users with the opportunity to download, use, and modify new processing methods on demand. EMERALD includes data acquisition tools allowing direct importation of seismic data, and also imports data from a number of existing seismic file formats. Pre-processed clean sets of data can be exported as standard sac files with user-defined file naming and directory organization, for use with existing processing codes. The EMERALD system incorporates existing acquisition and processing tools, including SOD, TauP, GMT, and FISSURES/DHI, making much of the functionality of those tools available in a unified system with a user-friendly web browser interface. EMERALD is now in beta test. See emerald.asu.edu or contact john.d.west@asu.edu for more details.

Formats and Network Protocols for Browser Access to 2D Raster Data

NASA Astrophysics Data System (ADS)

Plesea, L.

2015-12-01

Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

Automatically assisting human memory: a SenseCam browser.

PubMed

Doherty, Aiden R; Moulin, Chris J A; Smeaton, Alan F

2011-10-01

SenseCams have many potential applications as tools for lifelogging, including the possibility of use as a memory rehabilitation tool. Given that a SenseCam can log hundreds of thousands of images per year, it is critical that these be presented to the viewer in a manner that supports the aims of memory rehabilitation. In this article we report a software browser constructed with the aim of using the characteristics of memory to organise SenseCam images into a form that makes the wealth of information stored on SenseCam more accessible. To enable a large amount of visual information to be easily and quickly assimilated by a user, we apply a series of automatic content analysis techniques to structure the images into "events", suggest their relative importance, and select representative images for each. This minimises effort when browsing and searching. We provide anecdotes on use of such a system and emphasise the need for SenseCam images to be meaningfully sorted using such a browser.

Performance evaluation of a distance learning program.

PubMed

Dailey, D J; Eno, K R; Brinkley, J F

1994-01-01

This paper presents a performance metric which uses a single number to characterize the response time for a non-deterministic client-server application operating over the Internet. When applied to a Macintosh-based distance learning application called the Digital Anatomist Browser, the metric allowed us to observe that "A typical student doing a typical mix of Browser commands on a typical data set will experience the same delay if they use a slow Macintosh on a local network or a fast Macintosh on the other side of the country accessing the data over the Internet." The methodology presented is applicable to other client-server applications that are rapidly appearing on the Internet.

Advantages to Geoscience and Disaster Response from QuakeSim Implementation of Interferometric Radar Maps in a GIS Database System

NASA Astrophysics Data System (ADS)

Parker, Jay; Donnellan, Andrea; Glasscoe, Margaret; Fox, Geoffrey; Wang, Jun; Pierce, Marlon; Ma, Yu

2015-08-01

High-resolution maps of earth surface deformation are available in public archives for scientific interpretation, but are primarily available as bulky downloads on the internet. The NASA uninhabited aerial vehicle synthetic aperture radar (UAVSAR) archive of airborne radar interferograms delivers very high resolution images (approximately seven meter pixels) making remote handling of the files that much more pressing. Data exploration requiring data selection and exploratory analysis has been tedious. QuakeSim has implemented an archive of UAVSAR data in a web service and browser system based on GeoServer (http://geoserver.org). This supports a variety of services that supply consistent maps, raster image data and geographic information systems (GIS) objects including standard earthquake faults. Browsing the database is supported by initially displaying GIS-referenced thumbnail images of the radar displacement maps. Access is also provided to image metadata and links for full file downloads. One of the most widely used features is the QuakeSim line-of-sight profile tool, which calculates the radar-observed displacement (from an unwrapped interferogram product) along a line specified through a web browser. Displacement values along a profile are updated to a plot on the screen as the user interactively redefines the endpoints of the line and the sampling density. The profile and also a plot of the ground height are available as CSV (text) files for further examination, without any need to download the full radar file. Additional tools allow the user to select a polygon overlapping the radar displacement image, specify a downsampling rate and extract a modest sized grid of observations for display or for inversion, for example, the QuakeSim simplex inversion tool which estimates a consistent fault geometry and slip model.

Chapter 35: Describing Data and Data Collections in the VO

NASA Astrophysics Data System (ADS)

Kent, B. R.; Hanisch, R. J.; Williams, R. D.

The list of numbers: 19.22, 17.23, 18.11, 16.98, and 15.11, is of little intrinsic interest without information about the context in which they appear. For instance, are these daily closing stock prices for your favorite investment, or are they hourly photometric measurements of an increasingly bright quasar? The information needed to define this context is called metadata. Metadata are data about data. Astronomers are familiar with metadata through the headers of FITS files and the names and units associated with columns in a table or database. In the VO, metadata describe the contents of tables, images, and spectra, as well as aggregate collections of data (archives, surveys) and computational services. Moreover, VO metadata are constructed according to rules that avoid ambiguity and make it clear whether, in the example above, the stock prices are in dollars or euros, or the photometry is Johnson V or Sloan g. Organization of data is important in any scientific discipline. Equally crucial are the descriptions of that data: the organization publishing the data, its creator or the person making it available, what instruments were used, units assigned to measurement, calibration status, and data quality assessment. The Virtual Observatory metadata scheme not only applies to datasets, but to resources as well, including data archive facilities, searchable web forms, and online analysis and display tools. Since the scientific output flowing from large datasets depends greatly on how well the data are described, it is important for users to understand the basics of the metadata scheme in order to locate the data that they want and use it correctly. Metadata are the key to data discovery and data and service interoperability in the Virtual Observatory.

Towards a semantic medical Web: HealthCyberMap's tool for building an RDF metadata base of health information resources based on the Qualified Dublin Core Metadata Set.

PubMed

Boulos, Maged N; Roudsari, Abdul V; Carson, Ewart R

2002-07-01

HealthCyberMap (http://healthcybermap.semanticweb.org/) aims at mapping Internet health information resources in novel ways for enhanced retrieval and navigation. This is achieved by collecting appropriate resource metadata in an unambiguous form that preserves semantics. We modelled a qualified Dublin Core (DC) metadata set ontology with extra elements for resource quality and geographical provenance in Prot g -2000. A metadata collection form helps acquiring resource instance data within Prot g . The DC subject field is populated with UMLS terms directly imported from UMLS Knowledge Source Server using UMLS tab, a Prot g -2000 plug-in. The project is saved in RDFS/RDF. The ontology and associated form serve as a free tool for building and maintaining an RDF medical resource metadata base. The UMLS tab enables browsing and searching for concepts that best describe a resource, and importing them to DC subject fields. The resultant metadata base can be used with a search and inference engine, and have textual and/or visual navigation interface(s) applied to it, to ultimately build a medical Semantic Web portal. Different ways of exploiting Prot g -2000 RDF output are discussed. By making the context and semantics of resources, not merely their raw text and formatting, amenable to computer 'understanding,' we can build a Semantic Web that is more useful to humans than the current Web. This requires proper use of metadata and ontologies. Clinical codes can reliably describe the subjects of medical resources, establish the semantic relationships (as defined by underlying coding scheme) between related resources, and automate their topical categorisation.

Ridge 2000 Data Management System

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.; Carbotte, S. M.; Arko, R. A.; Haxby, W. F.; Ryan, W. B.; Chayes, D. N.; Lehnert, K. A.; Shank, T. M.

2005-12-01

Hosted at Lamont by the marine geoscience Data Management group, mgDMS, the NSF-funded Ridge 2000 electronic database, http://www.marine-geo.org/ridge2000/, is a key component of the Ridge 2000 multi-disciplinary program. The database covers each of the three Ridge 2000 Integrated Study Sites: Endeavour Segment, Lau Basin, and 8-11N Segment. It promotes the sharing of information to the broader community, facilitates integration of the suite of information collected at each study site, and enables comparisons between sites. The Ridge 2000 data system provides easy web access to a relational database that is built around a catalogue of cruise metadata. Any web browser can be used to perform a versatile text-based search which returns basic cruise and submersible dive information, sample and data inventories, navigation, and other relevant metadata such as shipboard personnel and links to NSF program awards. In addition, non-proprietary data files, images, and derived products which are hosted locally or in national repositories, as well as science and technical reports, can be freely downloaded. On the Ridge 2000 database page, our Data Link allows users to search the database using a broad range of parameters including data type, cruise ID, chief scientist, geographical location. The first Ridge 2000 field programs sailed in 2004 and, in addition to numerous data sets collected prior to the Ridge 2000 program, the database currently contains information on fifteen Ridge 2000-funded cruises and almost sixty Alvin dives. Track lines can be viewed using a recently- implemented Web Map Service button labelled Map View. The Ridge 2000 database is fully integrated with databases hosted by the mgDMS group for MARGINS and the Antarctic multibeam and seismic reflection data initiatives. Links are provided to partner databases including PetDB, SIOExplorer, and the ODP Janus system. Improved inter-operability with existing and new partner repositories continues to be strengthened. One major effort involves the gradual unification of the metadata across these partner databases. Standardised electronic metadata forms that can be filled in at sea are available from our web site. Interactive map-based exploration and visualisation of the Ridge 2000 database is provided by GeoMapApp, a freely-available Java(tm) application being developed within the mgDMS group. GeoMapApp includes high-resolution bathymetric grids for the 8-11N EPR segment and allows customised maps and grids for any of the Ridge 2000 ISS to be created. Vent and instrument locations can be plotted and saved as images, and Alvin dive photos are also available.

Digital Pathology Evaluation in the Multicenter Nephrotic Syndrome Study Network (NEPTUNE)

PubMed Central

Nast, Cynthia C.; Jennette, J. Charles; Hodgin, Jeffrey B.; Herzenberg, Andrew M.; Lemley, Kevin V.; Conway, Catherine M.; Kopp, Jeffrey B.; Kretzler, Matthias; Lienczewski, Christa; Avila-Casado, Carmen; Bagnasco, Serena; Sethi, Sanjeev; Tomaszewski, John; Gasim, Adil H.

2013-01-01

Summary Pathology consensus review for clinical trials and disease classification has historically been performed by manual light microscopy with sequential section review by study pathologists, or multi-headed microscope review. Limitations of this approach include high intra- and inter-reader variability, costs, and delays for slide mailing and consensus reviews. To improve this, the Nephrotic Syndrome Study Network (NEPTUNE) is systematically applying digital pathology review in a multicenter study using renal biopsy whole slide imaging (WSI) for observation-based data collection. Study pathology materials are acquired, scanned, uploaded, and stored in a web-based information system that is accessed through a web-browser interface. Quality control includes metadata and image quality review. Initially, digital slides are annotated, with each glomerulus identified, given a unique number, and maintained in all levels until the glomerulus disappears or sections end. The software allows viewing and annotation of multiple slide sections concurrently. Analysis utilizes “descriptors” for patterns of injury, rather than diagnoses, in renal parenchymal compartments. This multidimensional representation via WSI, allows more accurate glomerular counting and identification of all lesions in each glomerulus, with data available in a searchable database. The use of WSI brings about efficiency critical to pathology review in a clinical trial setting, including independent review by multiple pathologists, improved intraobserver and interobserver reproducibility, efficiencies and risk reduction in slide circulation and mailing, centralized management of data integrity and slide images for current or future studies, and web-based consensus meetings. The overall effect is improved incorporation of pathology review in a budget neutral approach. PMID:23393107

Effective use of metadata in the integration and analysis of multi-dimensional optical data

NASA Astrophysics Data System (ADS)

Pastorello, G. Z.; Gamon, J. A.

2012-12-01

Data discovery and integration relies on adequate metadata. However, creating and maintaining metadata is time consuming and often poorly addressed or avoided altogether, leading to problems in later data analysis and exchange. This is particularly true for research fields in which metadata standards do not yet exist or are under development, or within smaller research groups without enough resources. Vegetation monitoring using in-situ and remote optical sensing is an example of such a domain. In this area, data are inherently multi-dimensional, with spatial, temporal and spectral dimensions usually being well characterized. Other equally important aspects, however, might be inadequately translated into metadata. Examples include equipment specifications and calibrations, field/lab notes and field/lab protocols (e.g., sampling regimen, spectral calibration, atmospheric correction, sensor view angle, illumination angle), data processing choices (e.g., methods for gap filling, filtering and aggregation of data), quality assurance, and documentation of data sources, ownership and licensing. Each of these aspects can be important as metadata for search and discovery, but they can also be used as key data fields in their own right. If each of these aspects is also understood as an "extra dimension," it is possible to take advantage of them to simplify the data acquisition, integration, analysis, visualization and exchange cycle. Simple examples include selecting data sets of interest early in the integration process (e.g., only data collected according to a specific field sampling protocol) or applying appropriate data processing operations to different parts of a data set (e.g., adaptive processing for data collected under different sky conditions). More interesting scenarios involve guided navigation and visualization of data sets based on these extra dimensions, as well as partitioning data sets to highlight relevant subsets to be made available for exchange. The DAX (Data Acquisition to eXchange) Web-based tool uses a flexible metadata representation model and takes advantage of multi-dimensional data structures to translate metadata types into data dimensions, effectively reshaping data sets according to available metadata. With that, metadata is tightly integrated into the acquisition-to-exchange cycle, allowing for more focused exploration of data sets while also increasing the value of, and incentives for, keeping good metadata. The tool is being developed and tested with optical data collected in different settings, including laboratory, field, airborne, and satellite platforms.

WHOI and SIO (I): Next Steps toward Multi-Institution Archiving of Shipboard and Deep Submergence Vehicle Data

NASA Astrophysics Data System (ADS)

Detrick, R. S.; Clark, D.; Gaylord, A.; Goldsmith, R.; Helly, J.; Lemmond, P.; Lerner, S.; Maffei, A.; Miller, S. P.; Norton, C.; Walden, B.

2005-12-01

The Scripps Institution of Oceanography (SIO) and the Woods Hole Oceanographic Institution (WHOI) have joined forces with the San Diego Supercomputer Center to build a testbed for multi-institutional archiving of shipboard and deep submergence vehicle data. Support has been provided by the Digital Archiving and Preservation program funded by NSF/CISE and the Library of Congress. In addition to the more than 92,000 objects stored in the SIOExplorer Digital Library, the testbed will provide access to data, photographs, video images and documents from WHOI ships, Alvin submersible and Jason ROV dives, and deep-towed vehicle surveys. An interactive digital library interface will allow combinations of distributed collections to be browsed, metadata inspected, and objects displayed or selected for download. The digital library architecture, and the search and display tools of the SIOExplorer project, are being combined with WHOI tools, such as the Alvin Framegrabber and the Jason Virtual Control Van, that have been designed using WHOI's GeoBrowser to handle the vast volumes of digital video and camera data generated by Alvin, Jason and other deep submergence vehicles. Notions of scalability will be tested, as data volumes range from 3 CDs per cruise to 200 DVDs per cruise. Much of the scalability of this proposal comes from an ability to attach digital library data and metadata acquisition processes to diverse sensor systems. We are able to run an entire digital library from a laptop computer as well as from supercomputer-center-size resources. It can be used, in the field, laboratory or classroom, covering data from acquisition-to-archive using a single coherent methodology. The design is an open architecture, supporting applications through well-defined external interfaces maintained as an open-source effort for community inclusion and enhancement.

Design and deployment of a large brain-image database for clinical and nonclinical research

NASA Astrophysics Data System (ADS)

Yang, Guo Liang; Lim, Choie Cheio Tchoyoson; Banukumar, Narayanaswami; Aziz, Aamer; Hui, Francis; Nowinski, Wieslaw L.

2004-04-01

An efficient database is an essential component of organizing diverse information on image metadata and patient information for research in medical imaging. This paper describes the design, development and deployment of a large database system serving as a brain image repository that can be used across different platforms in various medical researches. It forms the infrastructure that links hospitals and institutions together and shares data among them. The database contains patient-, pathology-, image-, research- and management-specific data. The functionalities of the database system include image uploading, storage, indexing, downloading and sharing as well as database querying and management with security and data anonymization concerns well taken care of. The structure of database is multi-tier client-server architecture with Relational Database Management System, Security Layer, Application Layer and User Interface. Image source adapter has been developed to handle most of the popular image formats. The database has a user interface based on web browsers and is easy to handle. We have used Java programming language for its platform independency and vast function libraries. The brain image database can sort data according to clinically relevant information. This can be effectively used in research from the clinicians" points of view. The database is suitable for validation of algorithms on large population of cases. Medical images for processing could be identified and organized based on information in image metadata. Clinical research in various pathologies can thus be performed with greater efficiency and large image repositories can be managed more effectively. The prototype of the system has been installed in a few hospitals and is working to the satisfaction of the clinicians.

A New Data Management System for Biological and Chemical Oceanography

NASA Astrophysics Data System (ADS)

Groman, R. C.; Chandler, C.; Allison, D.; Glover, D. M.; Wiebe, P. H.

2007-12-01

The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was created to serve PIs principally funded by NSF to conduct marine chemical and ecological research. The new office is dedicated to providing open access to data and information developed in the course of scientific research on short and intermediate time-frames. The data management system developed in support of U.S. JGOFS and U.S. GLOBEC programs is being modified to support the larger scope of the BCO-DMO effort, which includes ultimately providing a way to exchange data with other data systems. The open access system is based on a philosophy of data stewardship, support for existing and evolving data standards, and use of public domain software. The DMO staff work closely with originating PIs to manage data gathered as part of their individual programs. In the new BCO-DMO data system, project and data set metadata records designed to support re-use of the data are stored in a relational database (MySQL) and the data are stored in or made accessible by the JGOFS/GLOBEC object- oriented, relational, data management system. Data access will be provided via any standard Web browser client user interface through a GIS application (Open Source, OGC-compliant MapServer), a directory listing from the data holdings catalog, or a custom search engine that facilitates data discovery. In an effort to maximize data system interoperability, data will also be available via Web Services; and data set descriptions will be generated to comply with a variety of metadata content standards. The office is located at the Woods Hole Oceanographic Institution and web access is via http://www.bco-dmo.org.

TOPCAT: Tool for OPerations on Catalogues And Tables

NASA Astrophysics Data System (ADS)

Taylor, Mark

2011-01-01

TOPCAT is an interactive graphical viewer and editor for tabular data. Its aim is to provide most of the facilities that astronomers need for analysis and manipulation of source catalogues and other tables, though it can be used for non-astronomical data as well. It understands a number of different astronomically important formats (including FITS and VOTable) and more formats can be added. It offers a variety of ways to view and analyse tables, including a browser for the cell data themselves, viewers for information about table and column metadata, and facilities for 1-, 2-, 3- and higher-dimensional visualisation, calculating statistics and joining tables using flexible matching algorithms. Using a powerful and extensible Java-based expression language new columns can be defined and row subsets selected for separate analysis. Table data and metadata can be edited and the resulting modified table can be written out in a wide range of output formats. It is a stand-alone application which works quite happily with no network connection. However, because it uses Virtual Observatory (VO) standards, it can cooperate smoothly with other tools in the VO world and beyond, such as VODesktop, Aladin and ds9. Between 2006 and 2009 TOPCAT was developed within the AstroGrid project, and is offered as part of a standard suite of applications on the AstroGrid web site, where you can find information on several other VO tools. The program is written in pure Java and available under the GNU General Public Licence. It has been developed in the UK within the Starlink and AstroGrid projects, and under PPARC and STFC grants. Its underlying table processing facilities are provided by STIL.

Facilitating Stewardship of scientific data through standards based workflows

NASA Astrophysics Data System (ADS)

Bastrakova, I.; Kemp, C.; Potter, A. K.

2013-12-01

There are main suites of standards that can be used to define the fundamental scientific methodology of data, methods and results. These are firstly Metadata standards to enable discovery of the data (ISO 19115), secondly the Sensor Web Enablement (SWE) suite of standards that include the O&M and SensorML standards and thirdly Ontology that provide vocabularies to define the scientific concepts and relationships between these concepts. All three types of standards have to be utilised by the practicing scientist to ensure that those who ultimately have to steward the data stewards to ensure that the data can be preserved curated and reused and repurposed. Additional benefits of this approach include transparency of scientific processes from the data acquisition to creation of scientific concepts and models, and provision of context to inform data use. Collecting and recording metadata is the first step in scientific data flow. The primary role of metadata is to provide details of geographic extent, availability and high-level description of data suitable for its initial discovery through common search engines. The SWE suite provides standardised patterns to describe observations and measurements taken for these data, capture detailed information about observation or analytical methods, used instruments and define quality determinations. This information standardises browsing capability over discrete data types. The standardised patterns of the SWE standards simplify aggregation of observation and measurement data enabling scientists to transfer disintegrated data to scientific concepts. The first two steps provide a necessary basis for the reasoning about concepts of ';pure' science, building relationship between concepts of different domains (linked-data), and identifying domain classification and vocabularies. Geoscience Australia is re-examining its marine data flows, including metadata requirements and business processes, to achieve a clearer link between scientific data acquisition and analysis requirements and effective interoperable data management and delivery. This includes participating in national and international dialogue on development of standards, embedding data management activities in business processes, and developing scientific staff as effective data stewards. Similar approach is applied to the geophysical data. By ensuring the geophysical datasets at GA strictly follow metadata and industry standards we are able to implement a provenance based workflow where the data is easily discoverable, geophysical processing can be applied to it and results can be stored. The provenance based workflow enables metadata records for the results to be produced automatically from the input dataset metadata.

Enabling interspecies epigenomic comparison with CEpBrowser.

PubMed

Cao, Xiaoyi; Zhong, Sheng

2013-05-01

We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.

Gene Ontology Consortium: going forward

PubMed Central

2015-01-01

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. PMID:25428369

Ligandbook: an online repository for small and drug-like molecule force field parameters.

PubMed

Domanski, Jan; Beckstein, Oliver; Iorga, Bogdan I

2017-06-01

Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit. oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org . Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

mORCA: sailing bioinformatics world with mobile devices.

PubMed

Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

2018-03-01

Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

Panoptes: web-based exploration of large scale genome variation data.

PubMed

Vauterin, Paul; Jeffery, Ben; Miles, Alistair; Amato, Roberto; Hart, Lee; Wright, Ian; Kwiatkowski, Dominic

2017-10-15

The size and complexity of modern large-scale genome variation studies demand novel approaches for exploring and sharing the data. In order to unlock the potential of these data for a broad audience of scientists with various areas of expertise, a unified exploration framework is required that is accessible, coherent and user-friendly. Panoptes is an open-source software framework for collaborative visual exploration of large-scale genome variation data and associated metadata in a web browser. It relies on technology choices that allow it to operate in near real-time on very large datasets. It can be used to browse rich, hybrid content in a coherent way, and offers interactive visual analytics approaches to assist the exploration. We illustrate its application using genome variation data of Anopheles gambiae, Plasmodium falciparum and Plasmodium vivax. Freely available at https://github.com/cggh/panoptes, under the GNU Affero General Public License. paul.vauterin@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Developing a distributed HTML5-based search engine for geospatial resource discovery

NASA Astrophysics Data System (ADS)

ZHOU, N.; XIA, J.; Nebert, D.; Yang, C.; Gui, Z.; Liu, K.

2013-12-01

With explosive growth of data, Geospatial Cyberinfrastructure(GCI) components are developed to manage geospatial resources, such as data discovery and data publishing. However, the efficiency of geospatial resources discovery is still challenging in that: (1) existing GCIs are usually developed for users of specific domains. Users may have to visit a number of GCIs to find appropriate resources; (2) The complexity of decentralized network environment usually results in slow response and pool user experience; (3) Users who use different browsers and devices may have very different user experiences because of the diversity of front-end platforms (e.g. Silverlight, Flash or HTML). To address these issues, we developed a distributed and HTML5-based search engine. Specifically, (1)the search engine adopts a brokering approach to retrieve geospatial metadata from various and distributed GCIs; (2) the asynchronous record retrieval mode enhances the search performance and user interactivity; (3) the search engine based on HTML5 is able to provide unified access capabilities for users with different devices (e.g. tablet and smartphone).

Digital Investigations of AN Archaeological Smart Point Cloud: a Real Time Web-Based Platform to Manage the Visualisation of Semantical Queries

NASA Astrophysics Data System (ADS)

Poux, F.; Neuville, R.; Hallot, P.; Van Wersch, L.; Luczfalvy Jancsó, A.; Billen, R.

2017-05-01

While virtual copies of the real world tend to be created faster than ever through point clouds and derivatives, their working proficiency by all professionals' demands adapted tools to facilitate knowledge dissemination. Digital investigations are changing the way cultural heritage researchers, archaeologists, and curators work and collaborate to progressively aggregate expertise through one common platform. In this paper, we present a web application in a WebGL framework accessible on any HTML5-compatible browser. It allows real time point cloud exploration of the mosaics in the Oratory of Germigny-des-Prés, and emphasises the ease of use as well as performances. Our reasoning engine is constructed over a semantically rich point cloud data structure, where metadata has been injected a priori. We developed a tool that directly allows semantic extraction and visualisation of pertinent information for the end users. It leads to efficient communication between actors by proposing optimal 3D viewpoints as a basis on which interactions can grow.

MMI's Metadata and Vocabulary Solutions: 10 Years and Growing

NASA Astrophysics Data System (ADS)

Graybeal, J.; Gayanilo, F.; Rueda-Velasquez, C. A.

2014-12-01

The Marine Metadata Interoperability project (http://marinemetadata.org) held its public opening at AGU's 2004 Fall Meeting. For 10 years since that debut, the MMI guidance and vocabulary sites have served over 100,000 visitors, with 525 community members and continuous Steering Committee leadership. Originally funded by the National Science Foundation, over the years multiple organizations have supported the MMI mission: "Our goal is to support collaborative research in the marine science domain, by simplifying the incredibly complex world of metadata into specific, straightforward guidance. MMI encourages scientists and data managers at all levels to apply good metadata practices from the start of a project, by providing the best guidance and resources for data management, and developing advanced metadata tools and services needed by the community." Now hosted by the Harte Research Institute at Texas A&M University at Corpus Christi, MMI continues to provide guidance and services to the community, and is planning for marine science and technology needs for the next 10 years. In this presentation we will highlight our major accomplishments, describe our recent achievements and imminent goals, and propose a vision for improving marine data interoperability for the next 10 years, including Ontology Registry and Repository (http://mmisw.org/orr) advancements and applications (http://mmisw.org/cfsn).

Comparing ungulate dietary proxies using discriminant function analysis.

PubMed

Fraser, Danielle; Theodor, Jessica M

2011-12-01

A variety of tooth-wear and morphological dietary proxies have been proposed for ungulates. In turn, they have been applied to fossil specimens with the purpose of reconstructing the diets of extinct taxa. Although these dietary proxies have been used in isolation and in combination, a consistent set of statistical analyses has never been applied to all of the available datasets. The purpose of this study is to determine how well the most commonly used dietary proxies classify ungulates as browsers, grazers, and mixed feeders individually and in combination. Discriminant function analysis is applied to individual dietary proxies (hypsodonty, mesowear, microwear, and several cranial dietary proxies) and to combinations thereof to compare rates of successful dietary classification. In general, the tooth-wear dietary proxies (mesowear and microwear) perform better than morphological dietary proxies, though none are strong proxies in isolation. The success rates of the cranial dietary proxies are not increased substantially when ruminants and bovids are analyzed separately, and significance among the three dietary guilds is reduced when controlling for phylogenetic relatedness. The combination of hypsodonty, mesowear, and microwear is found to have a high rate of successful dietary classification, but a combination of all commonly used proxies increases the success rate to 100%. In most cases, mixed feeders bear the greatest resemblance to browsers suggesting that a morphology intermediate to browsers and grazers may represent a fitness valley resulting from the inability to exploit both browse and graze efficiently. These results are important for future paleoecological studies and should be used as a guide for determining which dietary proxies are appropriate to the research question. Copyright © 2011 Wiley-Liss, Inc.

Hyper Text Mark-up Language and Dublin Core metadata element set usage in websites of Iranian State Universities' libraries.

PubMed

Zare-Farashbandi, Firoozeh; Ramezan-Shirazi, Mahtab; Ashrafi-Rizi, Hasan; Nouri, Rasool

2014-01-01

Recent progress in providing innovative solutions in the organization of electronic resources and research in this area shows a global trend in the use of new strategies such as metadata to facilitate description, place for, organization and retrieval of resources in the web environment. In this context, library metadata standards have a special place; therefore, the purpose of the present study has been a comparative study on the Central Libraries' Websites of Iran State Universities for Hyper Text Mark-up Language (HTML) and Dublin Core metadata elements usage in 2011. The method of this study is applied-descriptive and data collection tool is the check lists created by the researchers. Statistical community includes 98 websites of the Iranian State Universities of the Ministry of Health and Medical Education and Ministry of Science, Research and Technology and method of sampling is the census. Information was collected through observation and direct visits to websites and data analysis was prepared by Microsoft Excel software, 2011. The results of this study indicate that none of the websites use Dublin Core (DC) metadata and that only a few of them have used overlaps elements between HTML meta tags and Dublin Core (DC) elements. The percentage of overlaps of DC elements centralization in the Ministry of Health were 56% for both description and keywords and, in the Ministry of Science, were 45% for the keywords and 39% for the description. But, HTML meta tags have moderate presence in both Ministries, as the most-used elements were keywords and description (56%) and the least-used elements were date and formatter (0%). It was observed that the Ministry of Health and Ministry of Science follows the same path for using Dublin Core standard on their websites in the future. Because Central Library Websites are an example of scientific web pages, special attention in designing them can help the researchers to achieve faster and more accurate information resources. Therefore, the influence of librarians' ideas on the awareness of web designers and developers will be important for using metadata elements as general, and specifically for applying such standards.

Hyper Text Mark-up Language and Dublin Core metadata element set usage in websites of Iranian State Universities’ libraries

PubMed Central

Zare-Farashbandi, Firoozeh; Ramezan-Shirazi, Mahtab; Ashrafi-Rizi, Hasan; Nouri, Rasool

2014-01-01

Introduction: Recent progress in providing innovative solutions in the organization of electronic resources and research in this area shows a global trend in the use of new strategies such as metadata to facilitate description, place for, organization and retrieval of resources in the web environment. In this context, library metadata standards have a special place; therefore, the purpose of the present study has been a comparative study on the Central Libraries’ Websites of Iran State Universities for Hyper Text Mark-up Language (HTML) and Dublin Core metadata elements usage in 2011. Materials and Methods: The method of this study is applied-descriptive and data collection tool is the check lists created by the researchers. Statistical community includes 98 websites of the Iranian State Universities of the Ministry of Health and Medical Education and Ministry of Science, Research and Technology and method of sampling is the census. Information was collected through observation and direct visits to websites and data analysis was prepared by Microsoft Excel software, 2011. Results: The results of this study indicate that none of the websites use Dublin Core (DC) metadata and that only a few of them have used overlaps elements between HTML meta tags and Dublin Core (DC) elements. The percentage of overlaps of DC elements centralization in the Ministry of Health were 56% for both description and keywords and, in the Ministry of Science, were 45% for the keywords and 39% for the description. But, HTML meta tags have moderate presence in both Ministries, as the most-used elements were keywords and description (56%) and the least-used elements were date and formatter (0%). Conclusion: It was observed that the Ministry of Health and Ministry of Science follows the same path for using Dublin Core standard on their websites in the future. Because Central Library Websites are an example of scientific web pages, special attention in designing them can help the researchers to achieve faster and more accurate information resources. Therefore, the influence of librarians’ ideas on the awareness of web designers and developers will be important for using metadata elements as general, and specifically for applying such standards. PMID:24741646

Compatibility Between Metadata Standards: Import Pipeline of CDISC ODM to the Samply.MDR.

PubMed

Kock-Schoppenhauer, Ann-Kristin; Ulrich, Hannes; Wagen-Zink, Stefanie; Duhm-Harbeck, Petra; Ingenerf, Josef; Neuhaus, Philipp; Dugas, Martin; Bruland, Philipp

2018-01-01

The establishment of a digital healthcare system is a national and community task. The Federal Ministry of Education and Research in Germany is providing funding for consortia consisting of university hospitals among others participating in the "Medical Informatics Initiative". Exchange of medical data between research institutions necessitates a place where meta information for this data is made accessible. Within these consortia different metadata registry solutions were chosen. To promote interoperability between these solutions, we have examined whether the portal of Medical Data Models is eligible for managing and communicating metadata and relevant information across different data integration centres of the Medical Informatics Initiative and beyond. Apart from the MDM-portal, some ISO 11179-based systems such as Samply.MDR as well as openEHR-based solutions are going to be applyed. In this paper, we have focused on the creation of a mapping model between the CDISC ODM standard and the Samply.MDR import format. In summary, it can be stated that the mapping model is feasible and promote the exchangeability between different metadata registry approaches.

Judo strategy. The competitive dynamics of Internet time.

PubMed

Yoffie, D B; Cusumano, M A

1999-01-01

Competition on the Internet is creating fierce battles between industry giants and small-scale start-ups. Smart start-ups can avoid those conflicts by moving quickly to uncontested ground and, when that's no longer possible, turning dominant players' strengths against them. The authors call this competitive approach judo strategy. They use the Netscape-Microsoft battles to illustrate the three main principles of judo strategy: rapid movement, flexibility, and leverage. In the early part of the browser wars, for instance, Netscape applied the principle of rapid movement by being the first company to offer a free stand-alone browser. This allowed Netscape to build market share fast and to set the market standard. Flexibility became a critical factor later in the browser wars. In December 1995, when Microsoft announced that it would "embrace and extend" competitors' Internet successes, Netscape failed to give way in the face of superior strength. Instead it squared off against Microsoft and even turned down numerous opportunities to craft deep partnerships with other companies. The result was that Netscape lost deal after deal when competing with Microsoft for common distribution channels. Netscape applied the principle of leverage by using Microsoft's strengths against it. Taking advantage of Microsoft's determination to convert the world to Windows or Windows NT, Netscape made its software compatible with existing UNIX systems. While it is true that these principles can't replace basic execution, say the authors, without speed, flexibility, and leverage, very few companies can compete successfully on Internet time.

A Policy Based Approach for the Management of Web Browser Resources to Prevent Anonymity Attacks in Tor

NASA Astrophysics Data System (ADS)

Navarro-Arribas, Guillermo; Garcia-Alfaro, Joaquin

Web browsers are becoming the universal interface to reach applications and services related with these systems. Different browsing contexts may be required in order to reach them, e.g., use of VPN tunnels, corporate proxies, anonymisers, etc. By browsing context we mean how the user browsers the Web, including mainly the concrete configuration of its browser. When the context of the browser changes, its security requirements also change. In this work, we present the use of authorisation policies to automatise the process of controlling the resources of a Web browser when its context changes. The objective of our proposal is oriented towards easing the adaptation to the security requirements of the new context and enforce them in the browser without the need for user intervention. We present a concrete application of our work as a plug-in for the adaption of security requirements in Mozilla/Firefox browser when a context of anonymous navigation through the Tor network is enabled.

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

Playing the Metadata Game: Technologies and Strategies Used by Climate Diagnostics Center for Cataloging and Distributing Climate Data.

NASA Astrophysics Data System (ADS)

Schweitzer, R. H.

2001-05-01

The Climate Diagnostics Center maintains a collection of gridded climate data primarily for use by local researchers. Because this data is available on fast digital storage and because it has been converted to netCDF using a standard metadata convention (called COARDS), we recognize that this data collection is also useful to the community at large. At CDC we try to use technology and metadata standards to reduce our costs associated with making these data available to the public. The World Wide Web has been an excellent technology platform for meeting that goal. Specifically we have developed Web-based user interfaces that allow users to search, plot and download subsets from the data collection. We have also been exploring use of the Pacific Marine Environment Laboratory's Live Access Server (LAS) as an engine for this task. This would result in further savings by allowing us to concentrate on customizing the LAS where needed, rather that developing and maintaining our own system. One such customization currently under development is the use of Java Servlets and JavaServer pages in conjunction with a metadata database to produce a hierarchical user interface to LAS. In addition to these Web-based user interfaces all of our data are available via the Distributed Oceanographic Data System (DODS). This allows other sites using LAS and individuals using DODS-enabled clients to use our data as if it were a local file. All of these technology systems are driven by metadata. When we began to create netCDF files, we collaborated with several other agencies to develop a netCDF convention (COARDS) for metadata. At CDC we have extended that convention to incorporate additional metadata elements to make the netCDF files as self-describing as possible. Part of the local metadata is a set of controlled names for the variable, level in the atmosphere and ocean, statistic and data set for each netCDF file. To allow searching and easy reorganization of these metadata, we loaded the metadata from the netCDF files into a mySQL database. The combination of the mySQL database and the controlled names makes it possible to automate the construction of user interfaces and standard format metadata descriptions, like Federal Geographic Data Committee (FGDC) and Directory Interchange Format (DIF). These standard descriptions also include an association between our controlled names and standard keywords such as those developed by the Global Change Master Directory (GCMD). This talk will give an overview of each of these technology and metadata standards as it applies to work at the Climate Diagnostics Center. The talk will also discuss the pros and cons of each approach and discuss areas for future development.

In-field Access to Geoscientific Metadata through GPS-enabled Mobile Phones

NASA Astrophysics Data System (ADS)

Hobona, Gobe; Jackson, Mike; Jordan, Colm; Butchart, Ben

2010-05-01

Fieldwork is an integral part of much geosciences research. But whilst geoscientists have physical or online access to data collections whilst in the laboratory or at base stations, equivalent in-field access is not standard or straightforward. The increasing availability of mobile internet and GPS-supported mobile phones, however, now provides the basis for addressing this issue. The SPACER project was commissioned by the Rapid Innovation initiative of the UK Joint Information Systems Committee (JISC) to explore the potential for GPS-enabled mobile phones to access geoscientific metadata collections. Metadata collections within the geosciences and the wider geospatial domain can be disseminated through web services based on the Catalogue Service for Web(CSW) standard of the Open Geospatial Consortium (OGC) - a global grouping of over 380 private, public and academic organisations aiming to improve interoperability between geospatial technologies. CSW offers an XML-over-HTTP interface for querying and retrieval of geospatial metadata. By default, the metadata returned by CSW is based on the ISO19115 standard and encoded in XML conformant to ISO19139. The SPACER project has created a prototype application that enables mobile phones to send queries to CSW containing user-defined keywords and coordinates acquired from GPS devices built-into the phones. The prototype has been developed using the free and open source Google Android platform. The mobile application offers views for listing titles, presenting multiple metadata elements and a Google Map with an overlay of bounding coordinates of datasets. The presentation will describe the architecture and approach applied in the development of the prototype.

A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human."

PubMed Central

2011-01-01

Background Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently no central repository for the depositing of data despite efforts by the Metabolomics Standard Initiative (MSI) to develop a standardised description of a metabolomic experiment. Findings In this manuscript we describe how the MSI description has been applied to a published dataset involving the identification of cross-species metabolic biomarkers associated with type II diabetes. The study describes sample collection of urine from mice, rats and human volunteers, and the subsequent acquisition of data by high resolution 1H NMR spectroscopy. The metadata is described to demonstrate how the MSI descriptions could be applied in a manuscript and the spectra have also been made available for the mouse and rat studies to allow others to process the data. Conclusions The intention of this manuscript is to stimulate discussion as to whether the MSI description is sufficient to describe the metadata associated with metabolomic experiments and encourage others to make their data available to other researchers. PMID:21801423

Exploring the enjoyment of playing browser games.

PubMed

Klimmt, Christoph; Schmid, Hannah; Orthmann, Julia

2009-04-01

Browser games--mostly persistent game worlds that can be used without client software and monetary cost with a Web browser--belong to the understudied digital game types, although they attract large player communities and motivate sustained play. The present work reports findings from an online survey of 8,203 players of a German strategy browser game ("Travian"). Results suggest that multiplayer browser games are enjoyed primarily because of the social relationships involved in game play and the specific time and flexibility characteristics ("easy-in, easy-out"). Competition, in contrast, seems to be less important for browser gamers than for users of other game types. Findings are discussed in terms of video game enjoyment and game addiction.

The AtChem On-line model and Electronic Laboratory Notebook (ELN): A free community modelling tool with provenance capture

NASA Astrophysics Data System (ADS)

Young, J. C.; Boronska, K.; Martin, C. J.; Rickard, A. R.; Vázquez Moreno, M.; Pilling, M. J.; Haji, M. H.; Dew, P. M.; Lau, L. M.; Jimack, P. K.

2010-12-01

AtChem On-line1 is a simple to use zero-dimensional box modelling toolkit, developed for use by laboratory, field and chamber scientists. Any set of chemical reactions can be simulated, in particular the whole Master Chemical Mechanism (MCM2) or any subset of it. Parameters and initial data can be provided through a self-explanatory web form and the resulting model is compiled and run on a dedicated server. The core part of the toolkit, providing a robust solver for thousands of chemical reactions, is written in Fortran and uses SUNDIALS3 CVODE libraries. Chemical systems can be constrained at multiple, user-determined timescales; this enabled studies of radical chemistry at one minute timescales. AtChem On-line is free to use and requires no installation - a web browser, text editor and any compressing software is all the user needs. CPU and storage are provided by the server (input and output data are saved indefinitely). An off-line version is also being developed, which will provide batch processing, an advanced graphical user interface and post-processing tools, for example, Rate of Production Analysis (ROPA) and chainlength analysis. The source code is freely available for advanced users wishing to adapt and run the program locally. Data management, dissemination and archiving are essential in all areas of science. In order to do this in an efficient and transparent way, there is a critical need to capture high quality metadata/provenance for modelling activities. An Electronic Laboratory Notebook (ELN) has been developed in parallel with AtChem Online as part of the EC EUROCHAMP24 project. In order to use controlled chamber experiments to evaluate the MCM, we need to be able to archive, track and search information on all associated chamber model runs, so that they can be used in subsequent mechanism development. Therefore it would be extremely useful if experiment and model metadata/provenance could be easily and automatically stored electronically. Archiving metadata/provenance via an ELN makes it easier to write a paper or thesis and for mechanism developers/evaluators/peer review to search for appropriate experimental and modelling results and conclusions. The development of an ELN in the context mechanism evaluation/development using large experimental chamber datasets is presented.

The MMI Device Ontology: Enabling Sensor Integration

NASA Astrophysics Data System (ADS)

Rueda, C.; Galbraith, N.; Morris, R. A.; Bermudez, L. E.; Graybeal, J.; Arko, R. A.; Mmi Device Ontology Working Group

2010-12-01

The Marine Metadata Interoperability (MMI) project has developed an ontology for devices to describe sensors and sensor networks. This ontology is implemented in the W3C Web Ontology Language (OWL) and provides an extensible conceptual model and controlled vocabularies for describing heterogeneous instrument types, with different data characteristics, and their attributes. It can help users populate metadata records for sensors; associate devices with their platforms, deployments, measurement capabilities and restrictions; aid in discovery of sensor data, both historic and real-time; and improve the interoperability of observational oceanographic data sets. We developed the MMI Device Ontology following a community-based approach. By building on and integrating other models and ontologies from related disciplines, we sought to facilitate semantic interoperability while avoiding duplication. Key concepts and insights from various communities, including the Open Geospatial Consortium (eg., SensorML and Observations and Measurements specifications), Semantic Web for Earth and Environmental Terminology (SWEET), and W3C Semantic Sensor Network Incubator Group, have significantly enriched the development of the ontology. Individuals ranging from instrument designers, science data producers and consumers to ontology specialists and other technologists contributed to the work. Applications of the MMI Device Ontology are underway for several community use cases. These include vessel-mounted multibeam mapping sonars for the Rolling Deck to Repository (R2R) program and description of diverse instruments on deepwater Ocean Reference Stations for the OceanSITES program. These trials involve creation of records completely describing instruments, either by individual instances or by manufacturer and model. Individual terms in the MMI Device Ontology can be referenced with their corresponding Uniform Resource Identifiers (URIs) in sensor-related metadata specifications (e.g., SensorML, NetCDF). These identifiers can be resolved through a web browser, or other client applications via HTTP against the MMI Ontology Registry and Repository (ORR), where the ontology is maintained. SPARQL-based query capabilities, which are enhanced with reasoning, along with several supported output formats, allow the effective interaction of diverse client applications with the semantic information associated with the device ontology. In this presentation we describe the process for the development of the MMI Device Ontology and illustrate extensions and applications that demonstrate the benefits of adopting this semantic approach, including example queries involving inference. We also highlight the issues encountered and future work.

Cyberspace for the Tenderfoot.

ERIC Educational Resources Information Center

Lemon, Donald K.

1997-01-01

Educators should plug into cyberspace to receive high-quality information, make connections to other people's ideas, and get answers applying to their work and personal interests. The K-12 Admin Listserv responded to a survey the author posted saying that certain features discussed here (web browser, newsgroup, e-mail, listserv, and gopher) were…

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata.

PubMed

Hu, Wei; Zaveri, Amrapali; Qiu, Honglei; Dumontier, Michel

2017-09-18

The ability to efficiently search and filter datasets depends on access to high quality metadata. While most biomedical repositories require data submitters to provide a minimal set of metadata, some such as the Gene Expression Omnibus (GEO) allows users to specify additional metadata in the form of textual key-value pairs (e.g. sex: female). However, since there is no structured vocabulary to guide the submitter regarding the metadata terms to use, consequently, the 44,000,000+ key-value pairs in GEO suffer from numerous quality issues including redundancy, heterogeneity, inconsistency, and incompleteness. Such issues hinder the ability of scientists to hone in on datasets that meet their requirements and point to a need for accurate, structured and complete description of the data. In this study, we propose a clustering-based approach to address data quality issues in biomedical, specifically gene expression, metadata. First, we present three different kinds of similarity measures to compare metadata keys. Second, we design a scalable agglomerative clustering algorithm to cluster similar keys together. Our agglomerative cluster algorithm identified metadata keys that were similar, based on (i) name, (ii) core concept and (iii) value similarities, to each other and grouped them together. We evaluated our method using a manually created gold standard in which 359 keys were grouped into 27 clusters based on six types of characteristics: (i) age, (ii) cell line, (iii) disease, (iv) strain, (v) tissue and (vi) treatment. As a result, the algorithm generated 18 clusters containing 355 keys (four clusters with only one key were excluded). In the 18 clusters, there were keys that were identified correctly to be related to that cluster, but there were 13 keys which were not related to that cluster. We compared our approach with four other published methods. Our approach significantly outperformed them for most metadata keys and achieved the best average F-Score (0.63). Our algorithm identified keys that were similar to each other and grouped them together. Our intuition that underpins cleaning by clustering is that, dividing keys into different clusters resolves the scalability issues for data observation and cleaning, and keys in the same cluster with duplicates and errors can easily be found. Our algorithm can also be applied to other biomedical data types.

Distributed metadata servers for cluster file systems using shared low latency persistent key-value metadata store

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bent, John M.; Faibish, Sorin; Pedone, Jr., James M.

A cluster file system is provided having a plurality of distributed metadata servers with shared access to one or more shared low latency persistent key-value metadata stores. A metadata server comprises an abstract storage interface comprising a software interface module that communicates with at least one shared persistent key-value metadata store providing a key-value interface for persistent storage of key-value metadata. The software interface module provides the key-value metadata to the at least one shared persistent key-value metadata store in a key-value format. The shared persistent key-value metadata store is accessed by a plurality of metadata servers. A metadata requestmore » can be processed by a given metadata server independently of other metadata servers in the cluster file system. A distributed metadata storage environment is also disclosed that comprises a plurality of metadata servers having an abstract storage interface to at least one shared persistent key-value metadata store.« less

A metadata approach for clinical data management in translational genomics studies in breast cancer.

PubMed

Papatheodorou, Irene; Crichton, Charles; Morris, Lorna; Maccallum, Peter; Davies, Jim; Brenton, James D; Caldas, Carlos

2009-11-30

In molecular profiling studies of cancer patients, experimental and clinical data are combined in order to understand the clinical heterogeneity of the disease: clinical information for each subject needs to be linked to tumour samples, macromolecules extracted, and experimental results. This may involve the integration of clinical data sets from several different sources: these data sets may employ different data definitions and some may be incomplete. In this work we employ semantic web techniques developed within the CancerGrid project, in particular the use of metadata elements and logic-based inference to annotate heterogeneous clinical information, integrate and query it. We show how this integration can be achieved automatically, following the declaration of appropriate metadata elements for each clinical data set; we demonstrate the practicality of this approach through application to experimental results and clinical data from five hospitals in the UK and Canada, undertaken as part of the METABRIC project (Molecular Taxonomy of Breast Cancer International Consortium). We describe a metadata approach for managing similarities and differences in clinical datasets in a standardized way that uses Common Data Elements (CDEs). We apply and evaluate the approach by integrating the five different clinical datasets of METABRIC.

Integrating Semantic Information in Metadata Descriptions for a Geoscience-wide Resource Inventory.

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Richard, S. M.; Gupta, A.; Valentine, D.; Whitenack, T.; Ozyurt, I. B.; Grethe, J. S.; Schachne, A.

2016-12-01

Integrating semantic information into legacy metadata catalogs is a challenging issue and so far has been mostly done on a limited scale. We present experience of CINERGI (Community Inventory of Earthcube Resources for Geoscience Interoperability), an NSF Earthcube Building Block project, in creating a large cross-disciplinary catalog of geoscience information resources to enable cross-domain discovery. The project developed a pipeline for automatically augmenting resource metadata, in particular generating keywords that describe metadata documents harvested from multiple geoscience information repositories or contributed by geoscientists through various channels including surveys and domain resource inventories. The pipeline examines available metadata descriptions using text parsing, vocabulary management and semantic annotation and graph navigation services of GeoSciGraph. GeoSciGraph, in turn, relies on a large cross-domain ontology of geoscience terms, which bridges several independently developed ontologies or taxonomies including SWEET, ENVO, YAGO, GeoSciML, GCMD, SWO, and CHEBI. The ontology content enables automatic extraction of keywords reflecting science domains, equipment used, geospatial features, measured properties, methods, processes, etc. We specifically focus on issues of cross-domain geoscience ontology creation, resolving several types of semantic conflicts among component ontologies or vocabularies, and constructing and managing facets for improved data discovery and navigation. The ontology and keyword generation rules are iteratively improved as pipeline results are presented to data managers for selective manual curation via a CINERGI Annotator user interface. We present lessons learned from applying CINERGI metadata augmentation pipeline to a number of federal agency and academic data registries, in the context of several use cases that require data discovery and integration across multiple earth science data catalogs of varying quality and completeness. The inventory is accessible at http://cinergi.sdsc.edu, and the CINERGI project web page is http://earthcube.org/group/cinergi

Design and implementation of a P300-based brain-computer interface for controlling an internet browser.

PubMed

Mugler, Emily M; Ruf, Carolin A; Halder, Sebastian; Bensch, Michael; Kubler, Andrea

2010-12-01

An electroencephalographic (EEG) brain-computer interface (BCI) internet browser was designed and evaluated with 10 healthy volunteers and three individuals with advanced amyotrophic lateral sclerosis (ALS), all of whom were given tasks to execute on the internet using the browser. Participants with ALS achieved an average accuracy of 73% and a subsequent information transfer rate (ITR) of 8.6 bits/min and healthy participants with no prior BCI experience over 90% accuracy and an ITR of 14.4 bits/min. We define additional criteria for unrestricted internet access for evaluation of the presented and future internet browsers, and we provide a review of the existing browsers in the literature. The P300-based browser provides unrestricted access and enables free web surfing for individuals with paralysis.

linkedISA: semantic representation of ISA-Tab experimental metadata.

PubMed

González-Beltrán, Alejandra; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While ISA-Tab works well mainly as a human readable format, we have also implemented a linked data approach to semantically define the ISA-Tab syntax. We present a semantic web representation of the ISA-Tab syntax that complements ISA-Tab's syntactic interoperability with semantic interoperability. We introduce the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata. We describe insights of the implementation and how annotations can be expanded driven by the metadata. We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions. Designed in a user-friendly manner, the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description to allow seamless interaction with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design. In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication. Our linked data approach has allowed us to: 1) make the ISA-Tab semantics explicit and machine-processable, 2) exploit the existing ontology-based annotations in the ISA-Tab experimental descriptions, 3) augment the ISA-Tab syntax with new descriptive elements, 4) visualise and query elements related to the experimental design. Reasoning over ISA-Tab metadata and associated data will facilitate data integration and knowledge discovery.

The VIS-AD data model: Integrating metadata and polymorphic display with a scientific programming language

NASA Technical Reports Server (NTRS)

Hibbard, William L.; Dyer, Charles R.; Paul, Brian E.

1994-01-01

The VIS-AD data model integrates metadata about the precision of values, including missing data indicators and the way that arrays sample continuous functions, with the data objects of a scientific programming language. The data objects of this data model form a lattice, ordered by the precision with which they approximate mathematical objects. We define a similar lattice of displays and study visualization processes as functions from data lattices to display lattices. Such functions can be applied to visualize data objects of all data types and are thus polymorphic.

The STP (Solar-Terrestrial Physics) Semantic Web based on the RSS1.0 and the RDF

NASA Astrophysics Data System (ADS)

Kubo, T.; Murata, K. T.; Kimura, E.; Ishikura, S.; Shinohara, I.; Kasaba, Y.; Watari, S.; Matsuoka, D.

2006-12-01

In the Solar-Terrestrial Physics (STP), it is pointed out that circulation and utilization of observation data among researchers are insufficient. To archive interdisciplinary researches, we need to overcome this circulation and utilization problems. Under such a background, authors' group has developed a world-wide database that manages meta-data of satellite and ground-based observation data files. It is noted that retrieving meta-data from the observation data and registering them to database have been carried out by hand so far. Our goal is to establish the STP Semantic Web. The Semantic Web provides a common framework that allows a variety of data shared and reused across applications, enterprises, and communities. We also expect that the secondary information related with observations, such as event information and associated news, are also shared over the networks. The most fundamental issue on the establishment is who generates, manages and provides meta-data in the Semantic Web. We developed an automatic meta-data collection system for the observation data using the RSS (RDF Site Summary) 1.0. The RSS1.0 is one of the XML-based markup languages based on the RDF (Resource Description Framework), which is designed for syndicating news and contents of news-like sites. The RSS1.0 is used to describe the STP meta-data, such as data file name, file server address and observation date. To describe the meta-data of the STP beyond RSS1.0 vocabulary, we defined original vocabularies for the STP resources using the RDF Schema. The RDF describes technical terms on the STP along with the Dublin Core Metadata Element Set, which is standard for cross-domain information resource descriptions. Researchers' information on the STP by FOAF, which is known as an RDF/XML vocabulary, creates a machine-readable metadata describing people. Using the RSS1.0 as a meta-data distribution method, the workflow from retrieving meta-data to registering them into the database is automated. This technique is applied for several database systems, such as the DARTS database system and NICT Space Weather Report Service. The DARTS is a science database managed by ISAS/JAXA in Japan. We succeeded in generating and collecting the meta-data automatically for the CDF (Common data Format) data, such as Reimei satellite data, provided by the DARTS. We also create an RDF service for space weather report and real-time global MHD simulation 3D data provided by the NICT. Our Semantic Web system works as follows: The RSS1.0 documents generated on the data sites (ISAS and NICT) are automatically collected by a meta-data collection agent. The RDF documents are registered and the agent extracts meta-data to store them in the Sesame, which is an open source RDF database with support for RDF Schema inferencing and querying. The RDF database provides advanced retrieval processing that has considered property and relation. Finally, the STP Semantic Web provides automatic processing or high level search for the data which are not only for observation data but for space weather news, physical events, technical terms and researches information related to the STP.

Rangeland mismanagement in South Africa: Failure to apply ecological knowledge

Treesearch

Andrew T. Hudak

1999-01-01

Chronic, heavy livestock grazing and concomitant fire suppression have caused the gradual replacement of palatable grass species by less palatable trees and woody shrubs in a rangeland degradation process termed bush encroachment in South Africa. Grazing policymakers and cattle farmers alike have not appreciated the ecological role fire and native browsers play in...

BrainBrowser: distributed, web-based neurological data visualization.

PubMed

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C

2014-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

BrainBrowser: distributed, web-based neurological data visualization

PubMed Central

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C.

2015-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible. PMID:25628562

Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

PubMed

Vempati, Uma D; Chung, Caty; Mader, Chris; Koleti, Amar; Datar, Nakul; Vidović, Dušica; Wrobel, David; Erickson, Sean; Muhlich, Jeremy L; Berriz, Gabriel; Benes, Cyril H; Subramanian, Aravind; Pillai, Ajay; Shamu, Caroline E; Schürer, Stephan C

2014-06-01

The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available. © 2014 Society for Laboratory Automation and Screening.

Log-less metadata management on metadata server for parallel file systems.

PubMed

Liao, Jianwei; Xiao, Guoqiang; Peng, Xiaoning

2014-01-01

This paper presents a novel metadata management mechanism on the metadata server (MDS) for parallel and distributed file systems. In this technique, the client file system backs up the sent metadata requests, which have been handled by the metadata server, so that the MDS does not need to log metadata changes to nonvolatile storage for achieving highly available metadata service, as well as better performance improvement in metadata processing. As the client file system backs up certain sent metadata requests in its memory, the overhead for handling these backup requests is much smaller than that brought by the metadata server, while it adopts logging or journaling to yield highly available metadata service. The experimental results show that this newly proposed mechanism can significantly improve the speed of metadata processing and render a better I/O data throughput, in contrast to conventional metadata management schemes, that is, logging or journaling on MDS. Besides, a complete metadata recovery can be achieved by replaying the backup logs cached by all involved clients, when the metadata server has crashed or gone into nonoperational state exceptionally.

Log-Less Metadata Management on Metadata Server for Parallel File Systems

PubMed Central

Xiao, Guoqiang; Peng, Xiaoning

2014-01-01

This paper presents a novel metadata management mechanism on the metadata server (MDS) for parallel and distributed file systems. In this technique, the client file system backs up the sent metadata requests, which have been handled by the metadata server, so that the MDS does not need to log metadata changes to nonvolatile storage for achieving highly available metadata service, as well as better performance improvement in metadata processing. As the client file system backs up certain sent metadata requests in its memory, the overhead for handling these backup requests is much smaller than that brought by the metadata server, while it adopts logging or journaling to yield highly available metadata service. The experimental results show that this newly proposed mechanism can significantly improve the speed of metadata processing and render a better I/O data throughput, in contrast to conventional metadata management schemes, that is, logging or journaling on MDS. Besides, a complete metadata recovery can be achieved by replaying the backup logs cached by all involved clients, when the metadata server has crashed or gone into nonoperational state exceptionally. PMID:24892093

Firefox add-ons for medical reference.

PubMed

Hoy, Matthew B

2010-07-01

Firefox is a Web browser created by the Mozilla project, an open-source software group. Features of the browser include automated updates, advanced security and standards compliance, and the ability to add functionality through add-ons and extensions. First introduced in 2004, Firefox now accounts for roughly 30% of the browser market. This article will focus primarily on add-ons and extensions available for the browser that are useful to medical researchers.

Gene Ontology Consortium: going forward.

PubMed

2015-01-01

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

STATS SRS v11.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piscotty, M A; Nazario, O L

2007-06-20

The objective of this project is the delivery of an application that will provide a unified, web-based system for collecting, verifying and analyzing the achievements for Laboratory employees. The application will enable individual Directorates to manage and report achievement record data for their employees using an LLNL standard web browser. In addition, cross directorate data reporting and analysis will be available for such organizations as LSTO and programmatic directorates. This system is intended to store reference data and metadata for employee achievements. Abstracts and entire publications will not be stored in this system.Directorates are expected to use this system atmore » all levels of management in preparing for Annual Self-Assessments, peer reviews, LDRD reviews, work force reviews, performance appraisals, and requests from sponsors. This document represents the primary deliverable for the Requirements Definition stage of system development. As part of a successful Requirements Definition, this document provides the development staff, the project sponsor, and the user community with a clear understanding of the product's operational, data, and other requirements. With this understanding, the development staff will take the opportunity to refine estimates regarding the cost, schedule, and deliverables reflected in it.« less

Web Browser Trends and Technologies.

ERIC Educational Resources Information Center

Goodwin-Jones, Bob

2000-01-01

Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

A Common Metadata System for Marine Data Portals

NASA Astrophysics Data System (ADS)

Wosniok, C.; Breitbach, G.; Lehfeldt, R.

2012-04-01

Processing and allocation of marine datasets depend on the nature of the data resulting from field campaigns, continuous monitoring and numerical modeling. Two research and development projects in northern Germany manage different types of marine data. Due to different data characteristics and institutional frameworks separate data portals are required. This paper describes the integration of distributed marine data in Germany. The Marine Data Infrastructure of Germany (MDI-DE) supports public authorities in the German coastal zone with the implementation of European directives like INSPIRE or the Marine Strategy Framework Directive. This is carried out through setting up standardized web services within a network of participating coastal agencies and the installation of a common data portal (http://www.mdi-de.org), which integrates distributed marine data concerning coastal engineering, coastal water protection and nature conservation in an interoperable and harmonized manner for administrative and scientific purposes as well as for information of the general public. The Coastal Observation System for Northern and Arctic Seas (COSYNA) aims at developing and testing analysis systems for the operational synoptic description of the environmental status of the North Sea and of Arctic coastal waters. This is done by establishing a network of monitoring facilities and the provision of its data in near-real-time. In situ measurements with poles, ferry boxes, and buoys, together with remote sensing measurements, and the data assimilation of these data into simulation results enables COSYNA to provide pre-operational 'products', that are beyond the present routinely applied techniques in observation and modelling. The data allocation in near-real-time requires thoroughly executed data validation, which is processed on the fly before data is passed on to the COSYNA portal (http://kofserver2.hzg.de/codm/). Both projects apply OGC standards such as Web Mapping Service (WMS), Web Feature Service (WFS) and Sensor Observation Service (SOS), which ensures interoperability and extensibility. In addition, metadata as crucial components for searching and finding information in large data infrastructures is provided via the Catalogue Web Service (CS-W). MDI-DE and COSYNA rely on the metadata information system for marine metadata NOKIS, which reflects a metadata profile tailored for marine data according to the specifications of German coastal authorities. In spite of this common software base, interoperability between the two data collections requires constant alignments of the diverse data processed by the two portals. While monitoring data in the MDI-DE is currently rather campaign-based, COSYNA has to fit constantly evolving time series into metadata sets. With all data following the same metadata profile, we now reach full interoperability between the different data collections. The distributed marine information system provides options to search, find and visualise the harmonised results from continuous monitoring, field campaigns, numerical modeling and other data in one web client.

Eco-Health Relationship Browser

EPA Science Inventory

The Eco-Health Relationship Browser (Browser) is a web tool designed to portray, in an engaging and intuitive way, the linkages between ecosystems, their services, and potential health outcomes that have been associated with those services in the literature. It functions an inte...

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

GeoNetwork powered GI-cat: a geoportal hybrid solution

NASA Astrophysics Data System (ADS)

Baldini, Alessio; Boldrini, Enrico; Santoro, Mattia; Mazzetti, Paolo

2010-05-01

To the aim of setting up a Spatial Data Infrastructures (SDI) the creation of a system for the metadata management and discovery plays a fundamental role. An effective solution is the use of a geoportal (e.g. FAO/ESA geoportal), that has the important benefit of being accessible from a web browser. With this work we present a solution based integrating two of the available frameworks: GeoNetwork and GI-cat. GeoNetwork is an opensource software designed to improve accessibility of a wide variety of data together with the associated ancillary information (metadata), at different scale and from multidisciplinary sources; data are organized and documented in a standard and consistent way. GeoNetwork implements both the Portal and Catalog components of a Spatial Data Infrastructure (SDI) defined in the OGC Reference Architecture. It provides tools for managing and publishing metadata on spatial data and related services. GeoNetwork allows harvesting of various types of web data sources e.g. OGC Web Services (e.g. CSW, WCS, WMS). GI-cat is a distributed catalog based on a service-oriented framework of modular components and can be customized and tailored to support different deployment scenarios. It can federate a multiplicity of catalogs services, as well as inventory and access services in order to discover and access heterogeneous ESS resources. The federated resources are exposed by GI-cat through several standard catalog interfaces (e.g. OGC CSW AP ISO, OpenSearch, etc.) and by the GI-cat extended interface. Specific components implement mediation services for interfacing heterogeneous service providers, each of which exposes a specific standard specification; such components are called Accessors. These mediating components solve providers data modelmultiplicity by mapping them onto the GI-cat internal data model which implements the ISO 19115 Core profile. Accessors also implement the query protocol mapping; first they translate the query requests expressed according to the interface protocols exposed by GI-cat into the multiple query dialects spoken by the resource service providers. Currently, a number of well-accepted catalog and inventory services are supported, including several OGC Web Services, THREDDS Data Server, SeaDataNet Common Data Index, GBIF and OpenSearch engines. A GeoNetwork powered GI-cat has been developed in order to exploit the best of the two frameworks. The new system uses a modified version of GeoNetwork web interface in order to add the capability of querying also the specified GI-cat catalog and not only the GeoNetwork internal database. The resulting system consists in a geoportal in which GI-cat plays the role of the search engine. This new system allows to distribute the query on the different types of data sources linked to a GI-cat. The metadata results of the query are then visualized by the Geonetwork web interface. This configuration was experimented in the framework of GIIDA, a project of the Italian National Research Council (CNR) focused on data accessibility and interoperability. A second advantage of this solution is achieved setting up a GeoNetwork catalog amongst the accessors of the GI-cat instance. Such a configuration will allow in turn GI-cat to run the query against the internal GeoNetwork database. This allows to have both the harvesting and the metadata editor functionalities provided by GeoNetwork and the distributed search functionality of GI-cat available in a consistent way through the same web interface.

DataSync - sharing data via filesystem

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Klump, Jens

2014-05-01

Usually research work is a cycle of to hypothesize, to collect data, to corroborate the hypothesis, and finally to publish the results. In this sequence there are possibilities to base the own work on the work of others. Maybe there are candidates of physical samples listed in the IGSN-Registry and there is no need to go on excursion to acquire physical samples. Hopefully the DataCite catalogue lists already metadata of datasets that meet the constraints of the hypothesis and that are now open for reappraisal. After all, working with the measured data to corroborate the hypothesis involves new methods, and proven methods as well as different software tools. A cohort of intermediate data is created that can be shared with colleagues to discuss the research progress and receive a first evaluation. In consequence, the intermediate data should be versioned to easily get back to valid intermediate data, when you notice you get on the wrong track. Things are different for project managers. They want to know what is currently done, what has been done, and what is the last valid data, if somebody has to continue the work. To make life of members of small science projects easier we developed Datasync [1] as a software for sharing and versioning data. Datasync is designed to synchronize directory trees between different computers of a research team over the internet. The software is developed as JAVA application and watches a local directory tree for changes that are replicated as eSciDoc-objects into an eSciDoc-infrastructure [2] using the eSciDoc REST API. Modifications to the local filesystem automatically create a new version of an eSciDoc-object inside the eSciDoc-infrastructure. This way individual folders can be shared between team members while project managers can get a general idea of current status by synchronizing whole project inventories. Additionally XML metadata from separate files can be managed together with data files inside the eSciDoc-objects. While Datasync's major task is to distribute directory trees, we complement its functionality with the PHP-based application panMetaDocs [3]. panMetaDocs is the successor to panMetaWorks [4] and inherits most of its functionality. Through an internet browser PanMetaDocs provides a web-based overview of the datasets inside the eSciDoc-infrastructure. The software allows to upload further data, to add and edit metadata using the metadata editor, and it disseminates metadata through various channels. In addition, previous versions of a file can be downloaded and access rights can be defined on files and folders to control visibility of files for users of both panMetaDocs and Datasync. panMetaDocs serves as a publication agent for datasets and it serves as a registration agent for dataset DOIs. The application stack presented here allows sharing, versioning, and central storage of data from the very beginning of project activities by using the file synchronization service Datasync. The web-application panMetaDocs complements the functionality of DataSync by providing a dataset publication agent and other tools to handle administrative tasks on the data. [1] http://github.com/ulbricht/datasync [2] http://github.com/escidoc [3] http://panmetadocs.sf.net [4] http://metaworks.pangaea.de

Exchanging the Context between OGC Geospatial Web clients and GIS applications using Atom

NASA Astrophysics Data System (ADS)

Maso, Joan; Díaz, Paula; Riverola, Anna; Pons, Xavier

2013-04-01

Currently, the discovery and sharing of geospatial information over the web still presents difficulties. News distribution through website content was simplified by the use of Really Simple Syndication (RSS) and Atom syndication formats. This communication exposes an extension of Atom to redistribute references to geospatial information in a Spatial Data Infrastructure distributed environment. A geospatial client can save the status of an application that involves several OGC services of different kind and direct data and share this status with other users that need the same information and use different client vendor products in an interoperable way. The extensibility of the Atom format was essential to define a format that could be used in RSS enabled web browser, Mass Market map viewers and emerging geospatial enable integrated clients that support Open Geospatial Consortium (OGC) services. Since OWS Context has been designed as an Atom extension, it is possible to see the document in common places where Atom documents are valid. Internet web browsers are able to present the document as a list of items with title, abstract, time, description and downloading features. OWS Context uses GeoRSS so that, the document can be to be interpreted by both Google maps and Bing Maps as items that have the extent represented in a dynamic map. Another way to explode a OWS Context is to develop an XSLT to transform the Atom feed into an HTML5 document that shows the exact status of the client view window that saved the context document. To accomplish so, we use the width and height of the client window, and the extent of the view in world (geographic) coordinates in order to calculate the scale of the map. Then, we can mix elements in world coordinates (such as CF-NetCDF files or GML) with elements in pixel coordinates (such as WMS maps, WMTS tiles and direct SVG content). A smarter map browser application called MiraMon Map Browser is able to write a context document and read it again to recover the context of the previous view or load a context generated by another application. The possibility to store direct links to direct files in OWS Context is particularly interesting for GIS desktop solutions. This communication also presents the development made in the MiraMon desktop GIS solution to include OWS Context. MiraMon software is able to deal either with local files, web services and database connections. As in any other GIS solution, MiraMon team designed its own file (MiraMon Map MMM) for storing and sharing the status of a GIS session. The new OWS Context format is now adopted as an interoperable substitution of the MMM. The extensibility of the format makes it possible to map concepts in the MMM to current OWS Context elements (such as titles, data links, extent, etc) and to generate new elements that are able to include all extra metadata not currently covered by OWS Context. These developments were done in the nine edition of the OpenGIS Web Services Interoperability Experiment (OWS-9) and are demonstrated in this communication.

Architecture for the Interdisciplinary Earth Data Alliance

NASA Astrophysics Data System (ADS)

Richard, S. M.

2016-12-01

The Interdisciplinary Earth Data Alliance (IEDA) is leading an EarthCube (EC) Integrative Activity to develop a governance structure and technology framework that enables partner data systems to share technology, infrastructure, and practice for documenting, curating, and accessing heterogeneous geoscience data. The IEDA data facility provides capabilities in an extensible framework that enables domain-specific requirements for each partner system in the Alliance to be integrated into standardized cross-domain workflows. The shared technology infrastructure includes a data submission hub, a domain-agnostic file-based repository, an integrated Alliance catalog and a Data Browser for data discovery across all partner holdings, as well as services for registering identifiers for datasets (DOI) and samples (IGSN). The submission hub will be a platform that facilitates acquisition of cross-domain resource documentation and channels users into domain and resource-specific workflows tailored for each partner community. We are exploring an event-based message bus architecture with a standardized plug-in interface for adding capabilities. This architecture builds on the EC CINERGI metadata pipeline as well as the message-based architecture of the SEAD project. Plug-in components for file introspection to match entities to a data type registry (extending EC Digital Crust and Research Data Alliance work), extract standardized keywords (using CINERGI components), location, cruise, personnel and other metadata linkage information (building on GeoLink and existing IEDA partner components). The submission hub will feed submissions to appropriate partner repositories and service endpoints targeted by domain and resource type for distribution. The Alliance governance will adopt patterns (vocabularies, operations, resource types) for self-describing data services using standard HTTP protocol for simplified data access (building on EC GeoWS and other `RESTful' approaches). Exposure of resource descriptions (datasets and service distributions) for harvesting by commercial search engines as well as geoscience-data focused crawlers (like EC B-Cube crawler) will increase discoverability of IEDA resources with minimal effort by curators.

Feature-Based Statistical Analysis of Combustion Simulation Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, J; Krishnamoorthy, V; Liu, S

2011-11-18

We present a new framework for feature-based statistical analysis of large-scale scientific data and demonstrate its effectiveness by analyzing features from Direct Numerical Simulations (DNS) of turbulent combustion. Turbulent flows are ubiquitous and account for transport and mixing processes in combustion, astrophysics, fusion, and climate modeling among other disciplines. They are also characterized by coherent structure or organized motion, i.e. nonlocal entities whose geometrical features can directly impact molecular mixing and reactive processes. While traditional multi-point statistics provide correlative information, they lack nonlocal structural information, and hence, fail to provide mechanistic causality information between organized fluid motion and mixing andmore » reactive processes. Hence, it is of great interest to capture and track flow features and their statistics together with their correlation with relevant scalar quantities, e.g. temperature or species concentrations. In our approach we encode the set of all possible flow features by pre-computing merge trees augmented with attributes, such as statistical moments of various scalar fields, e.g. temperature, as well as length-scales computed via spectral analysis. The computation is performed in an efficient streaming manner in a pre-processing step and results in a collection of meta-data that is orders of magnitude smaller than the original simulation data. This meta-data is sufficient to support a fully flexible and interactive analysis of the features, allowing for arbitrary thresholds, providing per-feature statistics, and creating various global diagnostics such as Cumulative Density Functions (CDFs), histograms, or time-series. We combine the analysis with a rendering of the features in a linked-view browser that enables scientists to interactively explore, visualize, and analyze the equivalent of one terabyte of simulation data. We highlight the utility of this new framework for combustion science; however, it is applicable to many other science domains.« less

Provenance for Runtime Workflow Steering and Validation in Computational Seismology

NASA Astrophysics Data System (ADS)

Spinuso, A.; Krischer, L.; Krause, A.; Filgueira, R.; Magnoni, F.; Muraleedharan, V.; David, M.

2014-12-01

Provenance systems may be offered by modern workflow engines to collect metadata about the data transformations at runtime. If combined with effective visualisation and monitoring interfaces, these provenance recordings can speed up the validation process of an experiment, suggesting interactive or automated interventions with immediate effects on the lifecycle of a workflow run. For instance, in the field of computational seismology, if we consider research applications performing long lasting cross correlation analysis and high resolution simulations, the immediate notification of logical errors and the rapid access to intermediate results, can produce reactions which foster a more efficient progress of the research. These applications are often executed in secured and sophisticated HPC and HTC infrastructures, highlighting the need for a comprehensive framework that facilitates the extraction of fine grained provenance and the development of provenance aware components, leveraging the scalability characteristics of the adopted workflow engines, whose enactment can be mapped to different technologies (MPI, Storm clusters, etc). This work looks at the adoption of W3C-PROV concepts and data model within a user driven processing and validation framework for seismic data, supporting also computational and data management steering. Validation needs to balance automation with user intervention, considering the scientist as part of the archiving process. Therefore, the provenance data is enriched with community-specific metadata vocabularies and control messages, making an experiment reproducible and its description consistent with the community understandings. Moreover, it can contain user defined terms and annotations. The current implementation of the system is supported by the EU-Funded VERCE (http://verce.eu). It provides, as well as the provenance generation mechanisms, a prototypal browser-based user interface and a web API built on top of a NoSQL storage technology, experimenting ways to ensure a rapid and flexible access to the lineage traces. It supports the users with the visualisation of graphical products and offers combined operations to access and download the data which may be selectively stored at runtime, into dedicated data archives.

Leveraging Open Standards and Technologies to Search and Display Planetary Image Data

NASA Astrophysics Data System (ADS)

Rose, M.; Schauer, C.; Quinol, M.; Trimble, J.

2011-12-01

Mars and the Moon have both been visited by multiple NASA spacecraft. A large number of images and other data have been gathered by the spacecraft and are publicly available in NASA's Planetary Data System. Through a collaboration with Google, Inc., the User Centered Technologies group at NASA Ames Resarch Center has developed at tool for searching and browsing among images from multiple Mars and Moon missions. Development of this tool was facilitated by the use of several open technologies and standards. First, an open-source full-text search engine is used to search both place names on the target and to find images matching a geographic region. Second, the published API of the Google Earth browser plugin is used to geolocate the images on a virtual globe and allow the user to navigate on the globe to see related images. The structure of the application also employs standard protocols and services. The back-end is exposed as RESTful APIs, which could be reused by other client systems in the future. Further, the communication between the front- and back-end portions of the system utilizes open data standards including XML and KML (Keyhole Markup Language) for representation of textual and geographic data. The creation of the search index was facilitated by reuse of existing, publicly available metadata, including the Gazetteer of Planetary Nomenclature from the USGS, available in KML format. And the image metadata was reused from standards-compliant archives in the Planetary Data System. The system also supports collaboration with other tools by allowing export of search results in KML, and the ability to display those results in the Google Earth desktop application. We will demonstrate the search and visualization capabilities of the system, with emphasis on how the system facilitates reuse of data and services through the adoption of open standards.

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E. W. H.; Overeem, I.; Syvitski, J. P.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) has a mission to enable model use and development for research in earth surface processes. CSDMS strives to expand the use of quantitative modeling techniques, promotes best practices in coding, and advocates for the use of open-source software. To streamline and standardize access to models, CSDMS has developed the Web Modeling Tool (WMT), a RESTful web application with a client-side graphical interface and a server-side database and API that allows users to build coupled surface dynamics models in a web browser on a personal computer or a mobile device, and run them in a high-performance computing (HPC) environment. With WMT, users can: Design a model from a set of components Edit component parameters Save models to a web-accessible server Share saved models with the community Submit runs to an HPC system Download simulation results The WMT client is an Ajax application written in Java with GWT, which allows developers to employ object-oriented design principles and development tools such as Ant, Eclipse and JUnit. For deployment on the web, the GWT compiler translates Java code to optimized and obfuscated JavaScript. The WMT client is supported on Firefox, Chrome, Safari, and Internet Explorer. The WMT server, written in Python and SQLite, is a layered system, with each layer exposing a web service API: wmt-db: database of component, model, and simulation metadata and output wmt-api: configure and connect components wmt-exe: launch simulations on remote execution servers The database server provides, as JSON-encoded messages, the metadata for users to couple model components, including descriptions of component exchange items, uses and provides ports, and input parameters. Execution servers are network-accessible computational resources, ranging from HPC systems to desktop computers, containing the CSDMS software stack for running a simulation. Once a simulation completes, its output, in NetCDF, is packaged and uploaded to a data server where it is stored and from which a user can download it as a single compressed archive file.

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

PubMed

Rideout, Jai Ram; Chase, John H; Bolyen, Evan; Ackermann, Gail; González, Antonio; Knight, Rob; Caporaso, J Gregory

2016-06-13

Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.

Web Services and Data Enhancements at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Lombard, P. N.; Allen, R. M.

2013-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, simple text, or MiniSEED depending on the service and selected output format. The NCEDC offers the following web services that are compliant with the International Federation of Digital Seismograph Networks (FDSN) web services specifications: (1) fdsn-dataselect: time series data delivered in MiniSEED format, (2) fdsn-station: station and channel metadata and time series availability delivered in StationXML format, (3) fdsn-event: earthquake event information delivered in QuakeML format. In addition, the NCEDC offers the the following IRIS-compatible web services: (1) sacpz: provide channel gains, poles, and zeros in SAC format, (2) resp: provide channel response information in RESP format, (3) dataless: provide station and channel metadata in Dataless SEED format. The NCEDC is also developing a web service to deliver timeseries from pre-assembled event waveform gathers. The NCEDC has waveform gathers for ~750,000 northern and central California events from 1984 to the present, many of which were created by the USGS NCSN prior to the establishment of the joint NCSS (Northern California Seismic System). We are currently adding waveforms to these older event gathers with time series from the UCB networks and other networks with waveforms archived at the NCEDC, and ensuring that the waveform for each channel in the event gathers have the highest quality waveform from the archive.

Metadata for Web Resources: How Metadata Works on the Web.

ERIC Educational Resources Information Center

Dillon, Martin

This paper discusses bibliographic control of knowledge resources on the World Wide Web. The first section sets the context of the inquiry. The second section covers the following topics related to metadata: (1) definitions of metadata, including metadata as tags and as descriptors; (2) metadata on the Web, including general metadata systems,…

Metadata Dictionary Database: A Proposed Tool for Academic Library Metadata Management

ERIC Educational Resources Information Center

Southwick, Silvia B.; Lampert, Cory

2011-01-01

This article proposes a metadata dictionary (MDD) be used as a tool for metadata management. The MDD is a repository of critical data necessary for managing metadata to create "shareable" digital collections. An operational definition of metadata management is provided. The authors explore activities involved in metadata management in…

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

PubMed

Martínez-Romero, Marcos; O'Connor, Martin J; Shankar, Ravi D; Panahiazar, Maryam; Willrett, Debra; Egyedi, Attila L; Gevaert, Olivier; Graybeal, John; Musen, Mark A

2017-01-01

In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository.

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations

PubMed Central

Martínez-Romero, Marcos; O’Connor, Martin J.; Shankar, Ravi D.; Panahiazar, Maryam; Willrett, Debra; Egyedi, Attila L.; Gevaert, Olivier; Graybeal, John; Musen, Mark A.

2017-01-01

In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository. PMID:29854196

A rapid prototyping/artificial intelligence approach to space station-era information management and access

NASA Technical Reports Server (NTRS)

Carnahan, Richard S., Jr.; Corey, Stephen M.; Snow, John B.

1989-01-01

Applications of rapid prototyping and Artificial Intelligence techniques to problems associated with Space Station-era information management systems are described. In particular, the work is centered on issues related to: (1) intelligent man-machine interfaces applied to scientific data user support, and (2) the requirement that intelligent information management systems (IIMS) be able to efficiently process metadata updates concerning types of data handled. The advanced IIMS represents functional capabilities driven almost entirely by the needs of potential users. Space Station-era scientific data projected to be generated is likely to be significantly greater than data currently processed and analyzed. Information about scientific data must be presented clearly, concisely, and with support features to allow users at all levels of expertise efficient and cost-effective data access. Additionally, mechanisms for allowing more efficient IIMS metadata update processes must be addressed. The work reported covers the following IIMS design aspects: IIMS data and metadata modeling, including the automatic updating of IIMS-contained metadata, IIMS user-system interface considerations, including significant problems associated with remote access, user profiles, and on-line tutorial capabilities, and development of an IIMS query and browse facility, including the capability to deal with spatial information. A working prototype has been developed and is being enhanced.

EMERALD: Coping with the Explosion of Seismic Data

NASA Astrophysics Data System (ADS)

West, J. D.; Fouch, M. J.; Arrowsmith, R.

2009-12-01

The geosciences are currently generating an unparalleled quantity of new public broadband seismic data with the establishment of large-scale seismic arrays such as the EarthScope USArray, which are enabling new and transformative scientific discoveries of the structure and dynamics of the Earth’s interior. Much of this explosion of data is a direct result of the formation of the IRIS consortium, which has enabled an unparalleled level of open exchange of seismic instrumentation, data, and methods. The production of these massive volumes of data has generated new and serious data management challenges for the seismological community. A significant challenge is the maintenance and updating of seismic metadata, which includes information such as station location, sensor orientation, instrument response, and clock timing data. This key information changes at unknown intervals, and the changes are not generally communicated to data users who have already downloaded and processed data. Another basic challenge is the ability to handle massive seismic datasets when waveform file volumes exceed the fundamental limitations of a computer’s operating system. A third, long-standing challenge is the difficulty of exchanging seismic processing codes between researchers; each scientist typically develops his or her own unique directory structure and file naming convention, requiring that codes developed by another researcher be rewritten before they can be used. To address these challenges, we are developing EMERALD (Explore, Manage, Edit, Reduce, & Analyze Large Datasets). The overarching goal of the EMERALD project is to enable more efficient and effective use of seismic datasets ranging from just a few hundred to millions of waveforms with a complete database-driven system, leading to higher quality seismic datasets for scientific analysis and enabling faster, more efficient scientific research. We will present a preliminary (beta) version of EMERALD, an integrated, extensible, standalone database server system based on the open-source PostgreSQL database engine. The system is designed for fast and easy processing of seismic datasets, and provides the necessary tools to manage very large datasets and all associated metadata. EMERALD provides methods for efficient preprocessing of seismic records; large record sets can be easily and quickly searched, reviewed, revised, reprocessed, and exported. EMERALD can retrieve and store station metadata and alert the user to metadata changes. The system provides many methods for visualizing data, analyzing dataset statistics, and tracking the processing history of individual datasets. EMERALD allows development and sharing of visualization and processing methods using any of 12 programming languages. EMERALD is designed to integrate existing software tools; the system provides wrapper functionality for existing widely-used programs such as GMT, SOD, and TauP. Users can interact with EMERALD via a web browser interface, or they can directly access their data from a variety of database-enabled external tools. Data can be imported and exported from the system in a variety of file formats, or can be directly requested and downloaded from the IRIS DMC from within EMERALD.

Harvesting NASA's Common Metadata Repository (CMR)

NASA Technical Reports Server (NTRS)

Shum, Dana; Durbin, Chris; Norton, James; Mitchell, Andrew

2017-01-01

As part of NASA's Earth Observing System Data and Information System (EOSDIS), the Common Metadata Repository (CMR) stores metadata for over 30,000 datasets from both NASA and international providers along with over 300M granules. This metadata enables sub-second discovery and facilitates data access. While the CMR offers a robust temporal, spatial and keyword search functionality to the general public and international community, it is sometimes more desirable for international partners to harvest the CMR metadata and merge the CMR metadata into a partner's existing metadata repository. This poster will focus on best practices to follow when harvesting CMR metadata to ensure that any changes made to the CMR can also be updated in a partner's own repository. Additionally, since each partner has distinct metadata formats they are able to consume, the best practices will also include guidance on retrieving the metadata in the desired metadata format using CMR's Unified Metadata Model translation software.

Harvesting NASA's Common Metadata Repository

NASA Astrophysics Data System (ADS)

Shum, D.; Mitchell, A. E.; Durbin, C.; Norton, J.

2017-12-01

As part of NASA's Earth Observing System Data and Information System (EOSDIS), the Common Metadata Repository (CMR) stores metadata for over 30,000 datasets from both NASA and international providers along with over 300M granules. This metadata enables sub-second discovery and facilitates data access. While the CMR offers a robust temporal, spatial and keyword search functionality to the general public and international community, it is sometimes more desirable for international partners to harvest the CMR metadata and merge the CMR metadata into a partner's existing metadata repository. This poster will focus on best practices to follow when harvesting CMR metadata to ensure that any changes made to the CMR can also be updated in a partner's own repository. Additionally, since each partner has distinct metadata formats they are able to consume, the best practices will also include guidance on retrieving the metadata in the desired metadata format using CMR's Unified Metadata Model translation software.

International Metadata Standards and Enterprise Data Quality Metadata Systems

NASA Astrophysics Data System (ADS)

Habermann, T.

2016-12-01

Well-documented data quality is critical in situations where scientists and decision-makers need to combine multiple datasets from different disciplines and collection systems to address scientific questions or difficult decisions. Standardized data quality metadata could be very helpful in these situations. Many efforts at developing data quality standards falter because of the diversity of approaches to measuring and reporting data quality. The "one size fits all" paradigm does not generally work well in this situation. The ISO data quality standard (ISO 19157) takes a different approach with the goal of systematically describing how data quality is measured rather than how it should be measured. It introduces the idea of standard data quality measures that can be well documented in a measure repository and used for consistently describing how data quality is measured across an enterprise. The standard includes recommendations for properties of these measures that include unique identifiers, references, illustrations and examples. Metadata records can reference these measures using the unique identifier and reuse them along with details (and references) that describe how the measure was applied to a particular dataset. A second important feature of ISO 19157 is the inclusion of citations to existing papers or reports that describe quality of a dataset. This capability allows users to find this information in a single location, i.e. the dataset metadata, rather than searching the web or other catalogs. I will describe these and other capabilities of ISO 19157 with examples of how they are being used to describe data quality across the NASA EOS Enterprise and also compare these approaches with other standards.

GenColors: annotation and comparative genomics of prokaryotes made easy.

PubMed

Romualdi, Alessandro; Felder, Marius; Rose, Dominic; Gausmann, Ulrike; Schilhabel, Markus; Glöckner, Gernot; Platzer, Matthias; Sühnel, Jürgen

2007-01-01

GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.

Genomes as geography: using GIS technology to build interactive genome feature maps

PubMed Central

Dolan, Mary E; Holden, Constance C; Beard, M Kate; Bult, Carol J

2006-01-01

Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. Results We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. Conclusion Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries. PMID:16984652

CERESVis: A QC Tool for CERES that Leverages Browser Technology for Data Validation

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Doelling, D.

2015-12-01

In this poster, we are going to present three user interfaces that CERES team uses to validate pixel-level data. Besides our home grown tools, we will aslo present the browser technology that we use to provide interactive interfaces, such as jquery, HighCharts and Google Earth. We pass data to the users' browsers and use the browsers to do some simple computations. The three user interfaces are: Thumbnails -- it displays hundrends images to allow users to browse 24-hour data files in few seconds. Multiple-synchronized cursors -- it allows users to compare multiple images side by side. Bounding Boxes and Histograms -- it allows users to draw multiple bounding boxes on an image and the browser computes/display the histograms.

Simplified Metadata Curation via the Metadata Management Tool

NASA Astrophysics Data System (ADS)

Shum, D.; Pilone, D.

2015-12-01

The Metadata Management Tool (MMT) is the newest capability developed as part of NASA Earth Observing System Data and Information System's (EOSDIS) efforts to simplify metadata creation and improve metadata quality. The MMT was developed via an agile methodology, taking into account inputs from GCMD's science coordinators and other end-users. In its initial release, the MMT uses the Unified Metadata Model for Collections (UMM-C) to allow metadata providers to easily create and update collection records in the ISO-19115 format. Through a simplified UI experience, metadata curators can create and edit collections without full knowledge of the NASA Best Practices implementation of ISO-19115 format, while still generating compliant metadata. More experienced users are also able to access raw metadata to build more complex records as needed. In future releases, the MMT will build upon recent work done in the community to assess metadata quality and compliance with a variety of standards through application of metadata rubrics. The tool will provide users with clear guidance as to how to easily change their metadata in order to improve their quality and compliance. Through these features, the MMT allows data providers to create and maintain compliant and high quality metadata in a short amount of time.

Navigating protected genomics data with UCSC Genome Browser in a Box.

PubMed

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

2015-03-01

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

Enriched Video Semantic Metadata: Authorization, Integration, and Presentation.

ERIC Educational Resources Information Center

Mu, Xiangming; Marchionini, Gary

2003-01-01

Presents an enriched video metadata framework including video authorization using the Video Annotation and Summarization Tool (VAST)-a video metadata authorization system that integrates both semantic and visual metadata-- metadata integration, and user level applications. Results demonstrated that the enriched metadata were seamlessly…

Tools and Methods for Visualization of Mesoscale Ocean Eddies

NASA Astrophysics Data System (ADS)

Bemis, K. G.; Liu, L.; Silver, D.; Kang, D.; Curchitser, E.

2017-12-01

Mesoscale ocean eddies form in the Gulf Stream and transport heat and nutrients across the ocean basin. The internal structure of these three-dimensional eddies and the kinematics with which they move are critical to a full understanding of their transport capacity. A series of visualization tools have been developed to extract, characterize, and track ocean eddies from 3D modeling results, to visually show the ocean eddy story by applying various illustrative visualization techniques, and to interactively view results stored on a server from a conventional browser. In this work, we apply a feature-based method to track instances of ocean eddies through the time steps of a high-resolution multidecadal regional ocean model and generate a series of eddy paths which reflect the life cycle of individual eddy instances. The basic method uses the Okubu-Weiss parameter to define eddy cores but could be adapted to alternative specifications of an eddy. Stored results include pixel-lists for each eddy instance, tracking metadata for eddy paths, and physical and geometric properties. In the simplest view, isosurfaces are used to display eddies along an eddy path. Individual eddies can then be selected and viewed independently or an eddy path can be viewed in the context of all eddy paths (longer than a specified duration) and the ocean basin. To tell the story of mesoscale ocean eddies, we combined illustrative visualization techniques, including visual effectiveness enhancement, focus+context, and smart visibility, with the extracted volume features to explore eddy characteristics at multiple scales from ocean basin to individual eddy. An evaluation by domain experts indicates that combining our feature-based techniques with illustrative visualization techniques provides an insight into the role eddies play in ocean circulation. A web-based GUI is under development to facilitate easy viewing of stored results. The GUI provides the user control to choose amongst available datasets, to specify the variables (such as temperature or salinity) to display on the isosurfaces, and to choose the scale and orientation of the view. These techniques allow an oceanographer to browse the data based on eddy paths and individual eddies rather than slices or volumes of data.

Serious Games for Health: The Potential of Metadata.

PubMed

Göbel, Stefan; Maddison, Ralph

2017-02-01

Numerous serious games and health games exist, either as commercial products (typically with a focus on entertaining a broad user group) or smaller games and game prototypes, often resulting from research projects (typically tailored to a smaller user group with a specific health characteristic). A major drawback of existing health games is that they are not very well described and attributed with (machine-readable, quantitative, and qualitative) metadata such as the characterizing goal of the game, the target user group, or expected health effects well proven in scientific studies. This makes it difficult or even impossible for end users to find and select the most appropriate game for a specific situation (e.g., health needs). Therefore, the aim of this article was to motivate the need and potential/benefit of metadata for the description and retrieval of health games and to describe a descriptive model for the qualitative description of games for health. It was not the aim of the article to describe a stable, running system (portal) for health games. This will be addressed in future work. Building on previous work toward a metadata format for serious games, a descriptive model for the formal description of games for health is introduced. For the conceptualization of this model, classification schemata of different existing health game repositories are considered. The classification schema consists of three levels: a core set of mandatory descriptive fields relevant for all games for health application areas, a detailed level with more comprehensive, optional information about the games, and so-called extension as level three with specific descriptive elements relevant for dedicated health games application areas, for example, cardio training. A metadata format provides a technical framework to describe, find, and select appropriate health games matching the needs of the end user. Future steps to improve, apply, and promote the metadata format in the health games market are discussed.

Partnerships To Mine Unexploited Sources of Metadata.

ERIC Educational Resources Information Center

Reynolds, Regina Romano

This paper discusses the metadata created for other purposes as a potential source of bibliographic data. The first section addresses collecting metadata by means of templates, including the Nordic Metadata Project's Dublin Core Metadata Template. The second section considers potential partnerships for re-purposing metadata for bibliographic use,…

47 CFR 14.61 - Obligations with respect to internet browsers built into mobile phones.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false Obligations with respect to internet browsers... GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Internet... internet browsers built into mobile phones. (a) Accessibility. If on or after October 8, 2013 a...

47 CFR 14.61 - Obligations with respect to internet browsers built into mobile phones.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 1 2013-10-01 2013-10-01 false Obligations with respect to internet browsers... GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Internet... internet browsers built into mobile phones. (a) Accessibility. If on or after October 8, 2013 a...

Ajax and Firefox: New Web Applications and Browsers

ERIC Educational Resources Information Center

Godwin-Jones, Bob

2005-01-01

Alternative browsers are gaining significant market share, and both Apple and Microsoft are releasing OS upgrades which portend some interesting changes in Web development. Of particular interest for language learning professionals may be new developments in the area of Web browser based applications, particularly using an approach dubbed "Ajax."…

A Window to the World: Lessons Learned from NASA's Collaborative Metadata Curation Effort

NASA Astrophysics Data System (ADS)

Bugbee, K.; Dixon, V.; Baynes, K.; Shum, D.; le Roux, J.; Ramachandran, R.

2017-12-01

Well written descriptive metadata adds value to data by making data easier to discover as well as increases the use of data by providing the context or appropriateness of use. While many data centers acknowledge the importance of correct, consistent and complete metadata, allocating resources to curate existing metadata is often difficult. To lower resource costs, many data centers seek guidance on best practices for curating metadata but struggle to identify those recommendations. In order to assist data centers in curating metadata and to also develop best practices for creating and maintaining metadata, NASA has formed a collaborative effort to improve the Earth Observing System Data and Information System (EOSDIS) metadata in the Common Metadata Repository (CMR). This effort has taken significant steps in building consensus around metadata curation best practices. However, this effort has also revealed gaps in EOSDIS enterprise policies and procedures within the core metadata curation task. This presentation will explore the mechanisms used for building consensus on metadata curation, the gaps identified in policies and procedures, the lessons learned from collaborating with both the data centers and metadata curation teams, and the proposed next steps for the future.

Programmatic access to data and information at the IRIS DMC via web services

NASA Astrophysics Data System (ADS)

Weertman, B. R.; Trabant, C.; Karstens, R.; Suleiman, Y. Y.; Ahern, T. K.; Casey, R.; Benson, R. B.

2011-12-01

The IRIS Data Management Center (DMC) has developed a suite of web services that provide access to the DMC's time series holdings, their related metadata and earthquake catalogs. In addition, services are available to perform simple, on-demand time series processing at the DMC prior to being shipped to the user. The primary goal is to provide programmatic access to data and processing services in a manner usable by and useful to the research community. The web services are relatively simple to understand and use and will form the foundation on which future DMC access tools will be built. Based on standard Web technologies they can be accessed programmatically with a wide range of programming languages (e.g. Perl, Python, Java), command line utilities such as wget and curl or with any web browser. We anticipate these services being used for everything from simple command line access, used in shell scripts and higher programming languages to being integrated within complex data processing software. In addition to improving access to our data by the seismological community the web services will also make our data more accessible to other disciplines. The web services available from the DMC include ws-bulkdataselect for the retrieval of large volumes of miniSEED data, ws-timeseries for the retrieval of individual segments of time series data in a variety of formats (miniSEED, SAC, ASCII, audio WAVE, and PNG plots) with optional signal processing, ws-station for station metadata in StationXML format, ws-resp for the retrieval of instrument response in RESP format, ws-sacpz for the retrieval of sensor response in the SAC poles and zeros convention and ws-event for the retrieval of earthquake catalogs. To make the services even easier to use, the DMC is developing a library that allows Java programmers to seamlessly retrieve and integrate DMC information into their own programs. The library will handle all aspects of dealing with the services and will parse the returned data. By using this library a developer will not need to learn the details of the service interfaces or understand the data formats returned. This library will be used to build the software bridge needed to request data and information from within MATLAB°. We also provide several client scripts written in Perl for the retrieval of waveform data, metadata and earthquake catalogs using command line programs. For more information on the DMC's web services please visit http://www.iris.edu/ws/

Passenger baggage object database (PBOD)

NASA Astrophysics Data System (ADS)

Gittinger, Jaxon M.; Suknot, April N.; Jimenez, Edward S.; Spaulding, Terry W.; Wenrich, Steve A.

2018-04-01

Detection of anomalies of interest in x-ray images is an ever-evolving problem that requires the rapid development of automatic detection algorithms. Automatic detection algorithms are developed using machine learning techniques, which would require developers to obtain the x-ray machine that was used to create the images being trained on, and compile all associated metadata for those images by hand. The Passenger Baggage Object Database (PBOD) and data acquisition application were designed and developed for acquiring and persisting 2-D and 3-D x-ray image data and associated metadata. PBOD was specifically created to capture simulated airline passenger "stream of commerce" luggage data, but could be applied to other areas of x-ray imaging to utilize machine-learning methods.

PACS on mobile devices

NASA Astrophysics Data System (ADS)

Parikh, Ashesh; Mehta, Nihal

2015-03-01

Recent advances in internet browser technologies makes it possible to incorporate advanced functionality of a traditional PACS for viewing DICOM medical images on standard web browsers without the need to pre-install any plug-ins, apps or software. We demonstrate some of the capabilities of standard web browsers setting the stage for a cloud-based PACS.

YADBrowser: A Browser for Web-Based Educational Applications

ERIC Educational Resources Information Center

Zaldivar, Vicente Arturo Romero; Arandia, Jon Ander Elorriaga; Brito, Mateo Lezcano

2005-01-01

In this article, the main characteristics of the educational browser YADBrowser are described. One of the main objectives of this project is to define new languages and object models which facilitate the creation of educational applications for the Internet. The fundamental characteristics of the object model of the browser are also described.…

ISO 19115 Experiences in NASA's Earth Observing System (EOS) ClearingHOuse (ECHO)

NASA Astrophysics Data System (ADS)

Cechini, M. F.; Mitchell, A.

2011-12-01

Metadata is an important entity in the process of cataloging, discovering, and describing earth science data. As science research and the gathered data increases in complexity, so does the complexity and importance of descriptive metadata. To meet these growing needs, the metadata models required utilize richer and more mature metadata attributes. Categorizing, standardizing, and promulgating these metadata models to a politically, geographically, and scientifically diverse community is a difficult process. An integral component of metadata management within NASA's Earth Observing System Data and Information System (EOSDIS) is the Earth Observing System (EOS) ClearingHOuse (ECHO). ECHO is the core metadata repository for the EOSDIS data centers providing a centralized mechanism for metadata and data discovery and retrieval. ECHO has undertaken an internal restructuring to meet the changing needs of scientists, the consistent advancement in technology, and the advent of new standards such as ISO 19115. These improvements were based on the following tenets for data discovery and retrieval: + There exists a set of 'core' metadata fields recommended for data discovery. + There exists a set of users who will require the entire metadata record for advanced analysis. + There exists a set of users who will require a 'core' set metadata fields for discovery only. + There will never be a cessation of new formats or a total retirement of all old formats. + Users should be presented metadata in a consistent format of their choosing. In order to address the previously listed items, ECHO's new metadata processing paradigm utilizes the following approach: + Identify a cross-format set of 'core' metadata fields necessary for discovery. + Implement format-specific indexers to extract the 'core' metadata fields into an optimized query capability. + Archive the original metadata in its entirety for presentation to users requiring the full record. + Provide on-demand translation of 'core' metadata to any supported result format. Lessons learned by the ECHO team while implementing its new metadata approach to support usage of the ISO 19115 standard will be presented. These lessons learned highlight some discovered strengths and weaknesses in the ISO 19115 standard as it is introduced to an existing metadata processing system.

Metadata squared: enhancing its usability for volunteered geographic information and the GeoWeb

USGS Publications Warehouse

Poore, Barbara S.; Wolf, Eric B.; Sui, Daniel Z.; Elwood, Sarah; Goodchild, Michael F.

2013-01-01

The Internet has brought many changes to the way geographic information is created and shared. One aspect that has not changed is metadata. Static spatial data quality descriptions were standardized in the mid-1990s and cannot accommodate the current climate of data creation where nonexperts are using mobile phones and other location-based devices on a continuous basis to contribute data to Internet mapping platforms. The usability of standard geospatial metadata is being questioned by academics and neogeographers alike. This chapter analyzes current discussions of metadata to demonstrate how the media shift that is occurring has affected requirements for metadata. Two case studies of metadata use are presented—online sharing of environmental information through a regional spatial data infrastructure in the early 2000s, and new types of metadata that are being used today in OpenStreetMap, a map of the world created entirely by volunteers. Changes in metadata requirements are examined for usability, the ease with which metadata supports coproduction of data by communities of users, how metadata enhances findability, and how the relationship between metadata and data has changed. We argue that traditional metadata associated with spatial data infrastructures is inadequate and suggest several research avenues to make this type of metadata more interactive and effective in the GeoWeb.

Evolutions in Metadata Quality

NASA Astrophysics Data System (ADS)

Gilman, J.

2016-12-01

Metadata Quality is one of the chief drivers of discovery and use of NASA EOSDIS (Earth Observing System Data and Information System) data. Issues with metadata such as lack of completeness, inconsistency, and use of legacy terms directly hinder data use. As the central metadata repository for NASA Earth Science data, the Common Metadata Repository (CMR) has a responsibility to its users to ensure the quality of CMR search results. This talk will cover how we encourage metadata authors to improve the metadata through the use of integrated rubrics of metadata quality and outreach efforts. In addition we'll demonstrate Humanizers, a technique for dealing with the symptoms of metadata issues. Humanizers allow CMR administrators to identify specific metadata issues that are fixed at runtime when the data is indexed. An example Humanizer is the aliasing of processing level "Level 1" to "1" to improve consistency across collections. The CMR currently indexes 35K collections and 300M granules.

Metadata Means Communication: The Challenges of Producing Useful Metadata

NASA Astrophysics Data System (ADS)

Edwards, P. N.; Batcheller, A. L.

2010-12-01

Metadata are increasingly perceived as an important component of data sharing systems. For instance, metadata accompanying atmospheric model output may indicate the grid size, grid type, and parameter settings used in the model configuration. We conducted a case study of a data portal in the atmospheric sciences using in-depth interviews, document review, and observation. OUr analysis revealed a number of challenges in producing useful metadata. First, creating and managing metadata required considerable effort and expertise, yet responsibility for these tasks was ill-defined and diffused among many individuals, leading to errors, failure to capture metadata, and uncertainty about the quality of the primary data. Second, metadata ended up stored in many different forms and software tools, making it hard to manage versions and transfer between formats. Third, the exact meanings of metadata categories remained unsettled and misunderstood even among a small community of domain experts -- an effect we expect to be exacerbated when scientists from other disciplines wish to use these data. In practice, we found that metadata problems due to these obstacles are often overcome through informal, personal communication, such as conversations or email. We conclude that metadata serve to communicate the context of data production from the people who produce data to those who wish to use it. Thus while formal metadata systems are often public, critical elements of metadata (those embodied in informal communication) may never be recorded. Therefore, efforts to increase data sharing should include ways to facilitate inter-investigator communication. Instead of tackling metadata challenges only on the formal level, we can improve data usability for broader communities by better supporting metadata communication.

The role of metadata in managing large environmental science datasets. Proceedings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melton, R.B.; DeVaney, D.M.; French, J. C.

1995-06-01

The purpose of this workshop was to bring together computer science researchers and environmental sciences data management practitioners to consider the role of metadata in managing large environmental sciences datasets. The objectives included: establishing a common definition of metadata; identifying categories of metadata; defining problems in managing metadata; and defining problems related to linking metadata with primary data.

Information-Flow-Based Access Control for Web Browsers

NASA Astrophysics Data System (ADS)

Yoshihama, Sachiko; Tateishi, Takaaki; Tabuchi, Naoshi; Matsumoto, Tsutomu

The emergence of Web 2.0 technologies such as Ajax and Mashup has revealed the weakness of the same-origin policy[1], the current de facto standard for the Web browser security model. We propose a new browser security model to allow fine-grained access control in the client-side Web applications for secure mashup and user-generated contents. We propose a browser security model that is based on information-flow-based access control (IBAC) to overcome the dynamic nature of the client-side Web applications and to accurately determine the privilege of scripts in the event-driven programming model.

Introduction to the fathead minnow genome browser and ...

EPA Pesticide Factsheets

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minnow genomic sequence. This work is meant to extend the utility of fathead minnow genome as a resource and enable the continued development of this species as a model organism. The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporti

Evolution of Web Services in EOSDIS: Search and Order Metadata Registry (ECHO)

NASA Technical Reports Server (NTRS)

Mitchell, Andrew; Ramapriyan, Hampapuram; Lowe, Dawn

2009-01-01

During 2005 through 2008, NASA defined and implemented a major evolutionary change in it Earth Observing system Data and Information System (EOSDIS) to modernize its capabilities. This implementation was based on a vision for 2015 developed during 2005. The EOSDIS 2015 Vision emphasizes increased end-to-end data system efficiency and operability; increased data usability; improved support for end users; and decreased operations costs. One key feature of the Evolution plan was achieving higher operational maturity (ingest, reconciliation, search and order, performance, error handling) for the NASA s Earth Observing System Clearinghouse (ECHO). The ECHO system is an operational metadata registry through which the scientific community can easily discover and exchange NASA's Earth science data and services. ECHO contains metadata for 2,726 data collections comprising over 87 million individual data granules and 34 million browse images, consisting of NASA s EOSDIS Data Centers and the United States Geological Survey's Landsat Project holdings. ECHO is a middleware component based on a Service Oriented Architecture (SOA). The system is comprised of a set of infrastructure services that enable the fundamental SOA functions: publish, discover, and access Earth science resources. It also provides additional services such as user management, data access control, and order management. The ECHO system has a data registry and a services registry. The data registry enables organizations to publish EOS and other Earth-science related data holdings to a common metadata model. These holdings are described through metadata in terms of datasets (types of data) and granules (specific data items of those types). ECHO also supports browse images, which provide a visual representation of the data. The published metadata can be mapped to and from existing standards (e.g., FGDC, ISO 19115). With ECHO, users can find the metadata stored in the data registry and then access the data either directly online or through a brokered order to the data archive organization. ECHO stores metadata from a variety of science disciplines and domains, including Climate Variability and Change, Carbon Cycle and Ecosystems, Earth Surface and Interior, Atmospheric Composition, Weather, and Water and Energy Cycle. ECHO also has a services registry for community-developed search services and data services. ECHO provides a platform for the publication, discovery, understanding and access to NASA s Earth Observation resources (data, service and clients). In their native state, these data, service and client resources are not necessarily targeted for use beyond their original mission. However, with the proper interoperability mechanisms, users of these resources can expand their value, by accessing, combining and applying them in unforeseen ways.

An Asynchronous P300-Based Brain-Computer Interface Web Browser for Severely Disabled People.

PubMed

Martinez-Cagigal, Victor; Gomez-Pilar, Javier; Alvarez, Daniel; Hornero, Roberto

2017-08-01

This paper presents an electroencephalographic (EEG) P300-based brain-computer interface (BCI) Internet browser. The system uses the "odd-ball" row-col paradigm for generating the P300 evoked potentials on the scalp of the user, which are immediately processed and translated into web browser commands. There were previous approaches for controlling a BCI web browser. However, to the best of our knowledge, none of them was focused on an assistive context, failing to test their applications with a suitable number of end users. In addition, all of them were synchronous applications, where it was necessary to introduce a "read-mode" command in order to avoid a continuous command selection. Thus, the aim of this study is twofold: 1) to test our web browser with a population of multiple sclerosis (MS) patients in order to assess the usefulness of our proposal to meet their daily communication needs; and 2) to overcome the aforementioned limitation by adding a threshold that discerns between control and non-control states, allowing the user to calmly read the web page without undesirable selections. The browser was tested with sixteen MS patients and five healthy volunteers. Both quantitative and qualitative metrics were obtained. MS participants reached an average accuracy of 84.14%, whereas 95.75% was achieved by control subjects. Results show that MS patients can successfully control the BCI web browser, improving their personal autonomy.

Building Format-Agnostic Metadata Repositories

NASA Astrophysics Data System (ADS)

Cechini, M.; Pilone, D.

2010-12-01

This presentation will discuss the problems that surround persisting and discovering metadata in multiple formats; a set of tenets that must be addressed in a solution; and NASA’s Earth Observing System (EOS) ClearingHOuse’s (ECHO) proposed approach. In order to facilitate cross-discipline data analysis, Earth Scientists will potentially interact with more than one data source. The most common data discovery paradigm relies on services and/or applications facilitating the discovery and presentation of metadata. What may not be common are the formats in which the metadata are formatted. As the number of sources and datasets utilized for research increases, it becomes more likely that a researcher will encounter conflicting metadata formats. Metadata repositories, such as the EOS ClearingHOuse (ECHO), along with data centers, must identify ways to address this issue. In order to define the solution to this problem, the following tenets are identified: - There exists a set of ‘core’ metadata fields recommended for data discovery. - There exists a set of users who will require the entire metadata record for advanced analysis. - There exists a set of users who will require a ‘core’ set of metadata fields for discovery only. - There will never be a cessation of new formats or a total retirement of all old formats. - Users should be presented metadata in a consistent format. ECHO has undertaken an effort to transform its metadata ingest and discovery services in order to support the growing set of metadata formats. In order to address the previously listed items, ECHO’s new metadata processing paradigm utilizes the following approach: - Identify a cross-format set of ‘core’ metadata fields necessary for discovery. - Implement format-specific indexers to extract the ‘core’ metadata fields into an optimized query capability. - Archive the original metadata in its entirety for presentation to users requiring the full record. - Provide on-demand translation of ‘core’ metadata to any supported result format. With this identified approach, the Earth Scientist is provided with a consistent data representation as they interact with a variety of datasets that utilize multiple metadata formats. They are then able to focus their efforts on the more critical research activities which they are undertaking.

Making Metadata Better with CMR and MMT

NASA Technical Reports Server (NTRS)

Gilman, Jason Arthur; Shum, Dana

2016-01-01

Ensuring complete, consistent and high quality metadata is a challenge for metadata providers and curators. The CMR and MMT systems provide providers and curators options to build in metadata quality from the start and also assess and improve the quality of already existing metadata.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

PubMed

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

Evolution in Metadata Quality: Common Metadata Repository's Role in NASA Curation Efforts

NASA Technical Reports Server (NTRS)

Gilman, Jason; Shum, Dana; Baynes, Katie

2016-01-01

Metadata Quality is one of the chief drivers of discovery and use of NASA EOSDIS (Earth Observing System Data and Information System) data. Issues with metadata such as lack of completeness, inconsistency, and use of legacy terms directly hinder data use. As the central metadata repository for NASA Earth Science data, the Common Metadata Repository (CMR) has a responsibility to its users to ensure the quality of CMR search results. This poster covers how we use humanizers, a technique for dealing with the symptoms of metadata issues, as well as our plans for future metadata validation enhancements. The CMR currently indexes 35K collections and 300M granules.

Speech Recognition for A Digital Video Library.

ERIC Educational Resources Information Center

Witbrock, Michael J.; Hauptmann, Alexander G.

1998-01-01

Production of the meta-data supporting the Informedia Digital Video Library interface is automated using techniques derived from artificial intelligence research. Speech recognition and natural-language processing, information retrieval, and image analysis are applied to produce an interface that helps users locate information and navigate more…

The Primate Life History Database: A unique shared ecological data resource

PubMed Central

Strier, Karen B.; Altmann, Jeanne; Brockman, Diane K.; Bronikowski, Anne M.; Cords, Marina; Fedigan, Linda M.; Lapp, Hilmar; Liu, Xianhua; Morris, William F.; Pusey, Anne E.; Stoinski, Tara S.; Alberts, Susan C.

2011-01-01

Summary The importance of data archiving, data sharing, and public access to data has received considerable attention. Awareness is growing among scientists that collaborative databases can facilitate these activities.We provide a detailed description of the collaborative life history database developed by our Working Group at the National Evolutionary Synthesis Center (NESCent) to address questions about life history patterns and the evolution of mortality and demographic variability in wild primates.Examples from each of the seven primate species included in our database illustrate the range of data incorporated and the challenges, decision-making processes, and criteria applied to standardize data across diverse field studies. In addition to the descriptive and structural metadata associated with our database, we also describe the process metadata (how the database was designed and delivered) and the technical specifications of the database.Our database provides a useful model for other researchers interested in developing similar types of databases for other organisms, while our process metadata may be helpful to other groups of researchers interested in developing databases for other types of collaborative analyses. PMID:21698066

CONNJUR R: An annotation strategy for fostering reproducibility in bio-NMR: protein spectral assignment

PubMed Central

Fenwick, Matthew; Hoch, Jeffrey C.; Ulrich, Eldon; Gryk, Michael R.

2015-01-01

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata. PMID:26253947

Describing environmental public health data: implementing a descriptive metadata standard on the environmental public health tracking network.

PubMed

Patridge, Jeff; Namulanda, Gonza

2008-01-01

The Environmental Public Health Tracking (EPHT) Network provides an opportunity to bring together diverse environmental and health effects data by integrating}?> local, state, and national databases of environmental hazards, environmental exposures, and health effects. To help users locate data on the EPHT Network, the network will utilize descriptive metadata that provide critical information as to the purpose, location, content, and source of these data. Since 2003, the Centers for Disease Control and Prevention's EPHT Metadata Subgroup has been working to initiate the creation and use of descriptive metadata. Efforts undertaken by the group include the adoption of a metadata standard, creation of an EPHT-specific metadata profile, development of an open-source metadata creation tool, and promotion of the creation of descriptive metadata by changing the perception of metadata in the public health culture.

Metadata: Standards for Retrieving WWW Documents (and Other Digitized and Non-Digitized Resources)

NASA Astrophysics Data System (ADS)

Rusch-Feja, Diann

The use of metadata for indexing digitized and non-digitized resources for resource discovery in a networked environment is being increasingly implemented all over the world. Greater precision is achieved using metadata than relying on universal search engines and furthermore, meta-data can be used as filtering mechanisms for search results. An overview of various metadata sets is given, followed by a more focussed presentation of Dublin Core Metadata including examples of sub-elements and qualifiers. Especially the use of the Dublin Core Relation element provides connections between the metadata of various related electronic resources, as well as the metadata for physical, non-digitized resources. This facilitates more comprehensive search results without losing precision and brings together different genres of information which would otherwise be only searchable in separate databases. Furthermore, the advantages of Dublin Core Metadata in comparison with library cataloging and the use of universal search engines are discussed briefly, followed by a listing of types of implementation of Dublin Core Metadata.

Department of the Interior metadata implementation guide—Framework for developing the metadata component for data resource management

USGS Publications Warehouse

Obuch, Raymond C.; Carlino, Jennifer; Zhang, Lin; Blythe, Jonathan; Dietrich, Christopher; Hawkinson, Christine

2018-04-12

The Department of the Interior (DOI) is a Federal agency with over 90,000 employees across 10 bureaus and 8 agency offices. Its primary mission is to protect and manage the Nation’s natural resources and cultural heritage; provide scientific and other information about those resources; and honor its trust responsibilities or special commitments to American Indians, Alaska Natives, and affiliated island communities. Data and information are critical in day-to-day operational decision making and scientific research. DOI is committed to creating, documenting, managing, and sharing high-quality data and metadata in and across its various programs that support its mission. Documenting data through metadata is essential in realizing the value of data as an enterprise asset. The completeness, consistency, and timeliness of metadata affect users’ ability to search for and discover the most relevant data for the intended purpose; and facilitates the interoperability and usability of these data among DOI bureaus and offices. Fully documented metadata describe data usability, quality, accuracy, provenance, and meaning.Across DOI, there are different maturity levels and phases of information and metadata management implementations. The Department has organized a committee consisting of bureau-level points-of-contacts to collaborate on the development of more consistent, standardized, and more effective metadata management practices and guidance to support this shared mission and the information needs of the Department. DOI’s metadata implementation plans establish key roles and responsibilities associated with metadata management processes, procedures, and a series of actions defined in three major metadata implementation phases including: (1) Getting started—Planning Phase, (2) Implementing and Maintaining Operational Metadata Management Phase, and (3) the Next Steps towards Improving Metadata Management Phase. DOI’s phased approach for metadata management addresses some of the major data and metadata management challenges that exist across the diverse missions of the bureaus and offices. All employees who create, modify, or use data are involved with data and metadata management. Identifying, establishing, and formalizing the roles and responsibilities associated with metadata management are key to institutionalizing a framework of best practices, methodologies, processes, and common approaches throughout all levels of the organization; these are the foundation for effective data resource management. For executives and managers, metadata management strengthens their overarching views of data assets, holdings, and data interoperability; and clarifies how metadata management can help accelerate the compliance of multiple policy mandates. For employees, data stewards, and data professionals, formalized metadata management will help with the consistency of definitions, and approaches addressing data discoverability, data quality,  and data lineage. In addition to data professionals and others  associated with information technology; data stewards and program subject matter experts take on important metadata management roles and responsibilities as data flow through their respective business and science-related workflows.  The responsibilities of establishing, practicing, and  governing the actions associated with their specific metadata management roles are critical to successful metadata implementation.

Distributed health care imaging information systems

NASA Astrophysics Data System (ADS)

Thompson, Mary R.; Johnston, William E.; Guojun, Jin; Lee, Jason; Tierney, Brian; Terdiman, Joseph F.

1997-05-01

We have developed an ATM network-based system to collect and catalogue cardio-angiogram videos from the source at a Kaiser central facility and make them available for viewing by doctors at primary care Kaiser facilities. This an example of the general problem of diagnostic data being generated at tertiary facilities, while the images, or other large data objects they produce, need to be used from a variety of other locations such as doctor's offices or local hospitals. We describe the use of a highly distributed computing and storage architecture to provide all aspects of collecting, storing, analyzing, and accessing such large data-objects in a metropolitan area ATM network. Our large data-object management system provides network interface between the object sources, the data management system and the user of the data. As the data is being stored, a cataloguing system automatically creates and stores condensed versions of the data, textural metadata and pointers to the original data. The catalogue system provides a Web-based graphical interface to the data. The user is able the view the low-resolution data with a standard Internet connection and Web browser. If high-resolution is required, a high-speed connection and special application programs can be used to view the high-resolution original data.

GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

PubMed

Laird, Matthew R; Langille, Morgan G I; Brinkman, Fiona S L

2015-10-15

A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. brinkman@sfu.ca. © The Author 2015. Published by Oxford University Press.

HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

Lexicon Sextant: Modeling a Mnemonic System for Customizable Browser Information Organization and Management

ERIC Educational Resources Information Center

Shen, Siu-Tsen

2016-01-01

This paper presents an ongoing study of the development of a customizable web browser information organization and management system, which the author has named Lexicon Sextant (LS). LS is a user friendly, graphical web based add-on to the latest generation of web browsers, such as Google Chrome, making it easier and more intuitive to store and…

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.

PubMed

Hallin, Peter F; Stærfeldt, Hans-Henrik; Rotenberg, Eva; Binnewies, Tim T; Benham, Craig J; Ussery, David W

2009-09-25

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/.

GraphMeta: Managing HPC Rich Metadata in Graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dai, Dong; Chen, Yong; Carns, Philip

High-performance computing (HPC) systems face increasingly critical metadata management challenges, especially in the approaching exascale era. These challenges arise not only from exploding metadata volumes, but also from increasingly diverse metadata, which contains data provenance and arbitrary user-defined attributes in addition to traditional POSIX metadata. This ‘rich’ metadata is becoming critical to supporting advanced data management functionality such as data auditing and validation. In our prior work, we identified a graph-based model as a promising solution to uniformly manage HPC rich metadata due to its flexibility and generality. However, at the same time, graph-based HPC rich metadata anagement also introducesmore » significant challenges to the underlying infrastructure. In this study, we first identify the challenges on the underlying infrastructure to support scalable, high-performance rich metadata management. Based on that, we introduce GraphMeta, a graphbased engine designed for this use case. It achieves performance scalability by introducing a new graph partitioning algorithm and a write-optimal storage engine. We evaluate GraphMeta under both synthetic and real HPC metadata workloads, compare it with other approaches, and demonstrate its advantages in terms of efficiency and usability for rich metadata management in HPC systems.« less

Key Provenance of Earth Science Observational Data Products

NASA Astrophysics Data System (ADS)

Conover, H.; Plale, B.; Aktas, M.; Ramachandran, R.; Purohit, P.; Jensen, S.; Graves, S. J.

2011-12-01

As the sheer volume of data increases, particularly evidenced in the earth and environmental sciences, local arrangements for sharing data need to be replaced with reliable records about the what, who, how, and where of a data set or collection. This is frequently called the provenance of a data set. While observational data processing systems in the earth sciences have a long history of capturing metadata about the processing pipeline, current processes are limited in both what is captured and how it is disseminated to the science community. Provenance capture plays a role in scientific data preservation and stewardship precisely because it can automatically capture and represent a coherent picture of the what, how and who of a particular scientific collection. It reflects the transformations that a data collection underwent prior to its current form and the sequence of tasks that were executed and data products applied to generate a new product. In the NASA-funded Instant Karma project, we examine provenance capture in earth science applications, specifically the Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E) Science Investigator-led Processing system (SIPS). The project is integrating the Karma provenance collection and representation tool into the AMSR-E SIPS production environment, with an initial focus on Sea Ice. This presentation will describe capture and representation of provenance that is guided by the Open Provenance Model (OPM). Several things have become clear during the course of the project to date. One is that core OPM entities and relationships are not adequate for expressing the kinds of provenance that is of interest in the science domain. OPM supports name-value pair annotations that can be used to augment what is known about the provenance entities and relationships, but in Karma, annotations cannot be added during capture, but only after the fact. This limits the capture system's ability to record something it learned about an entity after the event of its creation in the provenance record. We will discuss extensions to the Open Provenance Model (OPM) and modifications to the Karma tool suite to address this issue, more efficient representations of earth science kinds of provenance, and definition of metadata structures for capturing related knowledge about the data products and science algorithms used to generate them. Use scenarios for provenance information is an active topic of investigation. It has additionally become clear through the project that not all provenance is created equal. In processing pipelines, some provenance is repetitive and uninteresting. Because of the volume of provenance, this obscures what are the interesting pieces of provenance. Methodologies to reveal science-relevant provenance will be presented, along with a preview of the AMSR-E Provenance Browser.

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

Since April 2004 the EarthScope USArray seismic network has grown to over 850 broadband stations that stream multi-channel data in near real-time to the Array Network Facility in San Diego. Providing secure, yet open, access to real-time and archived data for a broad range of audiences is best served by a series of platform agnostic low-latency web-based applications. We present a framework of tools that mediate between the world wide web and Boulder Real Time Technologies Antelope Environmental Monitoring System data acquisition and archival software. These tools provide comprehensive information to audiences ranging from network operators and geoscience researchers, to funding agencies and the general public. This ranges from network-wide to station-specific metadata, state-of-health metrics, event detection rates, archival data and dynamic report generation over a station's two year life span. Leveraging open source web-site development frameworks for both the server side (Perl, Python and PHP) and client-side (Flickr, Google Maps/Earth and jQuery) facilitates the development of a robust extensible architecture that can be tailored on a per-user basis, with rapid prototyping and development that adheres to web-standards. Typical seismic data warehouses allow online users to query and download data collected from regional networks, without the scientist directly visually assessing data coverage and/or quality. Using a suite of web-based protocols, we have recently developed an online seismic waveform interface that directly queries and displays data from a relational database through a web-browser. Using the Python interface to Datascope and the Python-based Twisted network package on the server side, and the jQuery Javascript framework on the client side to send and receive asynchronous waveform queries, we display broadband seismic data using the HTML Canvas element that is globally accessible by anyone using a modern web-browser. We are currently creating additional interface tools to create a rich-client interface for accessing and displaying seismic data that can be deployed to any system running the Antelope Real Time System. The software is freely available from the Antelope contributed code Git repository (http://www.antelopeusersgroup.org).

Data Model Management for Space Information Systems

NASA Technical Reports Server (NTRS)

Hughes, J. Steven; Crichton, Daniel J.; Ramirez, Paul; Mattmann, chris

2006-01-01

The Reference Architecture for Space Information Management (RASIM) suggests the separation of the data model from software components to promote the development of flexible information management systems. RASIM allows the data model to evolve independently from the software components and results in a robust implementation that remains viable as the domain changes. However, the development and management of data models within RASIM are difficult and time consuming tasks involving the choice of a notation, the capture of the model, its validation for consistency, and the export of the model for implementation. Current limitations to this approach include the lack of ability to capture comprehensive domain knowledge, the loss of significant modeling information during implementation, the lack of model visualization and documentation capabilities, and exports being limited to one or two schema types. The advent of the Semantic Web and its demand for sophisticated data models has addressed this situation by providing a new level of data model management in the form of ontology tools. In this paper we describe the use of a representative ontology tool to capture and manage a data model for a space information system. The resulting ontology is implementation independent. Novel on-line visualization and documentation capabilities are available automatically, and the ability to export to various schemas can be added through tool plug-ins. In addition, the ingestion of data instances into the ontology allows validation of the ontology and results in a domain knowledge base. Semantic browsers are easily configured for the knowledge base. For example the export of the knowledge base to RDF/XML and RDFS/XML and the use of open source metadata browsers provide ready-made user interfaces that support both text- and facet-based search. This paper will present the Planetary Data System (PDS) data model as a use case and describe the import of the data model into an ontology tool. We will also describe the current effort to provide interoperability with the European Space Agency (ESA)/Planetary Science Archive (PSA) which is critically dependent on a common data model.

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses

PubMed Central

Ara, Takeshi; Enomoto, Mitsuo; Arita, Masanori; Ikeda, Chiaki; Kera, Kota; Yamada, Manabu; Nishioka, Takaaki; Ikeda, Tasuku; Nihei, Yoshito; Shibata, Daisuke; Kanaya, Shigehiko; Sakurai, Nozomu

2015-01-01

Metabolomics – technology for comprehensive detection of small molecules in an organism – lags behind the other “omics” in terms of publication and dissemination of experimental data. Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated. To tackle these issues, we developed Metabolonote, a Semantic MediaWiki-based database designed specifically for managing metabolomic metadata. We also defined a metadata and data description format, called “Togo Metabolome Data” (TogoMD), with an ID system that is required for unique access to each level of the tree-structured metadata such as study purpose, sample, analytical method, and data analysis. Separation of the management of metadata from that of data and permission to attach related information to the metadata provide advantages for submitters, readers, and database developers. The metadata are enriched with information such as links to comparable data, thereby functioning as a hub of related data resources. They also enhance not only readers’ understanding and use of data but also submitters’ motivation to publish the data. The metadata are computationally shared among other systems via APIs, which facilitate the construction of novel databases by database developers. A permission system that allows publication of immature metadata and feedback from readers also helps submitters to improve their metadata. Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights. A total of 808 metadata for analyzed data obtained from 35 biological species are published currently. Metabolonote and related tools are available free of cost at http://metabolonote.kazusa.or.jp/. PMID:25905099

Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.

PubMed

Ara, Takeshi; Enomoto, Mitsuo; Arita, Masanori; Ikeda, Chiaki; Kera, Kota; Yamada, Manabu; Nishioka, Takaaki; Ikeda, Tasuku; Nihei, Yoshito; Shibata, Daisuke; Kanaya, Shigehiko; Sakurai, Nozomu

2015-01-01

Metabolomics - technology for comprehensive detection of small molecules in an organism - lags behind the other "omics" in terms of publication and dissemination of experimental data. Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated. To tackle these issues, we developed Metabolonote, a Semantic MediaWiki-based database designed specifically for managing metabolomic metadata. We also defined a metadata and data description format, called "Togo Metabolome Data" (TogoMD), with an ID system that is required for unique access to each level of the tree-structured metadata such as study purpose, sample, analytical method, and data analysis. Separation of the management of metadata from that of data and permission to attach related information to the metadata provide advantages for submitters, readers, and database developers. The metadata are enriched with information such as links to comparable data, thereby functioning as a hub of related data resources. They also enhance not only readers' understanding and use of data but also submitters' motivation to publish the data. The metadata are computationally shared among other systems via APIs, which facilitate the construction of novel databases by database developers. A permission system that allows publication of immature metadata and feedback from readers also helps submitters to improve their metadata. Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights. A total of 808 metadata for analyzed data obtained from 35 biological species are published currently. Metabolonote and related tools are available free of cost at http://metabolonote.kazusa.or.jp/.

Information integration for a sky survey by data warehousing

NASA Astrophysics Data System (ADS)

Luo, A.; Zhang, Y.; Zhao, Y.

The virtualization service of data system for a sky survey LAMOST is very important for astronomers The service needs to integrate information from data collections catalogs and references and support simple federation of a set of distributed files and associated metadata Data warehousing has been in existence for several years and demonstrated superiority over traditional relational database management systems by providing novel indexing schemes that supported efficient on-line analytical processing OLAP of large databases Now relational database systems such as Oracle etc support the warehouse capability which including extensions to the SQL language to support OLAP operations and a number of metadata management tools have been created The information integration of LAMOST by applying data warehousing is to effectively provide data and knowledge on-line

Architecture of the local spatial data infrastructure for regional climate change research

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny

2013-04-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, etc.) are actively used in modeling and analysis of climate change for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset studies in the area of climate and environmental change require a special software support based on SDI approach. A dedicated architecture of the local spatial data infrastructure aiming at regional climate change analysis using modern web mapping technologies is presented. Geoportal is a key element of any SDI, allowing searching of geoinformation resources (datasets and services) using metadata catalogs, producing geospatial data selections by their parameters (data access functionality) as well as managing services and applications of cartographical visualization. It should be noted that due to objective reasons such as big dataset volume, complexity of data models used, syntactic and semantic differences of various datasets, the development of environmental geodata access, processing and visualization services turns out to be quite a complex task. Those circumstances were taken into account while developing architecture of the local spatial data infrastructure as a universal framework providing geodata services. So that, the architecture presented includes: 1. Effective in terms of search, access, retrieval and subsequent statistical processing, model of storing big sets of regional georeferenced data, allowing in particular to store frequently used values (like monthly and annual climate change indices, etc.), thus providing different temporal views of the datasets 2. General architecture of the corresponding software components handling geospatial datasets within the storage model 3. Metadata catalog describing in detail using ISO 19115 and CF-convention standards datasets used in climate researches as a basic element of the spatial data infrastructure as well as its publication according to OGC CSW (Catalog Service Web) specification 4. Computational and mapping web services to work with geospatial datasets based on OWS (OGC Web Services) standards: WMS, WFS, WPS 5. Geoportal as a key element of thematic regional spatial data infrastructure providing also software framework for dedicated web applications development To realize web mapping services Geoserver software is used since it provides natural WPS implementation as a separate software module. To provide geospatial metadata services GeoNetwork Opensource (http://geonetwork-opensource.org) product is planned to be used for it supports ISO 19115/ISO 19119/ISO 19139 metadata standards as well as ISO CSW 2.0 profile for both client and server. To implement thematic applications based on geospatial web services within the framework of local SDI geoportal the following open source software have been selected: 1. OpenLayers JavaScript library, providing basic web mapping functionality for the thin client such as web browser 2. GeoExt/ExtJS JavaScript libraries for building client-side web applications working with geodata services. The web interface developed will be similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. The work is partially supported by RF Ministry of Education and Science grant 8345, SB RAS Program VIII.80.2.1 and IP 131.

Metadata (MD)

Treesearch

Robert E. Keane

2006-01-01

The Metadata (MD) table in the FIREMON database is used to record any information about the sampling strategy or data collected using the FIREMON sampling procedures. The MD method records metadata pertaining to a group of FIREMON plots, such as all plots in a specific FIREMON project. FIREMON plots are linked to metadata using a unique metadata identifier that is...

Documentation Resources on the ESIP Wiki

NASA Technical Reports Server (NTRS)

Habermann, Ted; Kozimor, John; Gordon, Sean

2017-01-01

The ESIP community includes data providers and users that communicate with one another through datasets and metadata that describe them. Improving this communication depends on consistent high-quality metadata. The ESIP Documentation Cluster and the wiki play an important central role in facilitating this communication. We will describe and demonstrate sections of the wiki that provide information about metadata concept definitions, metadata recommendation, metadata dialects, and guidance pages. We will also describe and demonstrate the ISO Explorer, a tool that the community is developing to help metadata creators.

Fast processing of digital imaging and communications in medicine (DICOM) metadata using multiseries DICOM format.

PubMed

Ismail, Mahmoud; Philbin, James

2015-04-01

The digital imaging and communications in medicine (DICOM) information model combines pixel data and its metadata in a single object. There are user scenarios that only need metadata manipulation, such as deidentification and study migration. Most picture archiving and communication system use a database to store and update the metadata rather than updating the raw DICOM files themselves. The multiseries DICOM (MSD) format separates metadata from pixel data and eliminates duplicate attributes. This work promotes storing DICOM studies in MSD format to reduce the metadata processing time. A set of experiments are performed that update the metadata of a set of DICOM studies for deidentification and migration. The studies are stored in both the traditional single frame DICOM (SFD) format and the MSD format. The results show that it is faster to update studies' metadata in MSD format than in SFD format because the bulk data is separated in MSD and is not retrieved from the storage system. In addition, it is space efficient to store the deidentified studies in MSD format as it shares the same bulk data object with the original study. In summary, separation of metadata from pixel data using the MSD format provides fast metadata access and speeds up applications that process only the metadata.

Transforming Dermatologic Imaging for the Digital Era: Metadata and Standards.

PubMed

Caffery, Liam J; Clunie, David; Curiel-Lewandrowski, Clara; Malvehy, Josep; Soyer, H Peter; Halpern, Allan C

2018-01-17

Imaging is increasingly being used in dermatology for documentation, diagnosis, and management of cutaneous disease. The lack of standards for dermatologic imaging is an impediment to clinical uptake. Standardization can occur in image acquisition, terminology, interoperability, and metadata. This paper presents the International Skin Imaging Collaboration position on standardization of metadata for dermatologic imaging. Metadata is essential to ensure that dermatologic images are properly managed and interpreted. There are two standards-based approaches to recording and storing metadata in dermatologic imaging. The first uses standard consumer image file formats, and the second is the file format and metadata model developed for the Digital Imaging and Communication in Medicine (DICOM) standard. DICOM would appear to provide an advantage over using consumer image file formats for metadata as it includes all the patient, study, and technical metadata necessary to use images clinically. Whereas, consumer image file formats only include technical metadata and need to be used in conjunction with another actor-for example, an electronic medical record-to supply the patient and study metadata. The use of DICOM may have some ancillary benefits in dermatologic imaging including leveraging DICOM network and workflow services, interoperability of images and metadata, leveraging existing enterprise imaging infrastructure, greater patient safety, and better compliance to legislative requirements for image retention.

Fast processing of digital imaging and communications in medicine (DICOM) metadata using multiseries DICOM format

PubMed Central

Ismail, Mahmoud; Philbin, James

2015-01-01

Abstract. The digital imaging and communications in medicine (DICOM) information model combines pixel data and its metadata in a single object. There are user scenarios that only need metadata manipulation, such as deidentification and study migration. Most picture archiving and communication system use a database to store and update the metadata rather than updating the raw DICOM files themselves. The multiseries DICOM (MSD) format separates metadata from pixel data and eliminates duplicate attributes. This work promotes storing DICOM studies in MSD format to reduce the metadata processing time. A set of experiments are performed that update the metadata of a set of DICOM studies for deidentification and migration. The studies are stored in both the traditional single frame DICOM (SFD) format and the MSD format. The results show that it is faster to update studies’ metadata in MSD format than in SFD format because the bulk data is separated in MSD and is not retrieved from the storage system. In addition, it is space efficient to store the deidentified studies in MSD format as it shares the same bulk data object with the original study. In summary, separation of metadata from pixel data using the MSD format provides fast metadata access and speeds up applications that process only the metadata. PMID:26158117

From the inside-out: Retrospectives on a metadata improvement process to advance the discoverability of NASÁs earth science data

NASA Astrophysics Data System (ADS)

Hernández, B. E.; Bugbee, K.; le Roux, J.; Beaty, T.; Hansen, M.; Staton, P.; Sisco, A. W.

2017-12-01

Earth observation (EO) data collected as part of NASA's Earth Observing System Data and Information System (EOSDIS) is now searchable via the Common Metadata Repository (CMR). The Analysis and Review of CMR (ARC) Team at Marshall Space Flight Center has been tasked with reviewing all NASA metadata records in the CMR ( 7,000 records). Each collection level record and constituent granule level metadata are reviewed for both completeness as well as compliance with the CMR's set of metadata standards, as specified in the Unified Metadata Model (UMM). NASA's Distributed Active Archive Centers (DAACs) have been harmonizing priority metadata records within the context of the inter-agency federal Big Earth Data Initiative (BEDI), which seeks to improve the discoverability, accessibility, and usability of EO data. Thus, the first phase of this project constitutes reviewing BEDI metadata records, while the second phase will constitute reviewing the remaining non-BEDI records in CMR. This presentation will discuss the ARC team's findings in terms of the overall quality of BEDI records across all DAACs as well as compliance with UMM standards. For instance, only a fifth of the collection-level metadata fields needed correction, compared to a quarter of the granule-level fields. It should be noted that the degree to which DAACs' metadata did not comply with the UMM standards may reflect multiple factors, such as recent changes in the UMM standards, and the utilization of different metadata formats (e.g. DIF 10, ECHO 10, ISO 19115-1) across the DAACs. Insights, constructive criticism, and lessons learned from this metadata review process will be contributed from both ORNL and SEDAC. Further inquiry along such lines may lead to insights which may improve the metadata curation process moving forward. In terms of the broader implications for metadata compliance with the UMM standards, this research has shown that a large proportion of the prioritized collections have already been made compliant, although the process of improving metadata quality is ongoing and iterative. Further research is also warranted into whether or not the gains in metadata quality are also driving gains in data use.

Forum Guide to Metadata: The Meaning behind Education Data. NFES 2009-805

ERIC Educational Resources Information Center

National Forum on Education Statistics, 2009

2009-01-01

The purpose of this guide is to empower people to more effectively use data as information. To accomplish this, the publication explains what metadata are; why metadata are critical to the development of sound education data systems; what components comprise a metadata system; what value metadata bring to data management and use; and how to…

Metadata Effectiveness in Internet Discovery: An Analysis of Digital Collection Metadata Elements and Internet Search Engine Keywords

ERIC Educational Resources Information Center

Yang, Le

2016-01-01

This study analyzed digital item metadata and keywords from Internet search engines to learn what metadata elements actually facilitate discovery of digital collections through Internet keyword searching and how significantly each metadata element affects the discovery of items in a digital repository. The study found that keywords from Internet…

Electricity Data Browser

EIA Publications

The Electricity Data Browser shows generation, consumption, fossil fuel receipts, stockpiles, retail sales, and electricity prices. The data appear on an interactive web page and are updated each month. The Electricity Data Browser includes all the datasets collected and published in EIA's Electric Power Monthly and allows users to perform dynamic charting of data sets as well as map the data by state. The data browser includes a series of reports that appear in the Electric Power Monthly and allows readers to drill down to plant level statistics, where available. All images and datasets are available for download. Users can also link to the data series in EIA's Application Programming Interface (API). An API makes our data machine-readable and more accessible to users.

A novel framework for assessing metadata quality in epidemiological and public health research settings

PubMed Central

McMahon, Christiana; Denaxas, Spiros

2016-01-01

Metadata are critical in epidemiological and public health research. However, a lack of biomedical metadata quality frameworks and limited awareness of the implications of poor quality metadata renders data analyses problematic. In this study, we created and evaluated a novel framework to assess metadata quality of epidemiological and public health research datasets. We performed a literature review and surveyed stakeholders to enhance our understanding of biomedical metadata quality assessment. The review identified 11 studies and nine quality dimensions; none of which were specifically aimed at biomedical metadata. 96 individuals completed the survey; of those who submitted data, most only assessed metadata quality sometimes, and eight did not at all. Our framework has four sections: a) general information; b) tools and technologies; c) usability; and d) management and curation. We evaluated the framework using three test cases and sought expert feedback. The framework can assess biomedical metadata quality systematically and robustly. PMID:27570670

A novel framework for assessing metadata quality in epidemiological and public health research settings.

PubMed

McMahon, Christiana; Denaxas, Spiros

2016-01-01

Metadata are critical in epidemiological and public health research. However, a lack of biomedical metadata quality frameworks and limited awareness of the implications of poor quality metadata renders data analyses problematic. In this study, we created and evaluated a novel framework to assess metadata quality of epidemiological and public health research datasets. We performed a literature review and surveyed stakeholders to enhance our understanding of biomedical metadata quality assessment. The review identified 11 studies and nine quality dimensions; none of which were specifically aimed at biomedical metadata. 96 individuals completed the survey; of those who submitted data, most only assessed metadata quality sometimes, and eight did not at all. Our framework has four sections: a) general information; b) tools and technologies; c) usability; and d) management and curation. We evaluated the framework using three test cases and sought expert feedback. The framework can assess biomedical metadata quality systematically and robustly.

CMO: Cruise Metadata Organizer for JAMSTEC Research Cruises

NASA Astrophysics Data System (ADS)

Fukuda, K.; Saito, H.; Hanafusa, Y.; Vanroosebeke, A.; Kitayama, T.

2011-12-01

JAMSTEC's Data Research Center for Marine-Earth Sciences manages and distributes a wide variety of observational data and samples obtained from JAMSTEC research vessels and deep sea submersibles. Generally, metadata are essential to identify data and samples were obtained. In JAMSTEC, cruise metadata include cruise information such as cruise ID, name of vessel, research theme, and diving information such as dive number, name of submersible and position of diving point. They are submitted by chief scientists of research cruises in the Microsoft Excel° spreadsheet format, and registered into a data management database to confirm receipt of observational data files, cruise summaries, and cruise reports. The cruise metadata are also published via "JAMSTEC Data Site for Research Cruises" within two months after end of cruise. Furthermore, these metadata are distributed with observational data, images and samples via several data and sample distribution websites after a publication moratorium period. However, there are two operational issues in the metadata publishing process. One is that duplication efforts and asynchronous metadata across multiple distribution websites due to manual metadata entry into individual websites by administrators. The other is that differential data types or representation of metadata in each website. To solve those problems, we have developed a cruise metadata organizer (CMO) which allows cruise metadata to be connected from the data management database to several distribution websites. CMO is comprised of three components: an Extensible Markup Language (XML) database, an Enterprise Application Integration (EAI) software, and a web-based interface. The XML database is used because of its flexibility for any change of metadata. Daily differential uptake of metadata from the data management database to the XML database is automatically processed via the EAI software. Some metadata are entered into the XML database using the web-based interface by a metadata editor in CMO as needed. Then daily differential uptake of metadata from the XML database to databases in several distribution websites is automatically processed using a convertor defined by the EAI software. Currently, CMO is available for three distribution websites: "Deep Sea Floor Rock Sample Database GANSEKI", "Marine Biological Sample Database", and "JAMSTEC E-library of Deep-sea Images". CMO is planned to provide "JAMSTEC Data Site for Research Cruises" with metadata in the future.

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Fei; Maslov, Sergei; Yoo, Shinjae

Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

DOE PAGES

He, Fei; Maslov, Sergei; Yoo, Shinjae; ...

2016-05-25

Here, transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset andmore » found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.« less

Analyzing handwriting biometrics in metadata context

NASA Astrophysics Data System (ADS)

Scheidat, Tobias; Wolf, Franziska; Vielhauer, Claus

2006-02-01

In this article, methods for user recognition by online handwriting are experimentally analyzed using a combination of demographic data of users in relation to their handwriting habits. Online handwriting as a biometric method is characterized by having high variations of characteristics that influences the reliance and security of this method. These variations have not been researched in detail so far. Especially in cross-cultural application it is urgent to reveal the impact of personal background to security aspects in biometrics. Metadata represent the background of writers, by introducing cultural, biological and conditional (changing) aspects like fist language, country of origin, gender, handedness, experiences the influence handwriting and language skills. The goal is the revelation of intercultural impacts on handwriting in order to achieve higher security in biometrical systems. In our experiments, in order to achieve a relatively high coverage, 48 different handwriting tasks have been accomplished by 47 users from three countries (Germany, India and Italy) have been investigated with respect to the relations of metadata and biometric recognition performance. For this purpose, hypotheses have been formulated and have been evaluated using the measurement of well-known recognition error rates from biometrics. The evaluation addressed both: system reliance and security threads by skilled forgeries. For the later purpose, a novel forgery type is introduced, which applies the personal metadata to security aspects and includes new methods of security tests. Finally in our paper, we formulate recommendations for specific user groups and handwriting samples.

An Intelligent Semantic E-Learning Framework Using Context-Aware Semantic Web Technologies

ERIC Educational Resources Information Center

Huang, Weihong; Webster, David; Wood, Dawn; Ishaya, Tanko

2006-01-01

Recent developments of e-learning specifications such as Learning Object Metadata (LOM), Sharable Content Object Reference Model (SCORM), Learning Design and other pedagogy research in semantic e-learning have shown a trend of applying innovative computational techniques, especially Semantic Web technologies, to promote existing content-focused…

Open Source Software Development and Lotka's Law: Bibliometric Patterns in Programming.

ERIC Educational Resources Information Center

Newby, Gregory B.; Greenberg, Jane; Jones, Paul

2003-01-01

Applies Lotka's Law to metadata on open source software development. Authoring patterns found in software development productivity are found to be comparable to prior studies of Lotka's Law for scientific and scholarly publishing, and offer promise in predicting aggregate behavior of open source developers. (Author/LRW)

Towards Data Value-Level Metadata for Clinical Studies.

PubMed

Zozus, Meredith Nahm; Bonner, Joseph

2017-01-01

While several standards for metadata describing clinical studies exist, comprehensive metadata to support traceability of data from clinical studies has not been articulated. We examine uses of metadata in clinical studies. We examine and enumerate seven sources of data value-level metadata in clinical studies inclusive of research designs across the spectrum of the National Institutes of Health definition of clinical research. The sources of metadata inform categorization in terms of metadata describing the origin of a data value, the definition of a data value, and operations to which the data value was subjected. The latter is further categorized into information about changes to a data value, movement of a data value, retrieval of a data value, and data quality checks, constraints or assessments to which the data value was subjected. The implications of tracking and managing data value-level metadata are explored.

Plugin free remote visualization in the browser

NASA Astrophysics Data System (ADS)

Tamm, Georg; Slusallek, Philipp

2015-01-01

Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

PubMed

Setti, E; Musumeci, R

2001-06-01

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

UCSC genome browser: deep support for molecular biomedical research.

PubMed

Mangan, Mary E; Williams, Jennifer M; Lathe, Scott M; Karolchik, Donna; Lathe, Warren C

2008-01-01

The volume and complexity of genomic sequence data, and the additional experimental data required for annotation of the genomic context, pose a major challenge for display and access for biomedical researchers. Genome browsers organize this data and make it available in various ways to extract useful information to advance research projects. The UCSC Genome Browser is one of these resources. The official sequence data for a given species forms the framework to display many other types of data such as expression, variation, cross-species comparisons, and more. Visual representations of the data are available for exploration. Data can be queried with sequences. Complex database queries are also easily achieved with the Table Browser interface. Associated tools permit additional query types or access to additional data sources such as images of in situ localizations. Support for solving researcher's issues is provided with active discussion mailing lists and by providing updated training materials. The UCSC Genome Browser provides a source of deep support for a wide range of biomedical molecular research (http://genome.ucsc.edu).

Reliability of SNOMED-CT Coding by Three Physicians using Two Terminology Browsers

PubMed Central

Chiang, Michael F.; Hwang, John C.; Yu, Alexander C.; Casper, Daniel S.; Cimino, James J.; Starren, Justin

2006-01-01

SNOMED-CT has been promoted as a reference terminology for electronic health record (EHR) systems. Many important EHR functions are based on the assumption that medical concepts will be coded consistently by different users. This study is designed to measure agreement among three physicians using two SNOMED-CT terminology browsers to encode 242 concepts from five ophthalmology case presentations in a publicly-available clinical journal. Inter-coder reliability, based on exact coding match by each physician, was 44% using one browser and 53% using the other. Intra-coder reliability testing revealed that a different SNOMED-CT code was obtained up to 55% of the time when the two browsers were used by one user to encode the same concept. These results suggest that the reliability of SNOMED-CT coding is imperfect, and may be a function of browsing methodology. A combination of physician training, terminology refinement, and browser improvement may help increase the reproducibility of SNOMED-CT coding. PMID:17238317

IMAGE EXPLORER: Astronomical Image Analysis on an HTML5-based Web Application

NASA Astrophysics Data System (ADS)

Gopu, A.; Hayashi, S.; Young, M. D.

2014-05-01

Large datasets produced by recent astronomical imagers cause the traditional paradigm for basic visual analysis - typically downloading one's entire image dataset and using desktop clients like DS9, Aladin, etc. - to not scale, despite advances in desktop computing power and storage. This paper describes Image Explorer, a web framework that offers several of the basic visualization and analysis functionality commonly provided by tools like DS9, on any HTML5 capable web browser on various platforms. It uses a combination of the modern HTML5 canvas, JavaScript, and several layers of lossless PNG tiles producted from the FITS image data. Astronomers are able to rapidly and simultaneously open up several images on their web-browser, adjust the intensity min/max cutoff or its scaling function, and zoom level, apply color-maps, view position and FITS header information, execute typically used data reduction codes on the corresponding FITS data using the FRIAA framework, and overlay tiles for source catalog objects, etc.

Managing Complex Change in Clinical Study Metadata

PubMed Central

Brandt, Cynthia A.; Gadagkar, Rohit; Rodriguez, Cesar; Nadkarni, Prakash M.

2004-01-01

In highly functional metadata-driven software, the interrelationships within the metadata become complex, and maintenance becomes challenging. We describe an approach to metadata management that uses a knowledge-base subschema to store centralized information about metadata dependencies and use cases involving specific types of metadata modification. Our system borrows ideas from production-rule systems in that some of this information is a high-level specification that is interpreted and executed dynamically by a middleware engine. Our approach is implemented in TrialDB, a generic clinical study data management system. We review approaches that have been used for metadata management in other contexts and describe the features, capabilities, and limitations of our system. PMID:15187070

WebVR: an interactive web browser for virtual environments

NASA Astrophysics Data System (ADS)

Barsoum, Emad; Kuester, Falko

2005-03-01

The pervasive nature of web-based content has lead to the development of applications and user interfaces that port between a broad range of operating systems and databases, while providing intuitive access to static and time-varying information. However, the integration of this vast resource into virtual environments has remained elusive. In this paper we present an implementation of a 3D Web Browser (WebVR) that enables the user to search the internet for arbitrary information and to seamlessly augment this information into virtual environments. WebVR provides access to the standard data input and query mechanisms offered by conventional web browsers, with the difference that it generates active texture-skins of the web contents that can be mapped onto arbitrary surfaces within the environment. Once mapped, the corresponding texture functions as a fully integrated web-browser that will respond to traditional events such as the selection of links or text input. As a result, any surface within the environment can be turned into a web-enabled resource that provides access to user-definable data. In order to leverage from the continuous advancement of browser technology and to support both static as well as streamed content, WebVR uses ActiveX controls to extract the desired texture skin from industry strength browsers, providing a unique mechanism for data fusion and extensibility.

A Digital Broadcast Item (DBI) enabling metadata repository for digital, interactive television (digiTV) feedback channel networks

NASA Astrophysics Data System (ADS)

Lugmayr, Artur R.; Mailaparampil, Anurag; Tico, Florina; Kalli, Seppo; Creutzburg, Reiner

2003-01-01

Digital television (digiTV) is an additional multimedia environment, where metadata is one key element for the description of arbitrary content. This implies adequate structures for content description, which is provided by XML metadata schemes (e.g. MPEG-7, MPEG-21). Content and metadata management is the task of a multimedia repository, from which digiTV clients - equipped with an Internet connection - can access rich additional multimedia types over an "All-HTTP" protocol layer. Within this research work, we focus on conceptual design issues of a metadata repository for the storage of metadata, accessible from the feedback channel of a local set-top box. Our concept describes the whole heterogeneous life-cycle chain of XML metadata from the service provider to the digiTV equipment, device independent representation of content, accessing and querying the metadata repository, management of metadata related to digiTV, and interconnection of basic system components (http front-end, relational database system, and servlet container). We present our conceptual test configuration of a metadata repository that is aimed at a real-world deployment, done within the scope of the future interaction (fiTV) project at the Digital Media Institute (DMI) Tampere (www.futureinteraction.tv).

Metazen – metadata capture for metagenomes

PubMed Central

2014-01-01

Background As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusions Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility. PMID:25780508

Metazen - metadata capture for metagenomes.

PubMed

Bischof, Jared; Harrison, Travis; Paczian, Tobias; Glass, Elizabeth; Wilke, Andreas; Meyer, Folker

2014-01-01

As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.

Improving Access to NASA Earth Science Data through Collaborative Metadata Curation

NASA Astrophysics Data System (ADS)

Sisco, A. W.; Bugbee, K.; Shum, D.; Baynes, K.; Dixon, V.; Ramachandran, R.

2017-12-01

The NASA-developed Common Metadata Repository (CMR) is a high-performance metadata system that currently catalogs over 375 million Earth science metadata records. It serves as the authoritative metadata management system of NASA's Earth Observing System Data and Information System (EOSDIS), enabling NASA Earth science data to be discovered and accessed by a worldwide user community. The size of the EOSDIS data archive is steadily increasing, and the ability to manage and query this archive depends on the input of high quality metadata to the CMR. Metadata that does not provide adequate descriptive information diminishes the CMR's ability to effectively find and serve data to users. To address this issue, an innovative and collaborative review process is underway to systematically improve the completeness, consistency, and accuracy of metadata for approximately 7,000 data sets archived by NASA's twelve EOSDIS data centers, or Distributed Active Archive Centers (DAACs). The process involves automated and manual metadata assessment of both collection and granule records by a team of Earth science data specialists at NASA Marshall Space Flight Center. The team communicates results to DAAC personnel, who then make revisions and reingest improved metadata into the CMR. Implementation of this process relies on a network of interdisciplinary collaborators leveraging a variety of communication platforms and long-range planning strategies. Curating metadata at this scale and resolving metadata issues through community consensus improves the CMR's ability to serve current and future users and also introduces best practices for stewarding the next generation of Earth Observing System data. This presentation will detail the metadata curation process, its outcomes thus far, and also share the status of ongoing curation activities.

CMR Metadata Curation

NASA Technical Reports Server (NTRS)

Shum, Dana; Bugbee, Kaylin

2017-01-01

This talk explains the ongoing metadata curation activities in the Common Metadata Repository. It explores tools that exist today which are useful for building quality metadata and also opens up the floor for discussions on other potentially useful tools.

Efficient processing of MPEG-21 metadata in the binary domain

NASA Astrophysics Data System (ADS)

Timmerer, Christian; Frank, Thomas; Hellwagner, Hermann; Heuer, Jörg; Hutter, Andreas

2005-10-01

XML-based metadata is widely adopted across the different communities and plenty of commercial and open source tools for processing and transforming are available on the market. However, all of these tools have one thing in common: they operate on plain text encoded metadata which may become a burden in constrained and streaming environments, i.e., when metadata needs to be processed together with multimedia content on the fly. In this paper we present an efficient approach for transforming such kind of metadata which are encoded using MPEG's Binary Format for Metadata (BiM) without additional en-/decoding overheads, i.e., within the binary domain. Therefore, we have developed an event-based push parser for BiM encoded metadata which transforms the metadata by a limited set of processing instructions - based on traditional XML transformation techniques - operating on bit patterns instead of cost-intensive string comparisons.

A model for enhancing Internet medical document retrieval with "medical core metadata".

PubMed

Malet, G; Munoz, F; Appleyard, R; Hersh, W

1999-01-01

Finding documents on the World Wide Web relevant to a specific medical information need can be difficult. The goal of this work is to define a set of document content description tags, or metadata encodings, that can be used to promote disciplined search access to Internet medical documents. The authors based their approach on a proposed metadata standard, the Dublin Core Metadata Element Set, which has recently been submitted to the Internet Engineering Task Force. Their model also incorporates the National Library of Medicine's Medical Subject Headings (MeSH) vocabulary and MEDLINE-type content descriptions. The model defines a medical core metadata set that can be used to describe the metadata for a wide variety of Internet documents. The authors propose that their medical core metadata set be used to assign metadata to medical documents to facilitate document retrieval by Internet search engines.

Developing Cyberinfrastructure Tools and Services for Metadata Quality Evaluation

NASA Astrophysics Data System (ADS)

Mecum, B.; Gordon, S.; Habermann, T.; Jones, M. B.; Leinfelder, B.; Powers, L. A.; Slaughter, P.

2016-12-01

Metadata and data quality are at the core of reusable and reproducible science. While great progress has been made over the years, much of the metadata collected only addresses data discovery, covering concepts such as titles and keywords. Improving metadata beyond the discoverability plateau means documenting detailed concepts within the data such as sampling protocols, instrumentation used, and variables measured. Given that metadata commonly do not describe their data at this level, how might we improve the state of things? Giving scientists and data managers easy to use tools to evaluate metadata quality that utilize community-driven recommendations is the key to producing high-quality metadata. To achieve this goal, we created a set of cyberinfrastructure tools and services that integrate with existing metadata and data curation workflows which can be used to improve metadata and data quality across the sciences. These tools work across metadata dialects (e.g., ISO19115, FGDC, EML, etc.) and can be used to assess aspects of quality beyond what is internal to the metadata such as the congruence between the metadata and the data it describes. The system makes use of a user-friendly mechanism for expressing a suite of checks as code in popular data science programming languages such as Python and R. This reduces the burden on scientists and data managers to learn yet another language. We demonstrated these services and tools in three ways. First, we evaluated a large corpus of datasets in the DataONE federation of data repositories against a metadata recommendation modeled after existing recommendations such as the LTER best practices and the Attribute Convention for Dataset Discovery (ACDD). Second, we showed how this service can be used to display metadata and data quality information to data producers during the data submission and metadata creation process, and to data consumers through data catalog search and access tools. Third, we showed how the centrally deployed DataONE quality service can achieve major efficiency gains by allowing member repositories to customize and use recommendations that fit their specific needs without having to create de novo infrastructure at their site.

The New Online Metadata Editor for Generating Structured Metadata

NASA Astrophysics Data System (ADS)

Devarakonda, R.; Shrestha, B.; Palanisamy, G.; Hook, L.; Killeffer, T.; Boden, T.; Cook, R. B.; Zolly, L.; Hutchison, V.; Frame, M. T.; Cialella, A. T.; Lazer, K.

2014-12-01

Nobody is better suited to "describe" data than the scientist who created it. This "description" about a data is called Metadata. In general terms, Metadata represents the who, what, when, where, why and how of the dataset. eXtensible Markup Language (XML) is the preferred output format for metadata, as it makes it portable and, more importantly, suitable for system discoverability. The newly developed ORNL Metadata Editor (OME) is a Web-based tool that allows users to create and maintain XML files containing key information, or metadata, about the research. Metadata include information about the specific projects, parameters, time periods, and locations associated with the data. Such information helps put the research findings in context. In addition, the metadata produced using OME will allow other researchers to find these data via Metadata clearinghouses like Mercury [1] [2]. Researchers simply use the ORNL Metadata Editor to enter relevant metadata into a Web-based form. How is OME helping Big Data Centers like ORNL DAAC? The ORNL DAAC is one of NASA's Earth Observing System Data and Information System (EOSDIS) data centers managed by the ESDIS Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological components of the Earth's environment. Typically data produced, archived and analyzed is at a scale of multiple petabytes, which makes the discoverability of the data very challenging. Without proper metadata associated with the data, it is difficult to find the data you are looking for and equally difficult to use and understand the data. OME will allow data centers like the ORNL DAAC to produce meaningful, high quality, standards-based, descriptive information about their data products in-turn helping with the data discoverability and interoperability.References:[1] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94. [2] Wilson, Bruce E., et al. "Mercury Toolset for Spatiotemporal Metadata." NASA Technical Reports Server (NTRS) (2010).

Metadata Wizard: an easy-to-use tool for creating FGDC-CSDGM metadata for geospatial datasets in ESRI ArcGIS Desktop

USGS Publications Warehouse

Ignizio, Drew A.; O'Donnell, Michael S.; Talbert, Colin B.

2014-01-01

Creating compliant metadata for scientific data products is mandated for all federal Geographic Information Systems professionals and is a best practice for members of the geospatial data community. However, the complexity of the The Federal Geographic Data Committee’s Content Standards for Digital Geospatial Metadata, the limited availability of easy-to-use tools, and recent changes in the ESRI software environment continue to make metadata creation a challenge. Staff at the U.S. Geological Survey Fort Collins Science Center have developed a Python toolbox for ESRI ArcDesktop to facilitate a semi-automated workflow to create and update metadata records in ESRI’s 10.x software. The U.S. Geological Survey Metadata Wizard tool automatically populates several metadata elements: the spatial reference, spatial extent, geospatial presentation format, vector feature count or raster column/row count, native system/processing environment, and the metadata creation date. Once the software auto-populates these elements, users can easily add attribute definitions and other relevant information in a simple Graphical User Interface. The tool, which offers a simple design free of esoteric metadata language, has the potential to save many government and non-government organizations a significant amount of time and costs by facilitating the development of The Federal Geographic Data Committee’s Content Standards for Digital Geospatial Metadata compliant metadata for ESRI software users. A working version of the tool is now available for ESRI ArcDesktop, version 10.0, 10.1, and 10.2 (downloadable at http:/www.sciencebase.gov/metadatawizard).

USGIN ISO metadata profile

NASA Astrophysics Data System (ADS)

Richard, S. M.

2011-12-01

The USGIN project has drafted and is using a specification for use of ISO 19115/19/39 metadata, recommendations for simple metadata content, and a proposal for a URI scheme to identify resources using resolvable http URI's(see http://lab.usgin.org/usgin-profiles). The principal target use case is a catalog in which resources can be registered and described by data providers for discovery by users. We are currently using the ESRI Geoportal (Open Source), with configuration files for the USGIN profile. The metadata offered by the catalog must provide sufficient content to guide search engines to locate requested resources, to describe the resource content, provenance, and quality so users can determine if the resource will serve for intended usage, and finally to enable human users and sofware clients to obtain or access the resource. In order to achieve an operational federated catalog system, provisions in the ISO specification must be restricted and usage clarified to reduce the heterogeneity of 'standard' metadata and service implementations such that a single client can search against different catalogs, and the metadata returned by catalogs can be parsed reliably to locate required information. Usage of the complex ISO 19139 XML schema allows for a great deal of structured metadata content, but the heterogenity in approaches to content encoding has hampered development of sophisticated client software that can take advantage of the rich metadata; the lack of such clients in turn reduces motivation for metadata producers to produce content-rich metadata. If the only significant use of the detailed, structured metadata is to format into text for people to read, then the detailed information could be put in free text elements and be just as useful. In order for complex metadata encoding and content to be useful, there must be clear and unambiguous conventions on the encoding that are utilized by the community that wishes to take advantage of advanced metadata content. The use cases for the detailed content must be well understood, and the degree of metadata complexity should be determined by requirements for those use cases. The ISO standard provides sufficient flexibility that relatively simple metadata records can be created that will serve for text-indexed search/discovery, resource evaluation by a user reading text content from the metadata, and access to the resource via http, ftp, or well-known service protocols (e.g. Thredds; OGC WMS, WFS, WCS).

Exploratory Visual Analytics of a Dynamically Built Network of Nodes in a WebGL-Enabled Browser

DTIC Science & Technology

2014-01-01

dimensionality reduction, feature extraction, high-dimensional data, t-distributed stochastic neighbor embedding, neighbor retrieval visualizer, visual...WebGL-enabled rendering is supported natively by browsers such as the latest Mozilla Firefox , Google Chrome, and Microsoft Internet Explorer 11. At the...appropriate names. The resultant 26-node network is displayed in a Mozilla Firefox browser in figure 2 (also see appendix B). 3 Figure 1. The

The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.

PubMed

Kapopoulou, Adamandia; Lew, Jocelyne M; Cole, Stewart T

2011-01-01

In this paper, we present the MycoBrowser portal (http://mycobrowser.epfl.ch/), a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. A central component of MycoBrowser is TubercuList (http://tuberculist.epfl.ch), which has recently benefited from a new data management system and web interface. These improvements were extended to all MycoBrowser databases. We provide an overview of the functionalities available and the different ways of interrogating the data then discuss how both the new information and the latest features are helping the mycobacterial research communities. Copyright © 2010 Elsevier Ltd. All rights reserved.

Improving Scientific Metadata Interoperability And Data Discoverability using OAI-PMH

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James M.; Wilson, Bruce E.

2010-12-01

While general-purpose search engines (such as Google or Bing) are useful for finding many things on the Internet, they are often of limited usefulness for locating Earth Science data relevant (for example) to a specific spatiotemporal extent. By contrast, tools that search repositories of structured metadata can locate relevant datasets with fairly high precision, but the search is limited to that particular repository. Federated searches (such as Z39.50) have been used, but can be slow and the comprehensiveness can be limited by downtime in any search partner. An alternative approach to improve comprehensiveness is for a repository to harvest metadata from other repositories, possibly with limits based on subject matter or access permissions. Searches through harvested metadata can be extremely responsive, and the search tool can be customized with semantic augmentation appropriate to the community of practice being served. However, there are a number of different protocols for harvesting metadata, with some challenges for ensuring that updates are propagated and for collaborations with repositories using differing metadata standards. The Open Archive Initiative Protocol for Metadata Handling (OAI-PMH) is a standard that is seeing increased use as a means for exchanging structured metadata. OAI-PMH implementations must support Dublin Core as a metadata standard, with other metadata formats as optional. We have developed tools which enable our structured search tool (Mercury; http://mercury.ornl.gov) to consume metadata from OAI-PMH services in any of the metadata formats we support (Dublin Core, Darwin Core, FCDC CSDGM, GCMD DIF, EML, and ISO 19115/19137). We are also making ORNL DAAC metadata available through OAI-PMH for other metadata tools to utilize, such as the NASA Global Change Master Directory, GCMD). This paper describes Mercury capabilities with multiple metadata formats, in general, and, more specifically, the results of our OAI-PMH implementations and the lessons learned. References: [1] R. Devarakonda, G. Palanisamy, B.E. Wilson, and J.M. Green, "Mercury: reusable metadata management data discovery and access system", Earth Science Informatics, vol. 3, no. 1, pp. 87-94, May 2010. [2] R. Devarakonda, G. Palanisamy, J.M. Green, B.E. Wilson, "Data sharing and retrieval using OAI-PMH", Earth Science Informatics DOI: 10.1007/s12145-010-0073-0, (2010). [3] Devarakonda, R.; Palanisamy, G.; Green, J.; Wilson, B. E. "Mercury: An Example of Effective Software Reuse for Metadata Management Data Discovery and Access", Eos Trans. AGU, 89(53), Fall Meet. Suppl., IN11A-1019 (2008).

An Approach to Information Management for AIR7000 with Metadata and Ontologies

DTIC Science & Technology

2009-10-01

metadata. We then propose an approach based on Semantic Technologies including the Resource Description Framework (RDF) and Upper Ontologies, for the...mandating specific metadata schemas can result in interoperability problems. For example, many standards within the ADO mandate the use of XML for metadata...such problems, we propose an archi- tecture in which different metadata schemes can inter operate. By using RDF (Resource Description Framework ) as a

Making Interoperability Easier with NASA's Metadata Management Tool (MMT)

NASA Technical Reports Server (NTRS)

Shum, Dana; Reese, Mark; Pilone, Dan; Baynes, Katie

2016-01-01

While the ISO-19115 collection level metadata format meets many users' needs for interoperable metadata, it can be cumbersome to create it correctly. Through the MMT's simple UI experience, metadata curators can create and edit collections which are compliant with ISO-19115 without full knowledge of the NASA Best Practices implementation of ISO-19115 format. Users are guided through the metadata creation process through a forms-based editor, complete with field information, validation hints and picklists. Once a record is completed, users can download the metadata in any of the supported formats with just 2 clicks.

Predicting structured metadata from unstructured metadata.

PubMed

Posch, Lisa; Panahiazar, Maryam; Dumontier, Michel; Gevaert, Olivier

2016-01-01

Enormous amounts of biomedical data have been and are being produced by investigators all over the world. However, one crucial and limiting factor in data reuse is accurate, structured and complete description of the data or data about the data-defined as metadata. We propose a framework to predict structured metadata terms from unstructured metadata for improving quality and quantity of metadata, using the Gene Expression Omnibus (GEO) microarray database. Our framework consists of classifiers trained using term frequency-inverse document frequency (TF-IDF) features and a second approach based on topics modeled using a Latent Dirichlet Allocation model (LDA) to reduce the dimensionality of the unstructured data. Our results on the GEO database show that structured metadata terms can be the most accurately predicted using the TF-IDF approach followed by LDA both outperforming the majority vote baseline. While some accuracy is lost by the dimensionality reduction of LDA, the difference is small for elements with few possible values, and there is a large improvement over the majority classifier baseline. Overall this is a promising approach for metadata prediction that is likely to be applicable to other datasets and has implications for researchers interested in biomedical metadata curation and metadata prediction. © The Author(s) 2016. Published by Oxford University Press.

Metazen – metadata capture for metagenomes

DOE PAGES

Bischof, Jared; Harrison, Travis; Paczian, Tobias; ...

2014-12-08

Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack themore » appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.« less

Metazen – metadata capture for metagenomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bischof, Jared; Harrison, Travis; Paczian, Tobias

Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack themore » appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.« less

Predicting structured metadata from unstructured metadata

PubMed Central

Posch, Lisa; Panahiazar, Maryam; Dumontier, Michel; Gevaert, Olivier

2016-01-01

Enormous amounts of biomedical data have been and are being produced by investigators all over the world. However, one crucial and limiting factor in data reuse is accurate, structured and complete description of the data or data about the data—defined as metadata. We propose a framework to predict structured metadata terms from unstructured metadata for improving quality and quantity of metadata, using the Gene Expression Omnibus (GEO) microarray database. Our framework consists of classifiers trained using term frequency-inverse document frequency (TF-IDF) features and a second approach based on topics modeled using a Latent Dirichlet Allocation model (LDA) to reduce the dimensionality of the unstructured data. Our results on the GEO database show that structured metadata terms can be the most accurately predicted using the TF-IDF approach followed by LDA both outperforming the majority vote baseline. While some accuracy is lost by the dimensionality reduction of LDA, the difference is small for elements with few possible values, and there is a large improvement over the majority classifier baseline. Overall this is a promising approach for metadata prediction that is likely to be applicable to other datasets and has implications for researchers interested in biomedical metadata curation and metadata prediction. Database URL: http://www.yeastgenome.org/ PMID:28637268

Pragmatic Metadata Management for Integration into Multiple Spatial Data Infrastructure Systems and Platforms

NASA Astrophysics Data System (ADS)

Benedict, K. K.; Scott, S.

2013-12-01

While there has been a convergence towards a limited number of standards for representing knowledge (metadata) about geospatial (and other) data objects and collections, there exist a variety of community conventions around the specific use of those standards and within specific data discovery and access systems. This combination of limited (but multiple) standards and conventions creates a challenge for system developers that aspire to participate in multiple data infrastrucutres, each of which may use a different combination of standards and conventions. While Extensible Markup Language (XML) is a shared standard for encoding most metadata, traditional direct XML transformations (XSLT) from one standard to another often result in an imperfect transfer of information due to incomplete mapping from one standard's content model to another. This paper presents the work at the University of New Mexico's Earth Data Analysis Center (EDAC) in which a unified data and metadata management system has been developed in support of the storage, discovery and access of heterogeneous data products. This system, the Geographic Storage, Transformation and Retrieval Engine (GSTORE) platform has adopted a polyglot database model in which a combination of relational and document-based databases are used to store both data and metadata, with some metadata stored in a custom XML schema designed as a superset of the requirements for multiple target metadata standards: ISO 19115-2/19139/19110/19119, FGCD CSDGM (both with and without remote sensing extensions) and Dublin Core. Metadata stored within this schema is complemented by additional service, format and publisher information that is dynamically "injected" into produced metadata documents when they are requested from the system. While mapping from the underlying common metadata schema is relatively straightforward, the generation of valid metadata within each target standard is necessary but not sufficient for integration into multiple data infrastructures, as has been demonstrated through EDAC's testing and deployment of metadata into multiple external systems: Data.Gov, the GEOSS Registry, the DataONE network, the DSpace based institutional repository at UNM and semantic mediation systems developed as part of the NASA ACCESS ELSeWEB project. Each of these systems requires valid metadata as a first step, but to make most effective use of the delivered metadata each also has a set of conventions that are specific to the system. This presentation will provide an overview of the underlying metadata management model, the processes and web services that have been developed to automatically generate metadata in a variety of standard formats and highlight some of the specific modifications made to the output metadata content to support the different conventions used by the multiple metadata integration endpoints.

In situ data analytics and indexing of protein trajectories.

PubMed

Johnston, Travis; Zhang, Boyu; Liwo, Adam; Crivelli, Silvia; Taufer, Michela

2017-06-15

The transition toward exascale computing will be accompanied by a performance dichotomy. Computational peak performance will rapidly increase; I/O performance will either grow slowly or be completely stagnant. Essentially, the rate at which data are generated will grow much faster than the rate at which data can be read from and written to the disk. MD simulations will soon face the I/O problem of efficiently writing to and reading from disk on the next generation of supercomputers. This article targets MD simulations at the exascale and proposes a novel technique for in situ data analysis and indexing of MD trajectories. Our technique maps individual trajectories' substructures (i.e., α-helices, β-strands) to metadata frame by frame. The metadata captures the conformational properties of the substructures. The ensemble of metadata can be used for automatic, strategic analysis within a trajectory or across trajectories, without manually identify those portions of trajectories in which critical changes take place. We demonstrate our technique's effectiveness by applying it to 26.3k helices and 31.2k strands from 9917 PDB proteins and by providing three empirical case studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Echo™ User Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, Dustin Yewell

Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reportingmore » and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.« less

Filament Chirality over an Entire Cycle Determined with an Automated Detection Module -- a Neat Surprise!

NASA Astrophysics Data System (ADS)

Martens, Petrus C.; Yeates, A. R.; Mackay, D.; Pillai, K. G.

2013-07-01

Using metadata produced by automated solar feature detection modules developed for SDO (Martens et al. 2012) we have discovered some trends in filament chirality and filament-sigmoid relations that are new and in part contradict the current consensus. Automated detection of solar features has the advantage over manual detection of having the detection criteria applied consistently, and in being able to deal with enormous amounts of data, like the 1 Terabyte per day that SDO produces. Here we use the filament detection module developed by Bernasconi, which has metadata from 2000 on, and the sigmoid sniffer, which has been producing metadata from AIA 94 A images since October 2011. The most interesting result we find is that the hemispheric chirality preference for filaments (dextral in the north, and v.v.), studied in detail for a three year period by Pevtsov et al. (2003) seems to disappear during parts of the decline of cycle 23 and during the extended solar minimum that followed. Moreover the hemispheric chirality rule seems to be much less pronounced during the onset of cycle 24. For sigmoids we find the expected correlation between chirality and handedness (S or Z) shape but not as strong as expected.

Doing Your Science While You're in Orbit

NASA Astrophysics Data System (ADS)

Green, Mark L.; Miller, Stephen D.; Vazhkudai, Sudharshan S.; Trater, James R.

2010-11-01

Large-scale neutron facilities such as the Spallation Neutron Source (SNS) located at Oak Ridge National Laboratory need easy-to-use access to Department of Energy Leadership Computing Facilities and experiment repository data. The Orbiter thick- and thin-client and its supporting Service Oriented Architecture (SOA) based services (available at https://orbiter.sns.gov) consist of standards-based components that are reusable and extensible for accessing high performance computing, data and computational grid infrastructure, and cluster-based resources easily from a user configurable interface. The primary Orbiter system goals consist of (1) developing infrastructure for the creation and automation of virtual instrumentation experiment optimization, (2) developing user interfaces for thin- and thick-client access, (3) provide a prototype incorporating major instrument simulation packages, and (4) facilitate neutron science community access and collaboration. The secure Orbiter SOA authentication and authorization is achieved through the developed Virtual File System (VFS) services, which use Role-Based Access Control (RBAC) for data repository file access, thin-and thick-client functionality and application access, and computational job workflow management. The VFS Relational Database Management System (RDMS) consists of approximately 45 database tables describing 498 user accounts with 495 groups over 432,000 directories with 904,077 repository files. Over 59 million NeXus file metadata records are associated to the 12,800 unique NeXus file field/class names generated from the 52,824 repository NeXus files. Services that enable (a) summary dashboards of data repository status with Quality of Service (QoS) metrics, (b) data repository NeXus file field/class name full text search capabilities within a Google like interface, (c) fully functional RBAC browser for the read-only data repository and shared areas, (d) user/group defined and shared metadata for data repository files, (e) user, group, repository, and web 2.0 based global positioning with additional service capabilities are currently available. The SNS based Orbiter SOA integration progress with the Distributed Data Analysis for Neutron Scattering Experiments (DANSE) software development project is summarized with an emphasis on DANSE Central Services and the Virtual Neutron Facility (VNF). Additionally, the DANSE utilization of the Orbiter SOA authentication, authorization, and data transfer services best practice implementations are presented.

Why can't I manage my digital images like MP3s? The evolution and intent of multimedia metadata

NASA Astrophysics Data System (ADS)

Goodrum, Abby; Howison, James

2005-01-01

This paper considers the deceptively simple question: Why can't digital images be managed in the simple and effective manner in which digital music files are managed? We make the case that the answer is different treatments of metadata in different domains with different goals. A central difference between the two formats stems from the fact that digital music metadata lookup services are collaborative and automate the movement from a digital file to the appropriate metadata, while image metadata services do not. To understand why this difference exists we examine the divergent evolution of metadata standards for digital music and digital images and observed that the processes differ in interesting ways according to their intent. Specifically music metadata was developed primarily for personal file management and community resource sharing, while the focus of image metadata has largely been on information retrieval. We argue that lessons from MP3 metadata can assist individuals facing their growing personal image management challenges. Our focus therefore is not on metadata for cultural heritage institutions or the publishing industry, it is limited to the personal libraries growing on our hard-drives. This bottom-up approach to file management combined with p2p distribution radically altered the music landscape. Might such an approach have a similar impact on image publishing? This paper outlines plans for improving the personal management of digital images-doing image metadata and file management the MP3 way-and considers the likelihood of success.

Why can't I manage my digital images like MP3s? The evolution and intent of multimedia metadata

NASA Astrophysics Data System (ADS)

Goodrum, Abby; Howison, James

2004-12-01

This paper considers the deceptively simple question: Why can"t digital images be managed in the simple and effective manner in which digital music files are managed? We make the case that the answer is different treatments of metadata in different domains with different goals. A central difference between the two formats stems from the fact that digital music metadata lookup services are collaborative and automate the movement from a digital file to the appropriate metadata, while image metadata services do not. To understand why this difference exists we examine the divergent evolution of metadata standards for digital music and digital images and observed that the processes differ in interesting ways according to their intent. Specifically music metadata was developed primarily for personal file management and community resource sharing, while the focus of image metadata has largely been on information retrieval. We argue that lessons from MP3 metadata can assist individuals facing their growing personal image management challenges. Our focus therefore is not on metadata for cultural heritage institutions or the publishing industry, it is limited to the personal libraries growing on our hard-drives. This bottom-up approach to file management combined with p2p distribution radically altered the music landscape. Might such an approach have a similar impact on image publishing? This paper outlines plans for improving the personal management of digital images-doing image metadata and file management the MP3 way-and considers the likelihood of success.

The Role of Metadata Standards in EOSDIS Search and Retrieval Applications

NASA Technical Reports Server (NTRS)

Pfister, Robin

1999-01-01

Metadata standards play a critical role in data search and retrieval systems. Metadata tie software to data so the data can be processed, stored, searched, retrieved and distributed. Without metadata these actions are not possible. The process of populating metadata to describe science data is an important service to the end user community so that a user who is unfamiliar with the data, can easily find and learn about a particular dataset before an order decision is made. Once a good set of standards are in place, the accuracy with which data search can be performed depends on the degree to which metadata standards are adhered during product definition. NASA's Earth Observing System Data and Information System (EOSDIS) provides examples of how metadata standards are used in data search and retrieval.

openPDS: protecting the privacy of metadata through SafeAnswers.

PubMed

de Montjoye, Yves-Alexandre; Shmueli, Erez; Wang, Samuel S; Pentland, Alex Sandy

2014-01-01

The rise of smartphones and web services made possible the large-scale collection of personal metadata. Information about individuals' location, phone call logs, or web-searches, is collected and used intensively by organizations and big data researchers. Metadata has however yet to realize its full potential. Privacy and legal concerns, as well as the lack of technical solutions for personal metadata management is preventing metadata from being shared and reconciled under the control of the individual. This lack of access and control is furthermore fueling growing concerns, as it prevents individuals from understanding and managing the risks associated with the collection and use of their data. Our contribution is two-fold: (1) we describe openPDS, a personal metadata management framework that allows individuals to collect, store, and give fine-grained access to their metadata to third parties. It has been implemented in two field studies; (2) we introduce and analyze SafeAnswers, a new and practical way of protecting the privacy of metadata at an individual level. SafeAnswers turns a hard anonymization problem into a more tractable security one. It allows services to ask questions whose answers are calculated against the metadata instead of trying to anonymize individuals' metadata. The dimensionality of the data shared with the services is reduced from high-dimensional metadata to low-dimensional answers that are less likely to be re-identifiable and to contain sensitive information. These answers can then be directly shared individually or in aggregate. openPDS and SafeAnswers provide a new way of dynamically protecting personal metadata, thereby supporting the creation of smart data-driven services and data science research.

openPDS: Protecting the Privacy of Metadata through SafeAnswers

PubMed Central

de Montjoye, Yves-Alexandre; Shmueli, Erez; Wang, Samuel S.; Pentland, Alex Sandy

2014-01-01

The rise of smartphones and web services made possible the large-scale collection of personal metadata. Information about individuals' location, phone call logs, or web-searches, is collected and used intensively by organizations and big data researchers. Metadata has however yet to realize its full potential. Privacy and legal concerns, as well as the lack of technical solutions for personal metadata management is preventing metadata from being shared and reconciled under the control of the individual. This lack of access and control is furthermore fueling growing concerns, as it prevents individuals from understanding and managing the risks associated with the collection and use of their data. Our contribution is two-fold: (1) we describe openPDS, a personal metadata management framework that allows individuals to collect, store, and give fine-grained access to their metadata to third parties. It has been implemented in two field studies; (2) we introduce and analyze SafeAnswers, a new and practical way of protecting the privacy of metadata at an individual level. SafeAnswers turns a hard anonymization problem into a more tractable security one. It allows services to ask questions whose answers are calculated against the metadata instead of trying to anonymize individuals' metadata. The dimensionality of the data shared with the services is reduced from high-dimensional metadata to low-dimensional answers that are less likely to be re-identifiable and to contain sensitive information. These answers can then be directly shared individually or in aggregate. openPDS and SafeAnswers provide a new way of dynamically protecting personal metadata, thereby supporting the creation of smart data-driven services and data science research. PMID:25007320

A System for Distributing Real-Time Customized (NEXRAD-Radar) Geosciences Data

NASA Astrophysics Data System (ADS)

Singh, Satpreet; McWhirter, Jeff; Krajewski, Witold; Kruger, Anton; Goska, Radoslaw; Seo, Bongchul; Domaszczynski, Piotr; Weber, Jeff

2010-05-01

Hydrometeorologists and hydrologists can benefit from (weather) radar derived rain products, including rain rates and accumulations. The Hydro-NEXRAD system (HNX1) has been in operation since 2006 at IIHR-Hydroscience and Engineering at The University of Iowa. It provides rapid and user-friendly access to such user-customized products, generated using archived Weather Surveillance Doppler Radar (WSR-88D) data from the NEXRAD weather radar network in the United States. HNX1 allows researchers to deal directly with radar-derived rain products, without the burden of the details of radar data collection, quality control, processing, and format conversion. A number of hydrologic applications can benefit from a continuous real-time feed of customized radar-derived rain products. We are currently developing such a system, Hydro-NEXRAD 2 (HNX2). HNX2 collects real-time, unprocessed data from multiple NEXRAD radars as they become available, processes them through a user-configurable pipeline of data-processing modules, and then publishes processed products at regular intervals. Modules in the data processing pipeline encapsulate algorithms such as non-meteorological echo detection, range correction, radar-reflectivity-rain rate (Z-R) conversion, advection correction, merging products from multiple radars, and grid transformations. HNX2's implementation presents significant challenges, including quality-control, error-handling, time-synchronization of data from multiple asynchronous sources, generation of multiple-radar metadata products, distribution of products to a user base with diverse needs and constraints, and scalability. For content management and distribution, HNX2 uses RAMADDA (Repository for Archiving, Managing and Accessing Diverse Data), developed by the UCAR/Unidata Program Center in the Unites States. RAMADDA allows HNX2 to publish products through automation and gives users multiple access methods to the published products, including simple web-browser based access, and OpenDAP access. The latter allows a user to set up automation at his/her end, and fetch new data from HNX2 at regular intervals. HNX2 uses a two-dimensional metadata structure called a mosaic for managing metadata of the rain products. Currently, HNX2 is in pre-production state and is serving near real-time rain-rate map data-products for individual radars and merged data-products from seven radars covering the state of Iowa in the United States. These products then drive a rainfall-runoff model called CUENCAS, which is used as part of the Iowa Flood Center (housed at The University of Iowa) real-time flood forecasting system. We are currently developing a generalized scalable framework that will run on inexpensive hardware and will provide products for basins anywhere in the continental United States.

Development of Web GIS for complex processing and visualization of climate geospatial datasets as an integral part of dedicated Virtual Research Environment

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Okladnikov, Igor; Titov, Alexander

2017-04-01

For comprehensive usage of large geospatial meteorological and climate datasets it is necessary to create a distributed software infrastructure based on the spatial data infrastructure (SDI) approach. Currently, it is generally accepted that the development of client applications as integrated elements of such infrastructure should be based on the usage of modern web and GIS technologies. The paper describes the Web GIS for complex processing and visualization of geospatial (mainly in NetCDF and PostGIS formats) datasets as an integral part of the dedicated Virtual Research Environment for comprehensive study of ongoing and possible future climate change, and analysis of their implications, providing full information and computing support for the study of economic, political and social consequences of global climate change at the global and regional levels. The Web GIS consists of two basic software parts: 1. Server-side part representing PHP applications of the SDI geoportal and realizing the functionality of interaction with computational core backend, WMS/WFS/WPS cartographical services, as well as implementing an open API for browser-based client software. Being the secondary one, this part provides a limited set of procedures accessible via standard HTTP interface. 2. Front-end part representing Web GIS client developed according to a "single page application" technology based on JavaScript libraries OpenLayers (http://openlayers.org/), ExtJS (https://www.sencha.com/products/extjs), GeoExt (http://geoext.org/). It implements application business logic and provides intuitive user interface similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Boundless/OpenGeo architecture was used as a basis for Web-GIS client development. According to general INSPIRE requirements to data visualization Web GIS provides such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. The specialized Web GIS client contains three basic tires: • Tier of NetCDF metadata in JSON format • Middleware tier of JavaScript objects implementing methods to work with: o NetCDF metadata o XML file of selected calculations configuration (XML task) o WMS/WFS/WPS cartographical services • Graphical user interface tier representing JavaScript objects realizing general application business logic Web-GIS developed provides computational processing services launching to support solving tasks in the area of environmental monitoring, as well as presenting calculation results in the form of WMS/WFS cartographical layers in raster (PNG, JPG, GeoTIFF), vector (KML, GML, Shape), and binary (NetCDF) formats. It has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical formats. The work is supported by the Russian Science Foundation grant No 16-19-10257.

Discovery of Marine Datasets and Geospatial Metadata Visualization

NASA Astrophysics Data System (ADS)

Schwehr, K. D.; Brennan, R. T.; Sellars, J.; Smith, S.

2009-12-01

NOAA's National Geophysical Data Center (NGDC) provides the deep archive of US multibeam sonar hydrographic surveys. NOAA stores the data as Bathymetric Attributed Grids (BAG; http://www.opennavsurf.org/) that are HDF5 formatted files containing gridded bathymetry, gridded uncertainty, and XML metadata. While NGDC provides the deep store and a basic ERSI ArcIMS interface to the data, additional tools need to be created to increase the frequency with which researchers discover hydrographic surveys that might be beneficial for their research. Using Open Source tools, we have created a draft of a Google Earth visualization of NOAA's complete collection of BAG files as of March 2009. Each survey is represented as a bounding box, an optional preview image of the survey data, and a pop up placemark. The placemark contains a brief summary of the metadata and links to directly download of the BAG survey files and the complete metadata file. Each survey is time tagged so that users can search both in space and time for surveys that meet their needs. By creating this visualization, we aim to make the entire process of data discovery, validation of relevance, and download much more efficient for research scientists who may not be familiar with NOAA's hydrographic survey efforts or the BAG format. In the process of creating this demonstration, we have identified a number of improvements that can be made to the hydrographic survey process in order to make the results easier to use especially with respect to metadata generation. With the combination of the NGDC deep archiving infrastructure, a Google Earth virtual globe visualization, and GeoRSS feeds of updates, we hope to increase the utilization of these high-quality gridded bathymetry. This workflow applies equally well to LIDAR topography and bathymetry. Additionally, with proper referencing and geotagging in journal publications, we hope to close the loop and help the community create a true “Geospatial Scholar” infrastructure.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

NASA Astrophysics Data System (ADS)

Naito, O.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

A user-centred evaluation framework for the Sealife semantic web browsers

PubMed Central

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-01-01

Background Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. Methods This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. Results It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Conclusion Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues. PMID:19796398

A user-centred evaluation framework for the Sealife semantic web browsers.

PubMed

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-10-01

Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues.

Progress in defining a standard for file-level metadata

NASA Technical Reports Server (NTRS)

Williams, Joel; Kobler, Ben

1996-01-01

In the following narrative, metadata required to locate a file on tape or collection of tapes will be referred to as file-level metadata. This paper discribes the rationale for and the history of the effort to define a standard for this metadata.

Achieving interoperability for metadata registries using comparative object modeling.

PubMed

Park, Yu Rang; Kim, Ju Han

2010-01-01

Achieving data interoperability between organizations relies upon agreed meaning and representation (metadata) of data. For managing and registering metadata, many organizations have built metadata registries (MDRs) in various domains based on international standard for MDR framework, ISO/IEC 11179. Following this trend, two pubic MDRs in biomedical domain have been created, United States Health Information Knowledgebase (USHIK) and cancer Data Standards Registry and Repository (caDSR), from U.S. Department of Health & Human Services and National Cancer Institute (NCI), respectively. Most MDRs are implemented with indiscriminate extending for satisfying organization-specific needs and solving semantic and structural limitation of ISO/IEC 11179. As a result it is difficult to address interoperability among multiple MDRs. In this paper, we propose an integrated metadata object model for achieving interoperability among multiple MDRs. To evaluate this model, we developed an XML Schema Definition (XSD)-based metadata exchange format. We created an XSD-based metadata exporter, supporting both the integrated metadata object model and organization-specific MDR formats.

Request queues for interactive clients in a shared file system of a parallel computing system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bent, John M.; Faibish, Sorin

Interactive requests are processed from users of log-in nodes. A metadata server node is provided for use in a file system shared by one or more interactive nodes and one or more batch nodes. The interactive nodes comprise interactive clients to execute interactive tasks and the batch nodes execute batch jobs for one or more batch clients. The metadata server node comprises a virtual machine monitor; an interactive client proxy to store metadata requests from the interactive clients in an interactive client queue; a batch client proxy to store metadata requests from the batch clients in a batch client queue;more » and a metadata server to store the metadata requests from the interactive client queue and the batch client queue in a metadata queue based on an allocation of resources by the virtual machine monitor. The metadata requests can be prioritized, for example, based on one or more of a predefined policy and predefined rules.« less

A browser-based event display for the CMS experiment at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hategan, M.; McCauley, T.; Nguyen, P.

2012-01-01

The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d.more » The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.« less

Evaluating Web accessibility at different processing phases

NASA Astrophysics Data System (ADS)

Fernandes, N.; Lopes, R.; Carriço, L.

2012-09-01

Modern Web sites use several techniques (e.g. DOM manipulation) that allow for the injection of new content into their Web pages (e.g. AJAX), as well as manipulation of the HTML DOM tree. This has the consequence that the Web pages that are presented to users (i.e. after browser processing) are different from the original structure and content that is transmitted through HTTP communication (i.e. after browser processing). This poses a series of challenges for Web accessibility evaluation, especially on automated evaluation software. This article details an experimental study designed to understand the differences posed by accessibility evaluation after Web browser processing. We implemented a Javascript-based evaluator, QualWeb, that can perform WCAG 2.0 based accessibility evaluations in the two phases of browser processing. Our study shows that, in fact, there are considerable differences between the HTML DOM trees in both phases, which have the consequence of having distinct evaluation results. We discuss the impact of these results in the light of the potential problems that these differences can pose to designers and developers that use accessibility evaluators that function before browser processing.

Making metadata usable in a multi-national research setting.

PubMed

Ellul, Claire; Foord, Joanna; Mooney, John

2013-11-01

SECOA (Solutions for Environmental Contrasts in Coastal Areas) is a multi-national research project examining the effects of human mobility on urban settlements in fragile coastal environments. This paper describes the setting up of a SECOA metadata repository for non-specialist researchers such as environmental scientists and tourism experts. Conflicting usability requirements of two groups - metadata creators and metadata users - are identified along with associated limitations of current metadata standards. A description is given of a configurable metadata system designed to grow as the project evolves. This work is of relevance for similar projects such as INSPIRE. Copyright © 2012 Elsevier Ltd and The Ergonomics Society. All rights reserved.

A case for user-generated sensor metadata

NASA Astrophysics Data System (ADS)

Nüst, Daniel

2015-04-01

Cheap and easy to use sensing technology and new developments in ICT towards a global network of sensors and actuators promise previously unthought of changes for our understanding of the environment. Large professional as well as amateur sensor networks exist, and they are used for specific yet diverse applications across domains such as hydrology, meteorology or early warning systems. However the impact this "abundance of sensors" had so far is somewhat disappointing. There is a gap between (community-driven) sensor networks that could provide very useful data and the users of the data. In our presentation, we argue this is due to a lack of metadata which allows determining the fitness of use of a dataset. Syntactic or semantic interoperability for sensor webs have made great progress and continue to be an active field of research, yet they often are quite complex, which is of course due to the complexity of the problem at hand. But still, we see the most generic information to determine fitness for use is a dataset's provenance, because it allows users to make up their own minds independently from existing classification schemes for data quality. In this work we will make the case how curated user-contributed metadata has the potential to improve this situation. This especially applies for scenarios in which an observed property is applicable in different domains, and for set-ups where the understanding about metadata concepts and (meta-)data quality differs between data provider and user. On the one hand a citizen does not understand the ISO provenance metadata. On the other hand a researcher might find issues in publicly accessible time series published by citizens, which the latter might not be aware of or care about. Because users will have to determine fitness for use for each application on their own anyway, we suggest an online collaboration platform for user-generated metadata based on an extremely simplified data model. In the most basic fashion, metadata generated by users can be boiled down to a basic property of the world wide web: many information items, such as news or blog posts, allow users to create comments and rate the content. Therefore we argue to focus a core data model on one text field for a textual comment, one optional numerical field for a rating, and a resolvable identifier for the dataset that is commented on. We present a conceptual framework that integrates user comments in existing standards and relevant applications of online sensor networks and discuss possible approaches, such as linked data, brokering, or standalone metadata portals. We relate this framework to existing work in user generated content, such as proprietary rating systems on commercial websites, microformats, the GeoViQua User Quality Model, the CHARMe annotations, or W3C Open Annotation. These systems are also explored for commonalities and based on their very useful concepts and ideas; we present an outline for future extensions of the minimal model. Building on this framework we present a concept how a simplistic comment-rating-system can be extended to capture provenance information for spatio-temporal observations in the sensor web, and how this framework can be evaluated.

Inter-University Upper Atmosphere Global Observation Network (IUGONET) Metadata Database and Its Interoperability

NASA Astrophysics Data System (ADS)

Yatagai, A. I.; Iyemori, T.; Ritschel, B.; Koyama, Y.; Hori, T.; Abe, S.; Tanaka, Y.; Shinbori, A.; Umemura, N.; Sato, Y.; Yagi, M.; Ueno, S.; Hashiguchi, N. O.; Kaneda, N.; Belehaki, A.; Hapgood, M. A.

2013-12-01

The IUGONET is a Japanese program to build a metadata database for ground-based observations of the upper atmosphere [1]. The project began in 2009 with five Japanese institutions which archive data observed by radars, magnetometers, photometers, radio telescopes and helioscopes, and so on, at various altitudes from the Earth's surface to the Sun. Systems have been developed to allow searching of the above described metadata. We have been updating the system and adding new and updated metadata. The IUGONET development team adopted the SPASE metadata model [2] to describe the upper atmosphere data. This model is used as the common metadata format by the virtual observatories for solar-terrestrial physics. It includes metadata referring to each data file (called a 'Granule'), which enable a search for data files as well as data sets. Further details are described in [2] and [3]. Currently, three additional Japanese institutions are being incorporated in IUGONET. Furthermore, metadata of observations of the troposphere, taken at the observatories of the middle and upper atmosphere radar at Shigaraki and the Meteor radar in Indonesia, have been incorporated. These additions will contribute to efficient interdisciplinary scientific research. In the beginning of 2013, the registration of the 'Observatory' and 'Instrument' metadata was completed, which makes it easy to overview of the metadata database. The number of registered metadata as of the end of July, totalled 8.8 million, including 793 observatories and 878 instruments. It is important to promote interoperability and/or metadata exchange between the database development groups. A memorandum of agreement has been signed with the European Near-Earth Space Data Infrastructure for e-Science (ESPAS) project, which has similar objectives to IUGONET with regard to a framework for formal collaboration. Furthermore, observations by satellites and the International Space Station are being incorporated with a view for making/linking metadata databases. The development of effective data systems will contribute to the progress of scientific research on solar terrestrial physics, climate and the geophysical environment. Any kind of cooperation, metadata input and feedback, especially for linkage of the databases, is welcomed. References 1. Hayashi, H. et al., Inter-university Upper Atmosphere Global Observation Network (IUGONET), Data Sci. J., 12, WDS179-184, 2013. 2. King, T. et al., SPASE 2.0: A standard data model for space physics. Earth Sci. Inform. 3, 67-73, 2010, doi:10.1007/s12145-010-0053-4. 3. Hori, T., et al., Development of IUGONET metadata format and metadata management system. J. Space Sci. Info. Jpn., 105-111, 2012. (in Japanese)

Towards Precise Metadata-set for Discovering 3D Geospatial Models in Geo-portals

NASA Astrophysics Data System (ADS)

Zamyadi, A.; Pouliot, J.; Bédard, Y.

2013-09-01

Accessing 3D geospatial models, eventually at no cost and for unrestricted use, is certainly an important issue as they become popular among participatory communities, consultants, and officials. Various geo-portals, mainly established for 2D resources, have tried to provide access to existing 3D resources such as digital elevation model, LIDAR or classic topographic data. Describing the content of data, metadata is a key component of data discovery in geo-portals. An inventory of seven online geo-portals and commercial catalogues shows that the metadata referring to 3D information is very different from one geo-portal to another as well as for similar 3D resources in the same geo-portal. The inventory considered 971 data resources affiliated with elevation. 51% of them were from three geo-portals running at Canadian federal and municipal levels whose metadata resources did not consider 3D model by any definition. Regarding the remaining 49% which refer to 3D models, different definition of terms and metadata were found, resulting in confusion and misinterpretation. The overall assessment of these geo-portals clearly shows that the provided metadata do not integrate specific and common information about 3D geospatial models. Accordingly, the main objective of this research is to improve 3D geospatial model discovery in geo-portals by adding a specific metadata-set. Based on the knowledge and current practices on 3D modeling, and 3D data acquisition and management, a set of metadata is proposed to increase its suitability for 3D geospatial models. This metadata-set enables the definition of genuine classes, fields, and code-lists for a 3D metadata profile. The main structure of the proposal contains 21 metadata classes. These classes are classified in three packages as General and Complementary on contextual and structural information, and Availability on the transition from storage to delivery format. The proposed metadata set is compared with Canadian Geospatial Data Infrastructure (CGDI) metadata which is an implementation of North American Profile of ISO-19115. The comparison analyzes the two metadata against three simulated scenarios about discovering needed 3D geo-spatial datasets. Considering specific metadata about 3D geospatial models, the proposed metadata-set has six additional classes on geometric dimension, level of detail, geometric modeling, topology, and appearance information. In addition classes on data acquisition, preparation, and modeling, and physical availability have been specialized for 3D geospatial models.

Interactive Visualization Systems and Data Integration Methods for Supporting Discovery in Collections of Scientific Information

DTIC Science & Technology

2011-05-01

iTunes illustrate the difference between the centralized approach of digital library systems and the distributed approach of container file formats...metadata in a container file format. Apple’s iTunes uses a centralized metadata approach and allows users to maintain song metadata in a single...one iTunes library to another the metadata must be copied separately or reentered in the new library. This demonstrates the utility of storing metadata

Collaborative Metadata Curation in Support of NASA Earth Science Data Stewardship

NASA Technical Reports Server (NTRS)

Sisco, Adam W.; Bugbee, Kaylin; le Roux, Jeanne; Staton, Patrick; Freitag, Brian; Dixon, Valerie

2018-01-01

Growing collection of NASA Earth science data is archived and distributed by EOSDIS’s 12 Distributed Active Archive Centers (DAACs). Each collection and granule is described by a metadata record housed in the Common Metadata Repository (CMR). Multiple metadata standards are in use, and core elements of each are mapped to and from a common model – the Unified Metadata Model (UMM). Work done by the Analysis and Review of CMR (ARC) Team.

Mitogenome metadata: current trends and proposed standards.

PubMed

Strohm, Jeff H T; Gwiazdowski, Rodger A; Hanner, Robert

2016-09-01

Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal Mitochondrial DNA between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes's GenBank record, would increase their research value.

Design and implementation of a fault-tolerant and dynamic metadata database for clinical trials

NASA Astrophysics Data System (ADS)

Lee, J.; Zhou, Z.; Talini, E.; Documet, J.; Liu, B.

2007-03-01

In recent imaging-based clinical trials, quantitative image analysis (QIA) and computer-aided diagnosis (CAD) methods are increasing in productivity due to higher resolution imaging capabilities. A radiology core doing clinical trials have been analyzing more treatment methods and there is a growing quantity of metadata that need to be stored and managed. These radiology centers are also collaborating with many off-site imaging field sites and need a way to communicate metadata between one another in a secure infrastructure. Our solution is to implement a data storage grid with a fault-tolerant and dynamic metadata database design to unify metadata from different clinical trial experiments and field sites. Although metadata from images follow the DICOM standard, clinical trials also produce metadata specific to regions-of-interest and quantitative image analysis. We have implemented a data access and integration (DAI) server layer where multiple field sites can access multiple metadata databases in the data grid through a single web-based grid service. The centralization of metadata database management simplifies the task of adding new databases into the grid and also decreases the risk of configuration errors seen in peer-to-peer grids. In this paper, we address the design and implementation of a data grid metadata storage that has fault-tolerance and dynamic integration for imaging-based clinical trials.

Metadata and Service at the GFZ ISDC Portal

NASA Astrophysics Data System (ADS)

Ritschel, B.

2008-05-01

The online service portal of the GFZ Potsdam Information System and Data Center (ISDC) is an access point for all manner of geoscientific geodata, its corresponding metadata, scientific documentation and software tools. At present almost 2000 national and international users and user groups have the opportunity to request Earth science data from a portfolio of 275 different products types and more than 20 Million single data files with an added volume of approximately 12 TByte. The majority of the data and information, the portal currently offers to the public, are global geomonitoring products such as satellite orbit and Earth gravity field data as well as geomagnetic and atmospheric data for the exploration. These products for Earths changing system are provided via state-of-the art retrieval techniques. The data product catalog system behind these techniques is based on the extensive usage of standardized metadata, which are describing the different geoscientific product types and data products in an uniform way. Where as all ISDC product types are specified by NASA's Directory Interchange Format (DIF), Version 9.0 Parent XML DIF metadata files, the individual data files are described by extended DIF metadata documents. Depending on the beginning of the scientific project, one part of data files are described by extended DIF, Version 6 metadata documents and the other part are specified by data Child XML DIF metadata documents. Both, the product type dependent parent DIF metadata documents and the data file dependent child DIF metadata documents are derived from a base-DIF.xsd xml schema file. The ISDC metadata philosophy defines a geoscientific product as a package consisting of mostly one or sometimes more than one data file plus one extended DIF metadata file. Because NASA's DIF metadata standard has been developed in order to specify a collection of data only, the extension of the DIF standard consists of new and specific attributes, which are necessary for an explicit identification of single data files and the set-up of a comprehensive Earth science data catalog. The huge ISDC data catalog is realized by product type dependent tables filled with data file related metadata, which have relations to corresponding metadata tables. The product type describing parent DIF XML metadata documents are stored and managed in ORACLE's XML storage structures. In order to improve the interoperability of the ISDC service portal, the existing proprietary catalog system will be extended by an ISO 19115 based web catalog service. In addition to this development there is ISDC related concerning semantic network of different kind of metadata resources, like different kind of standardized and not-standardized metadata documents and literature as well as Web 2.0 user generated information derived from tagging activities and social navigation data.

Mercury Toolset for Spatiotemporal Metadata

NASA Technical Reports Server (NTRS)

Wilson, Bruce E.; Palanisamy, Giri; Devarakonda, Ranjeet; Rhyne, B. Timothy; Lindsley, Chris; Green, James

2010-01-01

Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily) harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

Mercury Toolset for Spatiotemporal Metadata

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce; Rhyne, B. Timothy; Lindsley, Chris

2010-06-01

Mercury (http://mercury.ornl.gov) is a set of tools for federated harvesting, searching, and retrieving metadata, particularly spatiotemporal metadata. Version 3.0 of the Mercury toolset provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, facetted type search, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. It provides a single portal to very quickly search for data and information contained in disparate data management systems, each of which may use different metadata formats. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury periodically (typically daily)harvests metadata sources through a collection of interfaces and re-indexes these metadata to provide extremely rapid search capabilities, even over collections with tens of millions of metadata records. A number of both graphical and application interfaces have been constructed within Mercury, to enable both human users and other computer programs to perform queries. Mercury was also designed to support multiple different projects, so that the particular fields that can be queried and used with search filters are easy to configure for each different project.

Metadata Realities for Cyberinfrastructure: Data Authors as Metadata Creators

ERIC Educational Resources Information Center

Mayernik, Matthew Stephen

2011-01-01

As digital data creation technologies become more prevalent, data and metadata management are necessary to make data available, usable, sharable, and storable. Researchers in many scientific settings, however, have little experience or expertise in data and metadata management. In this dissertation, I explore the everyday data and metadata…

NetCDF4/HDF5 and Linked Data in the Real World - Enriching Geoscientific Metadata without Bloat

NASA Astrophysics Data System (ADS)

Ip, Alex; Car, Nicholas; Druken, Kelsey; Poudjom-Djomani, Yvette; Butcher, Stirling; Evans, Ben; Wyborn, Lesley

2017-04-01

NetCDF4 has become the dominant generic format for many forms of geoscientific data, leveraging (and constraining) the versatile HDF5 container format, while providing metadata conventions for interoperability. However, the encapsulation of detailed metadata within each file can lead to metadata "bloat", and difficulty in maintaining consistency where metadata is replicated to multiple locations. Complex conceptual relationships are also difficult to represent in simple key-value netCDF metadata. Linked Data provides a practical mechanism to address these issues by associating the netCDF files and their internal variables with complex metadata stored in Semantic Web vocabularies and ontologies, while complying with and complementing existing metadata conventions. One of the stated objectives of the netCDF4/HDF5 formats is that they should be self-describing: containing metadata sufficient for cataloguing and using the data. However, this objective can be regarded as only partially-met where details of conventions and definitions are maintained externally to the data files. For example, one of the most widely used netCDF community standards, the Climate and Forecasting (CF) Metadata Convention, maintains standard vocabularies for a broad range of disciplines across the geosciences, but this metadata is currently neither readily discoverable nor machine-readable. We have previously implemented useful Linked Data and netCDF tooling (ncskos) that associates netCDF files, and individual variables within those files, with concepts in vocabularies formulated using the Simple Knowledge Organization System (SKOS) ontology. NetCDF files contain Uniform Resource Identifier (URI) links to terms represented as SKOS Concepts, rather than plain-text representations of those terms, so we can use simple, standardised web queries to collect and use rich metadata for the terms from any Linked Data-presented SKOS vocabulary. Geoscience Australia (GA) manages a large volume of diverse geoscientific data, much of which is being translated from proprietary formats to netCDF at NCI Australia. This data is made available through the NCI National Environmental Research Data Interoperability Platform (NERDIP) for programmatic access and interdisciplinary analysis. The netCDF files contain both scientific data variables (e.g. gravity, magnetic or radiometric values), but also domain-specific operational values (e.g. specific instrument parameters) best described fully in formal vocabularies. Our ncskos codebase provides access to multiple stores of detailed external metadata in a standardised fashion. Geophysical datasets are generated from a "survey" event, and GA maintains corporate databases of all surveys and their associated metadata. It is impractical to replicate the full source survey metadata into each netCDF dataset so, instead, we link the netCDF files to survey metadata using public Linked Data URIs. These URIs link to Survey class objects which we model as a subclass of Activity objects as defined by the PROV Ontology, and we provide URI resolution for them via a custom Linked Data API which draws current survey metadata from GA's in-house databases. We have demonstrated that Linked Data is a practical way to associate netCDF data with detailed, external metadata. This allows us to ensure that catalogued metadata is kept consistent with metadata points-of-truth, and we can infer complex conceptual relationships not possible with netCDF key-value attributes alone.

Content Metadata Standards for Marine Science: A Case Study

USGS Publications Warehouse

Riall, Rebecca L.; Marincioni, Fausto; Lightsom, Frances L.

2004-01-01

The U.S. Geological Survey developed a content metadata standard to meet the demands of organizing electronic resources in the marine sciences for a broad, heterogeneous audience. These metadata standards are used by the Marine Realms Information Bank project, a Web-based public distributed library of marine science from academic institutions and government agencies. The development and deployment of this metadata standard serve as a model, complete with lessons about mistakes, for the creation of similarly specialized metadata standards for digital libraries.

Concurrent array-based queue

DOEpatents

Heidelberger, Philip; Steinmacher-Burow, Burkhard

2015-01-06

According to one embodiment, a method for implementing an array-based queue in memory of a memory system that includes a controller includes configuring, in the memory, metadata of the array-based queue. The configuring comprises defining, in metadata, an array start location in the memory for the array-based queue, defining, in the metadata, an array size for the array-based queue, defining, in the metadata, a queue top for the array-based queue and defining, in the metadata, a queue bottom for the array-based queue. The method also includes the controller serving a request for an operation on the queue, the request providing the location in the memory of the metadata of the queue.

WGISS-45 International Directory Network (IDN) Report

NASA Technical Reports Server (NTRS)

Morahan, Michael

2018-01-01

The objective of this presentation is to provide IDN (International Directory Network) updates on features and activities to the Committee on Earth Observation Satellites (CEOS) Working Group on Information Systems and Services (WGISS) and provider community. The following topics will be will be discussed during the presentation: Transition of Providers DIF-9 (Directory Interchange Format-9) to DIF-10 Metadata Records in the Common Metadata Repository (CMR); GCMD (Global Change Master Directory) Keyword Update; DIF-10 and UMM-C (Unified Metadata Model-Collections) Schema Changes; Metadata Validation of Provider Metadata; docBUILDER for Submitting IDN Metadata to the CMR (i.e. Registration); and Mapping WGClimate Essential Climate Variable (ECV) Inventory to IDN Records.

Explorative Analyses of Nursing Research Data.

PubMed

Kim, Hyeoneui; Jang, Imho; Quach, Jimmy; Richardson, Alex; Kim, Jaemin; Choi, Jeeyae

2016-10-26

As a first step of pursuing the vision of "big data science in nursing," we described the characteristics of nursing research data reported in 194 published nursing studies. We also explored how completely the Version 1 metadata specification of biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) represents these metadata. The metadata items of the nursing studies were all related to one or more of the bioCADDIE metadata entities. However, values of many metadata items of the nursing studies were not sufficiently represented through the bioCADDIE metadata. This was partly due to the differences in the scope of the content that the bioCADDIE metadata are designed to represent. The 194 nursing studies reported a total of 1,181 unique data items, the majority of which take non-numeric values. This indicates the importance of data standardization to enable the integrative analyses of these data to support big data science in nursing. © The Author(s) 2016.

A Model for Enhancing Internet Medical Document Retrieval with “Medical Core Metadata”

PubMed Central

Malet, Gary; Munoz, Felix; Appleyard, Richard; Hersh, William

1999-01-01

Objective: Finding documents on the World Wide Web relevant to a specific medical information need can be difficult. The goal of this work is to define a set of document content description tags, or metadata encodings, that can be used to promote disciplined search access to Internet medical documents. Design: The authors based their approach on a proposed metadata standard, the Dublin Core Metadata Element Set, which has recently been submitted to the Internet Engineering Task Force. Their model also incorporates the National Library of Medicine's Medical Subject Headings (MeSH) vocabulary and Medline-type content descriptions. Results: The model defines a medical core metadata set that can be used to describe the metadata for a wide variety of Internet documents. Conclusions: The authors propose that their medical core metadata set be used to assign metadata to medical documents to facilitate document retrieval by Internet search engines. PMID:10094069

MPEG-7: standard metadata for multimedia content

NASA Astrophysics Data System (ADS)

Chang, Wo

2005-08-01

The eXtensible Markup Language (XML) metadata technology of describing media contents has emerged as a dominant mode of making media searchable both for human and machine consumptions. To realize this premise, many online Web applications are pushing this concept to its fullest potential. However, a good metadata model does require a robust standardization effort so that the metadata content and its structure can reach its maximum usage between various applications. An effective media content description technology should also use standard metadata structures especially when dealing with various multimedia contents. A new metadata technology called MPEG-7 content description has merged from the ISO MPEG standards body with the charter of defining standard metadata to describe audiovisual content. This paper will give an overview of MPEG-7 technology and what impact it can bring forth to the next generation of multimedia indexing and retrieval applications.

Quality Assurance for Digital Learning Object Repositories: Issues for the Metadata Creation Process

ERIC Educational Resources Information Center

Currier, Sarah; Barton, Jane; O'Beirne, Ronan; Ryan, Ben

2004-01-01

Metadata enables users to find the resources they require, therefore it is an important component of any digital learning object repository. Much work has already been done within the learning technology community to assure metadata quality, focused on the development of metadata standards, specifications and vocabularies and their implementation…

Enhancing SCORM Metadata for Assessment Authoring in E-Learning

ERIC Educational Resources Information Center

Chang, Wen-Chih; Hsu, Hui-Huang; Smith, Timothy K.; Wang, Chun-Chia

2004-01-01

With the rapid development of distance learning and the XML technology, metadata play an important role in e-Learning. Nowadays, many distance learning standards, such as SCORM, AICC CMI, IEEE LTSC LOM and IMS, use metadata to tag learning materials. However, most metadata models are used to define learning materials and test problems. Few…

Development of Health Information Search Engine Based on Metadata and Ontology

PubMed Central

Song, Tae-Min; Jin, Dal-Lae

2014-01-01

Objectives The aim of the study was to develop a metadata and ontology-based health information search engine ensuring semantic interoperability to collect and provide health information using different application programs. Methods Health information metadata ontology was developed using a distributed semantic Web content publishing model based on vocabularies used to index the contents generated by the information producers as well as those used to search the contents by the users. Vocabulary for health information ontology was mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), and a list of about 1,500 terms was proposed. The metadata schema used in this study was developed by adding an element describing the target audience to the Dublin Core Metadata Element Set. Results A metadata schema and an ontology ensuring interoperability of health information available on the internet were developed. The metadata and ontology-based health information search engine developed in this study produced a better search result compared to existing search engines. Conclusions Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers. PMID:24872907

Development of health information search engine based on metadata and ontology.

PubMed

Song, Tae-Min; Park, Hyeoun-Ae; Jin, Dal-Lae

2014-04-01

The aim of the study was to develop a metadata and ontology-based health information search engine ensuring semantic interoperability to collect and provide health information using different application programs. Health information metadata ontology was developed using a distributed semantic Web content publishing model based on vocabularies used to index the contents generated by the information producers as well as those used to search the contents by the users. Vocabulary for health information ontology was mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), and a list of about 1,500 terms was proposed. The metadata schema used in this study was developed by adding an element describing the target audience to the Dublin Core Metadata Element Set. A metadata schema and an ontology ensuring interoperability of health information available on the internet were developed. The metadata and ontology-based health information search engine developed in this study produced a better search result compared to existing search engines. Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers.

Metadata in the Wild: An Empirical Survey of OPeNDAP-accessible Metadata and its Implications for Discovery

NASA Astrophysics Data System (ADS)

Hardy, D.; Janée, G.; Gallagher, J.; Frew, J.; Cornillon, P.

2006-12-01

The OPeNDAP Data Access Protocol (DAP) is a community standard for sharing scientific data across the Internet. Data providers using DAP have adopted a variety of metadata conventions to improve data utility, such as COARDS (1995) and CF (2003). Our results show, however, that metadata do not follow these conventions in practice. We collected metadata from over a hundred DAP servers, tens of thousands of data objects, and hundreds of collections. We found that a minority claim to adhere to a metadata convention, and a small percentage accurately adhere to their stated convention. We present descriptive statistics of our survey and highlight common traits such as well-populated attributes. Our empirical results indicate that unified search services cannot rely solely on metadata conventions. Although we encourage all providers to adopt a small subset of the CF convention for discovery purposes, we have no evidence to suggest that improved conventions would simplify the fundamental problem of heterogeneity. Large-scale discovery services must find methods for integrating incompatible metadata.

Using JavaScript and the FDSN web service to create an interactive earthquake information system

NASA Astrophysics Data System (ADS)

Fischer, Kasper D.

2015-04-01

The FDSN web service provides a web interface to access earthquake meta-data (e. g. event or station information) and waveform date over the internet. Requests are send to a server as URLs and the output is either XML or miniSEED. This makes it hard to read by humans but easy to process with different software. Different data centers are already supporting the FDSN web service, e. g. USGS, IRIS, ORFEUS. The FDSN web service is also part of the Seiscomp3 (http://www.seiscomp3.org) software. The Seismological Observatory of the Ruhr-University switched to Seiscomp3 as the standard software for the analysis of mining induced earthquakes at the beginning of 2014. This made it necessary to create a new web-based earthquake information service for the publication of results to the general public. This has be done by processing the output of a FDSN web service query by javascript running in a standard browser. The result is an interactive map presenting the observed events and further information of events and stations on a single web page as a table and on a map. In addition the user can download event information, waveform data and station data in different formats like miniSEED, quakeML or FDSNxml. The developed code and all used libraries are open source and freely available.

WILBER and PyWEED: Event-based Seismic Data Request Tools

NASA Astrophysics Data System (ADS)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

DOORS to the semantic web and grid with a PORTAL for biomedical computing.

PubMed

Taswell, Carl

2008-03-01

The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish web sites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. The Internet Registry Information Service (IRIS) registers [corrected] domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.

Mississippi State University Center for Air Sea Technology. FY93 and FY 94 Research Program in Navy Ocean Modeling and Prediction

DTIC Science & Technology

1994-09-30

relational versus object oriented DBMS, knowledge discovery, data models, rnetadata, data filtering, clustering techniques, and synthetic data. A secondary...The first was the investigation of Al/ES Lapplications (knowledge discovery, data mining, and clustering ). Here CAST collabo.rated with Dr. Fred Petry...knowledge discovery system based on clustering techniques; implemented an on-line data browser to the DBMS; completed preliminary efforts to apply object

47 CFR 14.60 - Applicability.

Code of Federal Regulations, 2013 CFR

2013-10-01

... BY PEOPLE WITH DISABILITIES Internet Browsers Built Into Telephones Used With Public Mobile Services... mobile services (as such term is defined in 47 U.S.C. 710(b)(4)(B)) that includes an Internet browser in...

47 CFR 14.60 - Applicability.

Code of Federal Regulations, 2014 CFR

2014-10-01

... BY PEOPLE WITH DISABILITIES Internet Browsers Built Into Telephones Used With Public Mobile Services... mobile services (as such term is defined in 47 U.S.C. 710(b)(4)(B)) that includes an Internet browser in...

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

Controlling EPICS from a web browser.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, K., Jr.

1999-04-13

An alternative to using a large graphical display manager like MEDM [1,2] to interface to a control system, is to use individual control objects, such as text boxes, meters, etc., running in a browser. This paper presents three implementations of this concept, one using ActiveX controls, one with Java applets, and another with Microsoft Agent. The ActiveX controls have performance nearing that of MEDM, but they only work on Windows platforms. The Java applets require a server to get around Web security restrictions and are not as fast, but they have the advantage of working on most platforms and withmore » both of the leading Web browsers. The agent works on Windows platforms with and without a browser and allows voice recognition and speech synthesis, making it somewhat more innovative than MEDM.« less

Genome Maps, a new generation genome browser.

PubMed

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Genome Maps, a new generation genome browser

PubMed Central

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-01-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

Interactive Analysis of General Beam Configurations using Finite Element Methods and JavaScript

NASA Astrophysics Data System (ADS)

Hernandez, Christopher

Advancements in computer technology have contributed to the widespread practice of modelling and solving engineering problems through the use of specialized software. The wide use of engineering software comes with the disadvantage to the user of costs from the required purchase of software licenses. The creation of accurate, trusted, and freely available applications capable of conducting meaningful analysis of engineering problems is a way to mitigate to the costs associated with every-day engineering computations. Writing applications in the JavaScript programming language allows the applications to run within any computer browser, without the need to install specialized software, since all internet browsers are equipped with virtual machines (VM) that allow the browsers to execute JavaScript code. The objective of this work is the development of an application that performs the analysis of a completely general beam through use of the finite element method. The app is written in JavaScript and embedded in a web page so it can be downloaded and executed by a user with an internet connection. This application allows the user to analyze any uniform or non-uniform beam, with any combination of applied forces, moments, distributed loads, and boundary conditions. Outputs for this application include lists the beam deformations and slopes, as well as lateral and slope deformation graphs, bending stress distributions, and shear and a moment diagrams. To validate the methodology of the GBeam finite element app, its results are verified using the results from obtained from two other established finite element solvers for fifteen separate test cases.

A standard for measuring metadata quality in spectral libraries

NASA Astrophysics Data System (ADS)

Rasaiah, B.; Jones, S. D.; Bellman, C.

2013-12-01

A standard for measuring metadata quality in spectral libraries Barbara Rasaiah, Simon Jones, Chris Bellman RMIT University Melbourne, Australia barbara.rasaiah@rmit.edu.au, simon.jones@rmit.edu.au, chris.bellman@rmit.edu.au ABSTRACT There is an urgent need within the international remote sensing community to establish a metadata standard for field spectroscopy that ensures high quality, interoperable metadata sets that can be archived and shared efficiently within Earth observation data sharing systems. Metadata are an important component in the cataloguing and analysis of in situ spectroscopy datasets because of their central role in identifying and quantifying the quality and reliability of spectral data and the products derived from them. This paper presents approaches to measuring metadata completeness and quality in spectral libraries to determine reliability, interoperability, and re-useability of a dataset. Explored are quality parameters that meet the unique requirements of in situ spectroscopy datasets, across many campaigns. Examined are the challenges presented by ensuring that data creators, owners, and data users ensure a high level of data integrity throughout the lifecycle of a dataset. Issues such as field measurement methods, instrument calibration, and data representativeness are investigated. The proposed metadata standard incorporates expert recommendations that include metadata protocols critical to all campaigns, and those that are restricted to campaigns for specific target measurements. The implication of semantics and syntax for a robust and flexible metadata standard are also considered. Approaches towards an operational and logistically viable implementation of a quality standard are discussed. This paper also proposes a way forward for adapting and enhancing current geospatial metadata standards to the unique requirements of field spectroscopy metadata quality. [0430] BIOGEOSCIENCES / Computational methods and data processing [0480] BIOGEOSCIENCES / Remote sensing [1904] INFORMATICS / Community standards [1912] INFORMATICS / Data management, preservation, rescue [1926] INFORMATICS / Geospatial [1930] INFORMATICS / Data and information governance [1946] INFORMATICS / Metadata [1952] INFORMATICS / Modeling [1976] INFORMATICS / Software tools and services [9810] GENERAL OR MISCELLANEOUS / New fields

Metadata Design in the New PDS4 Standards - Something for Everybody

NASA Astrophysics Data System (ADS)

Raugh, Anne C.; Hughes, John S.

2015-11-01

The Planetary Data System (PDS) archives, supports, and distributes data of diverse targets, from diverse sources, to diverse users. One of the core problems addressed by the PDS4 data standard redesign was that of metadata - how to accommodate the increasingly sophisticated demands of search interfaces, analytical software, and observational documentation into label standards without imposing limits and constraints that would impinge on the quality or quantity of metadata that any particular observer or team could supply. And yet, as an archive, PDS must have detailed documentation for the metadata in the labels it supports, or the institutional knowledge encoded into those attributes will be lost - putting the data at risk.The PDS4 metadata solution is based on a three-step approach. First, it is built on two key ISO standards: ISO 11179 "Information Technology - Metadata Registries", which provides a common framework and vocabulary for defining metadata attributes; and ISO 14721 "Space Data and Information Transfer Systems - Open Archival Information System (OAIS) Reference Model", which provides the framework for the information architecture that enforces the object-oriented paradigm for metadata modeling. Second, PDS has defined a hierarchical system that allows it to divide its metadata universe into namespaces ("data dictionaries", conceptually), and more importantly to delegate stewardship for a single namespace to a local authority. This means that a mission can develop its own data model with a high degree of autonomy and effectively extend the PDS model to accommodate its own metadata needs within the common ISO 11179 framework. Finally, within a single namespace - even the core PDS namespace - existing metadata structures can be extended and new structures added to the model as new needs are identifiedThis poster illustrates the PDS4 approach to metadata management and highlights the expected return on the development investment for PDS, users and data preparers.

A SensorML-based Metadata Model and Registry for Ocean Observatories: a Contribution from European Projects NeXOS and FixO3

NASA Astrophysics Data System (ADS)

Delory, E.; Jirka, S.

2016-02-01

Discovering sensors and observation data is important when enabling the exchange of oceanographic data between observatories and scientists that need the data sets for their work. To better support this discovery process, one task of the European project FixO3 (Fixed-point Open Ocean Observatories) is dealing with the question which elements are needed for developing a better registry for sensors. This has resulted in four items which are addressed by the FixO3 project in cooperation with further European projects such as NeXOS (http://www.nexosproject.eu/). 1.) Metadata description format: To store and retrieve information about sensors and platforms it is necessary to have a common approach how to provide and encode the metadata. For this purpose, the OGC Sensor Model Language (SensorML) 2.0 standard was selected. Especially the opportunity to distinguish between sensor types and instances offers new chances for a more efficient provision and maintenance of sensor metadata. 2.) Conversion of existing metadata into a SensorML 2.0 representation: In order to ensure a sustainable re-use of already provided metadata content (e.g. from ESONET-FixO3 yellow pages), it is important to provide a mechanism which is capable of transforming these already available metadata sets into the new SensorML 2.0 structure. 3.) Metadata editor: To create descriptions of sensors and platforms, it is not possible to expect users to manually edit XML-based description files. Thus, a visual interface is necessary to help during the metadata creation. We will outline a prototype of this editor, building upon the development of the ESONET sensor registry interface. 4.) Sensor Metadata Store: A server is needed that for storing and querying the created sensor descriptions. For this purpose different options exist which will be discussed. In summary, we will present a set of different elements enabling sensor discovery ranging from metadata formats, metadata conversion and editing to metadata storage. Furthermore, the current development status will be demonstrated.

Improving Metadata Compliance for Earth Science Data Records

NASA Astrophysics Data System (ADS)

Armstrong, E. M.; Chang, O.; Foster, D.

2014-12-01

One of the recurring challenges of creating earth science data records is to ensure a consistent level of metadata compliance at the granule level where important details of contents, provenance, producer, and data references are necessary to obtain a sufficient level of understanding. These details are important not just for individual data consumers but also for autonomous software systems. Two of the most popular metadata standards at the granule level are the Climate and Forecast (CF) Metadata Conventions and the Attribute Conventions for Dataset Discovery (ACDD). Many data producers have implemented one or both of these models including the Group for High Resolution Sea Surface Temperature (GHRSST) for their global SST products and the Ocean Biology Processing Group for NASA ocean color and SST products. While both the CF and ACDD models contain various level of metadata richness, the actual "required" attributes are quite small in number. Metadata at the granule level becomes much more useful when recommended or optional attributes are implemented that document spatial and temporal ranges, lineage and provenance, sources, keywords, and references etc. In this presentation we report on a new open source tool to check the compliance of netCDF and HDF5 granules to the CF and ACCD metadata models. The tool, written in Python, was originally implemented to support metadata compliance for netCDF records as part of the NOAA's Integrated Ocean Observing System. It outputs standardized scoring for metadata compliance for both CF and ACDD, produces an objective summary weight, and can be implemented for remote records via OPeNDAP calls. Originally a command-line tool, we have extended it to provide a user-friendly web interface. Reports on metadata testing are grouped in hierarchies that make it easier to track flaws and inconsistencies in the record. We have also extended it to support explicit metadata structures and semantic syntax for the GHRSST project that can be easily adapted to other satellite missions as well. Overall, we hope this tool will provide the community with a useful mechanism to improve metadata quality and consistency at the granule level by providing objective scoring and assessment, as well as encourage data producers to improve metadata quality and quantity.

Evolving Metadata in NASA Earth Science Data Systems

NASA Astrophysics Data System (ADS)

Mitchell, A.; Cechini, M. F.; Walter, J.

2011-12-01

NASA's Earth Observing System (EOS) is a coordinated series of satellites for long term global observations. NASA's Earth Observing System Data and Information System (EOSDIS) is a petabyte-scale archive of environmental data that supports global climate change research by providing end-to-end services from EOS instrument data collection to science data processing to full access to EOS and other earth science data. On a daily basis, the EOSDIS ingests, processes, archives and distributes over 3 terabytes of data from NASA's Earth Science missions representing over 3500 data products ranging from various types of science disciplines. EOSDIS is currently comprised of 12 discipline specific data centers that are collocated with centers of science discipline expertise. Metadata is used in all aspects of NASA's Earth Science data lifecycle from the initial measurement gathering to the accessing of data products. Missions use metadata in their science data products when describing information such as the instrument/sensor, operational plan, and geographically region. Acting as the curator of the data products, data centers employ metadata for preservation, access and manipulation of data. EOSDIS provides a centralized metadata repository called the Earth Observing System (EOS) ClearingHouse (ECHO) for data discovery and access via a service-oriented-architecture (SOA) between data centers and science data users. ECHO receives inventory metadata from data centers who generate metadata files that complies with the ECHO Metadata Model. NASA's Earth Science Data and Information System (ESDIS) Project established a Tiger Team to study and make recommendations regarding the adoption of the international metadata standard ISO 19115 in EOSDIS. The result was a technical report recommending an evolution of NASA data systems towards a consistent application of ISO 19115 and related standards including the creation of a NASA-specific convention for core ISO 19115 elements. Part of NASA's effort to continually evolve its data systems led ECHO to enhancing the method in which it receives inventory metadata from the data centers to allow for multiple metadata formats including ISO 19115. ECHO's metadata model will also be mapped to the NASA-specific convention for ingesting science metadata into the ECHO system. As NASA's new Earth Science missions and data centers are migrating to the ISO 19115 standards, EOSDIS is developing metadata management resources to assist in the reading, writing and parsing ISO 19115 compliant metadata. To foster interoperability with other agencies and international partners, NASA is working to ensure that a common ISO 19115 convention is developed, enhancing data sharing capabilities and other data analysis initiatives. NASA is also investigating the use of ISO 19115 standards to encode data quality, lineage and provenance with stored values. A common metadata standard across NASA's Earth Science data systems promotes interoperability, enhances data utilization and removes levels of uncertainty found in data products.

Metadata Management on the SCEC PetaSHA Project: Helping Users Describe, Discover, Understand, and Use Simulation Data in a Large-Scale Scientific Collaboration

NASA Astrophysics Data System (ADS)

Okaya, D.; Deelman, E.; Maechling, P.; Wong-Barnum, M.; Jordan, T. H.; Meyers, D.

2007-12-01

Large scientific collaborations, such as the SCEC Petascale Cyberfacility for Physics-based Seismic Hazard Analysis (PetaSHA) Project, involve interactions between many scientists who exchange ideas and research results. These groups must organize, manage, and make accessible their community materials of observational data, derivative (research) results, computational products, and community software. The integration of scientific workflows as a paradigm to solve complex computations provides advantages of efficiency, reliability, repeatability, choices, and ease of use. The underlying resource needed for a scientific workflow to function and create discoverable and exchangeable products is the construction, tracking, and preservation of metadata. In the scientific workflow environment there is a two-tier structure of metadata. Workflow-level metadata and provenance describe operational steps, identity of resources, execution status, and product locations and names. Domain-level metadata essentially define the scientific meaning of data, codes and products. To a large degree the metadata at these two levels are separate. However, between these two levels is a subset of metadata produced at one level but is needed by the other. This crossover metadata suggests that some commonality in metadata handling is needed. SCEC researchers are collaborating with computer scientists at SDSC, the USC Information Sciences Institute, and Carnegie Mellon Univ. in order to perform earthquake science using high-performance computational resources. A primary objective of the "PetaSHA" collaboration is to perform physics-based estimations of strong ground motion associated with real and hypothetical earthquakes located within Southern California. Construction of 3D earth models, earthquake representations, and numerical simulation of seismic waves are key components of these estimations. Scientific workflows are used to orchestrate the sequences of scientific tasks and to access distributed computational facilities such as the NSF TeraGrid. Different types of metadata are produced and captured within the scientific workflows. One workflow within PetaSHA ("Earthworks") performs a linear sequence of tasks with workflow and seismological metadata preserved. Downstream scientific codes ingest these metadata produced by upstream codes. The seismological metadata uses attribute-value pairing in plain text; an identified need is to use more advanced handling methods. Another workflow system within PetaSHA ("Cybershake") involves several complex workflows in order to perform statistical analysis of ground shaking due to thousands of hypothetical but plausible earthquakes. Metadata management has been challenging due to its construction around a number of legacy scientific codes. We describe difficulties arising in the scientific workflow due to the lack of this metadata and suggest corrective steps, which in some cases include the cultural shift of domain science programmers coding for metadata.

Evaluating the privacy properties of telephone metadata.

PubMed

Mayer, Jonathan; Mutchler, Patrick; Mitchell, John C

2016-05-17

Since 2013, a stream of disclosures has prompted reconsideration of surveillance law and policy. One of the most controversial principles, both in the United States and abroad, is that communications metadata receives substantially less protection than communications content. Several nations currently collect telephone metadata in bulk, including on their own citizens. In this paper, we attempt to shed light on the privacy properties of telephone metadata. Using a crowdsourcing methodology, we demonstrate that telephone metadata is densely interconnected, can trivially be reidentified, and can be used to draw sensitive inferences.

Studies of Big Data metadata segmentation between relational and non-relational databases

NASA Astrophysics Data System (ADS)

Golosova, M. V.; Grigorieva, M. A.; Klimentov, A. A.; Ryabinkin, E. A.; Dimitrov, G.; Potekhin, M.

2015-12-01

In recent years the concepts of Big Data became well established in IT. Systems managing large data volumes produce metadata that describe data and workflows. These metadata are used to obtain information about current system state and for statistical and trend analysis of the processes these systems drive. Over the time the amount of the stored metadata can grow dramatically. In this article we present our studies to demonstrate how metadata storage scalability and performance can be improved by using hybrid RDBMS/NoSQL architecture.

Evaluating the privacy properties of telephone metadata

PubMed Central

Mayer, Jonathan; Mutchler, Patrick; Mitchell, John C.

2016-01-01

Since 2013, a stream of disclosures has prompted reconsideration of surveillance law and policy. One of the most controversial principles, both in the United States and abroad, is that communications metadata receives substantially less protection than communications content. Several nations currently collect telephone metadata in bulk, including on their own citizens. In this paper, we attempt to shed light on the privacy properties of telephone metadata. Using a crowdsourcing methodology, we demonstrate that telephone metadata is densely interconnected, can trivially be reidentified, and can be used to draw sensitive inferences. PMID:27185922

Incorporating ISO Metadata Using HDF Product Designer

NASA Technical Reports Server (NTRS)

Jelenak, Aleksandar; Kozimor, John; Habermann, Ted

2016-01-01

The need to store in HDF5 files increasing amounts of metadata of various complexity is greatly overcoming the capabilities of the Earth science metadata conventions currently in use. Data producers until now did not have much choice but to come up with ad hoc solutions to this challenge. Such solutions, in turn, pose a wide range of issues for data managers, distributors, and, ultimately, data users. The HDF Group is experimenting on a novel approach of using ISO 19115 metadata objects as a catch-all container for all the metadata that cannot be fitted into the current Earth science data conventions. This presentation will showcase how the HDF Product Designer software can be utilized to help data producers include various ISO metadata objects in their products.

Comparing Commercial WWW Browsers.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

Four commercial World Wide Web browsers are evaluated for features such as handling of WWW protocols and different URLs: FTP, Telnet, Gopher and WAIS, and e-mail and news; bookmark capabilities; navigation features; file management; and security support. (JKP)

Detecting Heap-Spraying Code Injection Attacks in Malicious Web Pages Using Runtime Execution

NASA Astrophysics Data System (ADS)

Choi, Younghan; Kim, Hyoungchun; Lee, Donghoon

The growing use of web services is increasing web browser attacks exponentially. Most attacks use a technique called heap spraying because of its high success rate. Heap spraying executes a malicious code without indicating the exact address of the code by copying it into many heap objects. For this reason, the attack has a high potential to succeed if only the vulnerability is exploited. Thus, attackers have recently begun using this technique because it is easy to use JavaScript to allocate the heap memory area. This paper proposes a novel technique that detects heap spraying attacks by executing a heap object in a real environment, irrespective of the version and patch status of the web browser. This runtime execution is used to detect various forms of heap spraying attacks, such as encoding and polymorphism. Heap objects are executed after being filtered on the basis of patterns of heap spraying attacks in order to reduce the overhead of the runtime execution. Patterns of heap spraying attacks are based on analysis of how an web browser accesses benign web sites. The heap objects are executed forcibly by changing the instruction register into the address of them after being loaded into memory. Thus, we can execute the malicious code without having to consider the version and patch status of the browser. An object is considered to contain a malicious code if the execution reaches a call instruction and then the instruction accesses the API of system libraries, such as kernel32.dll and ws_32.dll. To change registers and monitor execution flow, we used a debugger engine. A prototype, named HERAD(HEap spRAying Detector), is implemented and evaluated. In experiments, HERAD detects various forms of exploit code that an emulation cannot detect, and some heap spraying attacks that NOZZLE cannot detect. Although it has an execution overhead, HERAD produces a low number of false alarms. The processing time of several minutes is negligible because our research focuses on detecting heap spraying. This research can be applied to existing systems that collect malicious codes, such as Honeypot.

US NDC Modernization Iteration E2 Prototyping Report: User Interface Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Jennifer E.; Palmer, Melanie A.; Vickers, James Wallace

2014-12-01

During the second iteration of the US NDC Modernization Elaboration phase (E2), the SNL US NDC Modernization project team completed follow-on Rich Client Platform (RCP) exploratory prototyping related to the User Interface Framework (UIF). The team also developed a survey of browser-based User Interface solutions and completed exploratory prototyping for selected solutions. This report presents the results of the browser-based UI survey, summarizes the E2 browser-based UI and RCP prototyping work, and outlines a path forward for the third iteration of the Elaboration phase (E3).

Managing biomedical image metadata for search and retrieval of similar images.

PubMed

Korenblum, Daniel; Rubin, Daniel; Napel, Sandy; Rodriguez, Cesar; Beaulieu, Chris

2011-08-01

Radiology images are generally disconnected from the metadata describing their contents, such as imaging observations ("semantic" metadata), which are usually described in text reports that are not directly linked to the images. We developed a system, the Biomedical Image Metadata Manager (BIMM) to (1) address the problem of managing biomedical image metadata and (2) facilitate the retrieval of similar images using semantic feature metadata. Our approach allows radiologists, researchers, and students to take advantage of the vast and growing repositories of medical image data by explicitly linking images to their associated metadata in a relational database that is globally accessible through a Web application. BIMM receives input in the form of standard-based metadata files using Web service and parses and stores the metadata in a relational database allowing efficient data query and maintenance capabilities. Upon querying BIMM for images, 2D regions of interest (ROIs) stored as metadata are automatically rendered onto preview images included in search results. The system's "match observations" function retrieves images with similar ROIs based on specific semantic features describing imaging observation characteristics (IOCs). We demonstrate that the system, using IOCs alone, can accurately retrieve images with diagnoses matching the query images, and we evaluate its performance on a set of annotated liver lesion images. BIMM has several potential applications, e.g., computer-aided detection and diagnosis, content-based image retrieval, automating medical analysis protocols, and gathering population statistics like disease prevalences. The system provides a framework for decision support systems, potentially improving their diagnostic accuracy and selection of appropriate therapies.

The Metadata Cloud: The Last Piece of a Distributed Data System Model

NASA Astrophysics Data System (ADS)

King, T. A.; Cecconi, B.; Hughes, J. S.; Walker, R. J.; Roberts, D.; Thieman, J. R.; Joy, S. P.; Mafi, J. N.; Gangloff, M.

2012-12-01

Distributed data systems have existed ever since systems were networked together. Over the years the model for distributed data systems have evolved from basic file transfer to client-server to multi-tiered to grid and finally to cloud based systems. Initially metadata was tightly coupled to the data either by embedding the metadata in the same file containing the data or by co-locating the metadata in commonly named files. As the sources of data multiplied, data volumes have increased and services have specialized to improve efficiency; a cloud system model has emerged. In a cloud system computing and storage are provided as services with accessibility emphasized over physical location. Computation and data clouds are common implementations. Effectively using the data and computation capabilities requires metadata. When metadata is stored separately from the data; a metadata cloud is formed. With a metadata cloud information and knowledge about data resources can migrate efficiently from system to system, enabling services and allowing the data to remain efficiently stored until used. This is especially important with "Big Data" where movement of the data is limited by bandwidth. We examine how the metadata cloud completes a general distributed data system model, how standards play a role and relate this to the existing types of cloud computing. We also look at the major science data systems in existence and compare each to the generalized cloud system model.

Turning Data into Information: Assessing and Reporting GIS Metadata Integrity Using Integrated Computing Technologies

ERIC Educational Resources Information Center

Mulrooney, Timothy J.

2009-01-01

A Geographic Information System (GIS) serves as the tangible and intangible means by which spatially related phenomena can be created, analyzed and rendered. GIS metadata serves as the formal framework to catalog information about a GIS data set. Metadata is independent of the encoded spatial and attribute information. GIS metadata is a subset of…

Integrating XQuery-Enabled SCORM XML Metadata Repositories into an RDF-Based E-Learning P2P Network

ERIC Educational Resources Information Center

Qu, Changtao; Nejdl, Wolfgang

2004-01-01

Edutella is an RDF-based E-Learning P2P network that is aimed to accommodate heterogeneous learning resource metadata repositories in a P2P manner and further facilitate the exchange of metadata between these repositories based on RDF. Whereas Edutella provides RDF metadata repositories with a quite natural integration approach, XML metadata…

Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data.

PubMed

Bhandary, Priyanka; Seetharam, Arun S; Arendsee, Zebulun W; Hur, Manhoi; Wurtele, Eve Syrkin

2018-02-01

More than 15 petabases of raw RNAseq data is now accessible through public repositories. Acquisition of other 'omics data types is expanding, though most lack a centralized archival repository. Data-reuse provides tremendous opportunity to extract new knowledge from existing experiments, and offers a unique opportunity for robust, multi-'omics analyses by merging metadata (information about experimental design, biological samples, protocols) and data from multiple experiments. We illustrate how predictive research can be accelerated by meta-analysis with a study of orphan (species-specific) genes. Computational predictions are critical to infer orphan function because their coding sequences provide very few clues. The metadata in public databases is often confusing; a test case with Zea mays mRNA seq data reveals a high proportion of missing, misleading or incomplete metadata. This metadata morass significantly diminishes the insight that can be extracted from these data. We provide tips for data submitters and users, including specific recommendations to improve metadata quality by more use of controlled vocabulary and by metadata reviews. Finally, we advocate for a unified, straightforward metadata submission and retrieval system. Copyright © 2017 Elsevier B.V. All rights reserved.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

PubMed

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-09-18

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

PubMed Central

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-01-01

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. PMID:25990738

Science friction: data, metadata, and collaboration.

PubMed

Edwards, Paul N; Mayernik, Matthew S; Batcheller, Archer L; Bowker, Geoffrey C; Borgman, Christine L

2011-10-01

When scientists from two or more disciplines work together on related problems, they often face what we call 'science friction'. As science becomes more data-driven, collaborative, and interdisciplinary, demand increases for interoperability among data, tools, and services. Metadata--usually viewed simply as 'data about data', describing objects such as books, journal articles, or datasets--serve key roles in interoperability. Yet we find that metadata may be a source of friction between scientific collaborators, impeding data sharing. We propose an alternative view of metadata, focusing on its role in an ephemeral process of scientific communication, rather than as an enduring outcome or product. We report examples of highly useful, yet ad hoc, incomplete, loosely structured, and mutable, descriptions of data found in our ethnographic studies of several large projects in the environmental sciences. Based on this evidence, we argue that while metadata products can be powerful resources, usually they must be supplemented with metadata processes. Metadata-as-process suggests the very large role of the ad hoc, the incomplete, and the unfinished in everyday scientific work.

Recipes for Semantic Web Dog Food — The ESWC and ISWC Metadata Projects

NASA Astrophysics Data System (ADS)

Möller, Knud; Heath, Tom; Handschuh, Siegfried; Domingue, John

Semantic Web conferences such as ESWC and ISWC offer prime opportunities to test and showcase semantic technologies. Conference metadata about people, papers and talks is diverse in nature and neither too small to be uninteresting or too big to be unmanageable. Many metadata-related challenges that may arise in the Semantic Web at large are also present here. Metadata must be generated from sources which are often unstructured and hard to process, and may originate from many different players, therefore suitable workflows must be established. Moreover, the generated metadata must use appropriate formats and vocabularies, and be served in a way that is consistent with the principles of linked data. This paper reports on the metadata efforts from ESWC and ISWC, identifies specific issues and barriers encountered during the projects, and discusses how these were approached. Recommendations are made as to how these may be addressed in the future, and we discuss how these solutions may generalize to metadata production for the Semantic Web at large.

Metadata-driven Delphi rating on the Internet.

PubMed

Deshpande, Aniruddha M; Shiffman, Richard N; Nadkarni, Prakash M

2005-01-01

Paper-based data collection and analysis for consensus development is inefficient and error-prone. Computerized techniques that could improve efficiency, however, have been criticized as costly, inconvenient and difficult to use. We designed and implemented a metadata-driven Web-based Delphi rating and analysis tool, employing the flexible entity-attribute-value schema to create generic, reusable software. The software can be applied to various domains by altering the metadata; the programming code remains intact. This approach greatly reduces the marginal cost of re-using the software. We implemented our software to prepare for the Conference on Guidelines Standardization. Twenty-three invited experts completed the first round of the Delphi rating on the Web. For each participant, the software generated individualized reports that described the median rating and the disagreement index (calculated from the Interpercentile Range Adjusted for Symmetry) as defined by the RAND/UCLA Appropriateness Method. We evaluated the software with a satisfaction survey using a five-level Likert scale. The panelists felt that Web data entry was convenient (median 4, interquartile range [IQR] 4.0-5.0), acceptable (median 4.5, IQR 4.0-5.0) and easily accessible (median 5, IQR 4.0-5.0). We conclude that Web-based Delphi rating for consensus development is a convenient and acceptable alternative to the traditional paper-based method.

Research on key technologies for data-interoperability-based metadata, data compression and encryption, and their application

NASA Astrophysics Data System (ADS)

Yu, Xu; Shao, Quanqin; Zhu, Yunhai; Deng, Yuejin; Yang, Haijun

2006-10-01

With the development of informationization and the separation between data management departments and application departments, spatial data sharing becomes one of the most important objectives for the spatial information infrastructure construction, and spatial metadata management system, data transmission security and data compression are the key technologies to realize spatial data sharing. This paper discusses the key technologies for metadata based on data interoperability, deeply researches the data compression algorithms such as adaptive Huffman algorithm, LZ77 and LZ78 algorithm, studies to apply digital signature technique to encrypt spatial data, which can not only identify the transmitter of spatial data, but also find timely whether the spatial data are sophisticated during the course of network transmission, and based on the analysis of symmetric encryption algorithms including 3DES,AES and asymmetric encryption algorithm - RAS, combining with HASH algorithm, presents a improved mix encryption method for spatial data. Digital signature technology and digital watermarking technology are also discussed. Then, a new solution of spatial data network distribution is put forward, which adopts three-layer architecture. Based on the framework, we give a spatial data network distribution system, which is efficient and safe, and also prove the feasibility and validity of the proposed solution.

BASINS Metadata

EPA Pesticide Factsheets

Metadata or data about data describes the content, quality, condition, and other characteristics of data. Geospatial metadata are critical to data discovery and serves as the fuel for the Geospatial One-Stop data portal.

Visualization of JPEG Metadata

NASA Astrophysics Data System (ADS)

Malik Mohamad, Kamaruddin; Deris, Mustafa Mat

There are a lot of information embedded in JPEG image than just graphics. Visualization of its metadata would benefit digital forensic investigator to view embedded data including corrupted image where no graphics can be displayed in order to assist in evidence collection for cases such as child pornography or steganography. There are already available tools such as metadata readers, editors and extraction tools but mostly focusing on visualizing attribute information of JPEG Exif. However, none have been done to visualize metadata by consolidating markers summary, header structure, Huffman table and quantization table in a single program. In this paper, metadata visualization is done by developing a program that able to summarize all existing markers, header structure, Huffman table and quantization table in JPEG. The result shows that visualization of metadata helps viewing the hidden information within JPEG more easily.

GEO Label Web Services for Dynamic and Effective Communication of Geospatial Metadata Quality

NASA Astrophysics Data System (ADS)

Lush, Victoria; Nüst, Daniel; Bastin, Lucy; Masó, Joan; Lumsden, Jo

2014-05-01

We present demonstrations of the GEO label Web services and their integration into a prototype extension of the GEOSS portal (http://scgeoviqua.sapienzaconsulting.com/web/guest/geo_home), the GMU portal (http://gis.csiss.gmu.edu/GADMFS/) and a GeoNetwork catalog application (http://uncertdata.aston.ac.uk:8080/geonetwork/srv/eng/main.home). The GEO label is designed to communicate, and facilitate interrogation of, geospatial quality information with a view to supporting efficient and effective dataset selection on the basis of quality, trustworthiness and fitness for use. The GEO label which we propose was developed and evaluated according to a user-centred design (UCD) approach in order to maximise the likelihood of user acceptance once deployed. The resulting label is dynamically generated from producer metadata in ISO or FDGC format, and incorporates user feedback on dataset usage, ratings and discovered issues, in order to supply a highly informative summary of metadata completeness and quality. The label was easily incorporated into a community portal as part of the GEO Architecture Implementation Programme (AIP-6) and has been successfully integrated into a prototype extension of the GEOSS portal, as well as the popular metadata catalog and editor, GeoNetwork. The design of the GEO label was based on 4 user studies conducted to: (1) elicit initial user requirements; (2) investigate initial user views on the concept of a GEO label and its potential role; (3) evaluate prototype label visualizations; and (4) evaluate and validate physical GEO label prototypes. The results of these studies indicated that users and producers support the concept of a label with drill-down interrogation facility, combining eight geospatial data informational aspects, namely: producer profile, producer comments, lineage information, standards compliance, quality information, user feedback, expert reviews, and citations information. These are delivered as eight facets of a wheel-like label, which are coloured according to metadata availability and are clickable to allow a user to engage with the original metadata and explore specific aspects in more detail. To support this graphical representation and allow for wider deployment architectures we have implemented two Web services, a PHP and a Java implementation, that generate GEO label representations by combining producer metadata (from standard catalogues or other published locations) with structured user feedback. Both services accept encoded URLs of publicly available metadata documents or metadata XML files as HTTP POST and GET requests and apply XPath and XSLT mappings to transform producer and feedback XML documents into clickable SVG GEO label representations. The label and services are underpinned by two XML-based quality models. The first is a producer model that extends ISO 19115 and 19157 to allow fuller citation of reference data, presentation of pixel- and dataset- level statistical quality information, and encoding of 'traceability' information on the lineage of an actual quality assessment. The second is a user quality model (realised as a feedback server and client) which allows reporting and query of ratings, usage reports, citations, comments and other domain knowledge. Both services are Open Source and are available on GitHub at https://github.com/lushv/geolabel-service and https://github.com/52North/GEO-label-java. The functionality of these services can be tested using our GEO label generation demos, available online at http://www.geolabel.net/demo.html and http://geoviqua.dev.52north.org/glbservice/index.jsf.

Publishing datasets with eSciDoc and panMetaDocs

NASA Astrophysics Data System (ADS)

Ulbricht, D.; Klump, J.; Bertelmann, R.

2012-04-01

Currently serveral research institutions worldwide undertake considerable efforts to have their scientific datasets published and to syndicate them to data portals as extensively described objects identified by a persistent identifier. This is done to foster the reuse of data, to make scientific work more transparent, and to create a citable entity that can be referenced unambigously in written publications. GFZ Potsdam established a publishing workflow for file based research datasets. Key software components are an eSciDoc infrastructure [1] and multiple instances of the data curation tool panMetaDocs [2]. The eSciDoc repository holds data objects and their associated metadata in container objects, called eSciDoc items. A key metadata element in this context is the publication status of the referenced data set. PanMetaDocs, which is based on PanMetaWorks [3], is a PHP based web application that allows to describe data with any XML-based metadata schema. The metadata fields can be filled with static or dynamic content to reduce the number of fields that require manual entries to a minimum and make use of contextual information in a project setting. Access rights can be applied to set visibility of datasets to other project members and allow collaboration on and notifying about datasets (RSS) and interaction with the internal messaging system, that was inherited from panMetaWorks. When a dataset is to be published, panMetaDocs allows to change the publication status of the eSciDoc item from status "private" to "submitted" and prepare the dataset for verification by an external reviewer. After quality checks, the item publication status can be changed to "published". This makes the data and metadata available through the internet worldwide. PanMetaDocs is developed as an eSciDoc application. It is an easy to use graphical user interface to eSciDoc items, their data and metadata. It is also an application supporting a DOI publication agent during the process of publishing scientific datasets as electronic data supplements to research papers. Publication of research manuscripts has an already well established workflow that shares junctures with other processes and involves several parties in the process of dataset publication. Activities of the author, the reviewer, the print publisher and the data publisher have to be coordinated into a common data publication workflow. The case of data publication at GFZ Potsdam displays some specifics, e.g. the DOIDB webservice. The DOIDB is a proxy service at GFZ for the DataCite [4] DOI registration and its metadata store. DOIDB provides a local summary of the dataset DOIs registered through GFZ as a publication agent. An additional use case for the DOIDB is its function to enrich the datacite metadata with additional custom attributes, like a geographic reference in a DIF record. These attributes are at the moment not available in the datacite metadata schema but would be valuable elements for the compilation of data catalogues in the earth sciences and for dissemination of catalogue data via OAI-PMH. [1] http://www.escidoc.org , eSciDoc, FIZ Karlruhe, Germany [2] http://panmetadocs.sf.net , panMetaDocs, GFZ Potsdam, Germany [3] http://metaworks.pangaea.de , panMetaWorks, Dr. R. Huber, MARUM, Univ. Bremen, Germany [4] http://www.datacite.org

Use of a metadata documentation and search tool for large data volumes: The NGEE arctic example

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, Ranjeet; Hook, Leslie A; Killeffer, Terri S

The Online Metadata Editor (OME) is a web-based tool to help document scientific data in a well-structured, popular scientific metadata format. In this paper, we will discuss the newest tool that Oak Ridge National Laboratory (ORNL) has developed to generate, edit, and manage metadata and how it is helping data-intensive science centers and projects, such as the U.S. Department of Energy s Next Generation Ecosystem Experiments (NGEE) in the Arctic to prepare metadata and make their big data produce big science and lead to new discoveries.

Creating preservation metadata from XML-metadata profiles

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Bertelmann, Roland; Gebauer, Petra; Hasler, Tim; Klump, Jens; Kirchner, Ingo; Peters-Kottig, Wolfgang; Mettig, Nora; Rusch, Beate

2014-05-01

Registration of dataset DOIs at DataCite makes research data citable and comes with the obligation to keep data accessible in the future. In addition, many universities and research institutions measure data that is unique and not repeatable like the data produced by an observational network and they want to keep these data for future generations. In consequence, such data should be ingested in preservation systems, that automatically care for file format changes. Open source preservation software that is developed along the definitions of the ISO OAIS reference model is available but during ingest of data and metadata there are still problems to be solved. File format validation is difficult, because format validators are not only remarkably slow - due to variety in file formats different validators return conflicting identification profiles for identical data. These conflicts are hard to resolve. Preservation systems have a deficit in the support of custom metadata. Furthermore, data producers are sometimes not aware that quality metadata is a key issue for the re-use of data. In the project EWIG an university institute and a research institute work together with Zuse-Institute Berlin, that is acting as an infrastructure facility, to generate exemplary workflows for research data into OAIS compliant archives with emphasis on the geosciences. The Institute for Meteorology provides timeseries data from an urban monitoring network whereas GFZ Potsdam delivers file based data from research projects. To identify problems in existing preservation workflows the technical work is complemented by interviews with data practitioners. Policies for handling data and metadata are developed. Furthermore, university teaching material is created to raise the future scientists awareness of research data management. As a testbed for ingest workflows the digital preservation system Archivematica [1] is used. During the ingest process metadata is generated that is compliant to the Metadata Encoding and Transmission Standard (METS). To find datasets in future portals and to make use of this data in own scientific work, proper selection of discovery metadata and application metadata is very important. Some XML-metadata profiles are not suitable for preservation, because version changes are very fast and make it nearly impossible to automate the migration. For other XML-metadata profiles schema definitions are changed after publication of the profile or the schema definitions become inaccessible, which might cause problems during validation of the metadata inside the preservation system [2]. Some metadata profiles are not used widely enough and might not even exist in the future. Eventually, discovery and application metadata have to be embedded into the mdWrap-subtree of the METS-XML. [1] http://www.archivematica.org [2] http://dx.doi.org/10.2218/ijdc.v7i1.215

a Kml-Based Approach for Distributed Collaborative Interpretation of Remote Sensing Images in the Geo-Browser

NASA Astrophysics Data System (ADS)

Huang, L.; Zhu, X.; Guo, W.; Xiang, L.; Chen, X.; Mei, Y.

2012-07-01

Existing implementations of collaborative image interpretation have many limitations for very large satellite imageries, such as inefficient browsing, slow transmission, etc. This article presents a KML-based approach to support distributed, real-time, synchronous collaborative interpretation for remote sensing images in the geo-browser. As an OGC standard, KML (Keyhole Markup Language) has the advantage of organizing various types of geospatial data (including image, annotation, geometry, etc.) in the geo-browser. Existing KML elements can be used to describe simple interpretation results indicated by vector symbols. To enlarge its application, this article expands KML elements to describe some complex image processing operations, including band combination, grey transformation, geometric correction, etc. Improved KML is employed to describe and share interpretation operations and results among interpreters. Further, this article develops some collaboration related services that are collaboration launch service, perceiving service and communication service. The launch service creates a collaborative interpretation task and provides a unified interface for all participants. The perceiving service supports interpreters to share collaboration awareness. Communication service provides interpreters with written words communication. Finally, the GeoGlobe geo-browser (an extensible and flexible geospatial platform developed in LIESMARS) is selected to perform experiments of collaborative image interpretation. The geo-browser, which manage and visualize massive geospatial information, can provide distributed users with quick browsing and transmission. Meanwhile in the geo-browser, GIS data (for example DEM, DTM, thematic map and etc.) can be integrated to assist in improving accuracy of interpretation. Results show that the proposed method is available to support distributed collaborative interpretation of remote sensing image

Assisted editing od SensorML with EDI. A bottom-up scenario towards the definition of sensor profiles.

NASA Astrophysics Data System (ADS)

Oggioni, Alessandro; Tagliolato, Paolo; Fugazza, Cristiano; Bastianini, Mauro; Pavesi, Fabio; Pepe, Monica; Menegon, Stefano; Basoni, Anna; Carrara, Paola

2015-04-01

Sensor observation systems for environmental data have become increasingly important in the last years. The EGU's Informatics in Oceanography and Ocean Science track stressed the importance of management tools and solutions for marine infrastructures. We think that full interoperability among sensor systems is still an open issue and that the solution to this involves providing appropriate metadata. Several open source applications implement the SWE specification and, particularly, the Sensor Observation Services (SOS) standard. These applications allow for the exchange of data and metadata in XML format between computer systems. However, there is a lack of metadata editing tools supporting end users in this activity. Generally speaking, it is hard for users to provide sensor metadata in the SensorML format without dedicated tools. In particular, such a tool should ease metadata editing by providing, for standard sensors, all the invariant information to be included in sensor metadata, thus allowing the user to concentrate on the metadata items that are related to the specific deployment. RITMARE, the Italian flagship project on marine research, envisages a subproject, SP7, for the set-up of the project's spatial data infrastructure. SP7 developed EDI, a general purpose, template-driven metadata editor that is composed of a backend web service and an HTML5/javascript client. EDI can be customized for managing the creation of generic metadata encoded as XML. Once tailored to a specific metadata format, EDI presents the users a web form with advanced auto completion and validation capabilities. In the case of sensor metadata (SensorML versions 1.0.1 and 2.0), the EDI client is instructed to send an "insert sensor" request to an SOS endpoint in order to save the metadata in an SOS server. In the first phase of project RITMARE, EDI has been used to simplify the creation from scratch of SensorML metadata by the involved researchers and data managers. An interesting by-product of this ongoing work is currently constituting an archive of predefined sensor descriptions. This information is being collected in order to further ease metadata creation in the next phase of the project. Users will be able to choose among a number of sensor and sensor platform prototypes: These will be specific instances on which it will be possible to define, in a bottom-up approach, "sensor profiles". We report on the outcome of this activity.

3D Immersive Visualization with Astrophysical Data

NASA Astrophysics Data System (ADS)

Kent, Brian R.

2017-01-01

We present the refinement of a new 3D immersion technique for astrophysical data visualization.Methodology to create 360 degree spherical panoramas is reviewed. The 3D software package Blender coupled with Python and the Google Spatial Media module are used together to create the final data products. Data can be viewed interactively with a mobile phone or tablet or in a web browser. The technique can apply to different kinds of astronomical data including 3D stellar and galaxy catalogs, images, and planetary maps.

Improving throughput and user experience for information intensive websites by applying HTTP compression technique.

PubMed

Malla, Ratnakar

2008-11-06

HTTP compression is a technique specified as part of the W3C HTTP 1.0 standard. It allows HTTP servers to take advantage of GZIP compression technology that is built into latest browsers. A brief survey of medical informatics websites show that compression is not enabled. With compression enabled, downloaded files sizes are reduced by more than 50% and typical transaction time is also reduced from 20 to 8 minutes, thus providing a better user experience.

ODMedit: uniform semantic annotation for data integration in medicine based on a public metadata repository.

PubMed

Dugas, Martin; Meidt, Alexandra; Neuhaus, Philipp; Storck, Michael; Varghese, Julian

2016-06-01

The volume and complexity of patient data - especially in personalised medicine - is steadily increasing, both regarding clinical data and genomic profiles: Typically more than 1,000 items (e.g., laboratory values, vital signs, diagnostic tests etc.) are collected per patient in clinical trials. In oncology hundreds of mutations can potentially be detected for each patient by genomic profiling. Therefore data integration from multiple sources constitutes a key challenge for medical research and healthcare. Semantic annotation of data elements can facilitate to identify matching data elements in different sources and thereby supports data integration. Millions of different annotations are required due to the semantic richness of patient data. These annotations should be uniform, i.e., two matching data elements shall contain the same annotations. However, large terminologies like SNOMED CT or UMLS don't provide uniform coding. It is proposed to develop semantic annotations of medical data elements based on a large-scale public metadata repository. To achieve uniform codes, semantic annotations shall be re-used if a matching data element is available in the metadata repository. A web-based tool called ODMedit ( https://odmeditor.uni-muenster.de/ ) was developed to create data models with uniform semantic annotations. It contains ~800,000 terms with semantic annotations which were derived from ~5,800 models from the portal of medical data models (MDM). The tool was successfully applied to manually annotate 22 forms with 292 data items from CDISC and to update 1,495 data models of the MDM portal. Uniform manual semantic annotation of data models is feasible in principle, but requires a large-scale collaborative effort due to the semantic richness of patient data. A web-based tool for these annotations is available, which is linked to a public metadata repository.

ToxMystery

MedlinePlus

Accessibility - This is a link to an external javascript file that searchs for a flash browser plug-in and what version of the browser is being used. The javascript is functional ToxMystery uses Adobe Flash Player. If you cannot install Flash Player, please use ...

THE NEVADA GEOSPATIAL DATA BROWSER

EPA Science Inventory

The Nevada Geospatial Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) with the assistance and collaboration of the University of Idaho (Moscow, ID) and Lockheed-Martin Environmental Services (Las Vegas, NV).

NEVADA GEOSPATICAL DATA BROWSER

EPA Science Inventory

The Nevada Geospatial Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) with the assistance and collaboration of the University of Idaho (Moscow, ID) and Lockheed-Martin Environmental Services Office (Las Vegas,...

The PDS4 Metadata Management System

NASA Astrophysics Data System (ADS)

Raugh, A. C.; Hughes, J. S.

2018-04-01

We present the key features of the Planetary Data System (PDS) PDS4 Information Model as an extendable metadata management system for planetary metadata related to data structure, analysis/interpretation, and provenance.

Design of Community Resource Inventories as a Component of Scalable Earth Science Infrastructure: Experience of the Earthcube CINERGI Project

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Richard, S. M.; Valentine, D. W., Jr.; Grethe, J. S.; Hsu, L.; Malik, T.; Bermudez, L. E.; Gupta, A.; Lehnert, K. A.; Whitenack, T.; Ozyurt, I. B.; Condit, C.; Calderon, R.; Musil, L.

2014-12-01

EarthCube is envisioned as a cyberinfrastructure that fosters new, transformational geoscience by enabling sharing, understanding and scientifically-sound and efficient re-use of formerly unconnected data resources, software, models, repositories, and computational power. Its purpose is to enable science enterprise and workforce development via an extensible and adaptable collaboration and resource integration framework. A key component of this vision is development of comprehensive inventories supporting resource discovery and re-use across geoscience domains. The goal of the EarthCube CINERGI (Community Inventory of EarthCube Resources for Geoscience Interoperability) project is to create a methodology and assemble a large inventory of high-quality information resources with standard metadata descriptions and traceable provenance. The inventory is compiled from metadata catalogs maintained by geoscience data facilities, as well as from user contributions. The latter mechanism relies on community resource viewers: online applications that support update and curation of metadata records. Once harvested into CINERGI, metadata records from domain catalogs and community resource viewers are loaded into a staging database implemented in MongoDB, and validated for compliance with ISO 19139 metadata schema. Several types of metadata defects detected by the validation engine are automatically corrected with help of several information extractors or flagged for manual curation. The metadata harvesting, validation and processing components generate provenance statements using W3C PROV notation, which are stored in a Neo4J database. Thus curated metadata, along with the provenance information, is re-published and accessed programmatically and via a CINERGI online application. This presentation focuses on the role of resource inventories in a scalable and adaptable information infrastructure, and on the CINERGI metadata pipeline and its implementation challenges. Key project components are described at the project's website (http://workspace.earthcube.org/cinergi), which also provides access to the initial resource inventory, the inventory metadata model, metadata entry forms and a collection of the community resource viewers.

Metadata improvements driving new tools and services at a NASA data center

NASA Astrophysics Data System (ADS)

Moroni, D. F.; Hausman, J.; Foti, G.; Armstrong, E. M.

2011-12-01

The NASA Physical Oceanography DAAC (PO.DAAC) is responsible for distributing and maintaining satellite derived oceanographic data from a number of NASA and non-NASA missions for the physical disciplines of ocean winds, sea surface temperature, ocean topography and gravity. Currently its holdings consist of over 600 datasets with a data archive in excess of 200 Terrabytes. The PO.DAAC has recently embarked on a metadata quality and completeness project to migrate, update and improve metadata records for over 300 public datasets. An interactive database management tool has been developed to allow data scientists to enter, update and maintain metadata records. This tool communicates directly with PO.DAAC's Data Management and Archiving System (DMAS), which serves as the new archival and distribution backbone as well as a permanent repository of dataset and granule-level metadata. Although we will briefly discuss the tool, more important ramifications are the ability to now expose, propagate and leverage the metadata in a number of ways. First, the metadata are exposed directly through a faceted and free text search interface directly from drupal-based PO.DAAC web pages allowing for quick browsing and data discovery especially by "drilling" through the various facet levels that organize datasets by time/space resolution, processing level, sensor, measurement type etc. Furthermore, the metadata can now be exposed through web services to produce metadata records in a number of different formats such as FGDC and ISO 19115, or potentially propagated to visualization and subsetting tools, and other discovery interfaces. The fundamental concept is that the metadata forms the essential bridge between the user, and the tool or discovery mechanism for a broad range of ocean earth science data records.

EPA Metadata Style Guide Keywords and EPA Organization Names

EPA Pesticide Factsheets

The following keywords and EPA organization names listed below, along with EPA’s Metadata Style Guide, are intended to provide suggestions and guidance to assist with the standardization of metadata records.

THE NEVADA GEOSPATIAL DATA BROWSER

EPA Science Inventory

The Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) has developed the Nevada Geospatial Data Browser, a spatial data archive to centralize and distribute the geospatial data used to create the land cover, vertebrate habitat models, and land o...

SAN PEDRO GEODATA BROWSER

EPA Science Inventory

The San Pedro Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV). The goal of the Landscape Sciences Program is to improve decision-making relative to natural and human resource management through the development...

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.

PubMed

Harper, Lisa C; Schaeffer, Mary L; Thistle, Jordan; Gardiner, Jack M; Andorf, Carson M; Campbell, Darwin A; Cannon, Ethalinda K S; Braun, Bremen L; Birkett, Scott M; Lawrence, Carolyn J; Sen, Taner Z

2011-01-01

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is 'Using the MaizeGDB Genome Browser', which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database

The UCSC genome browser: what every molecular biologist should know.

PubMed

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C

2009-10-01

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one's understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes

PubMed Central

Lee, Moon Young; Park, Chanjae; Berent, Robyn M.; Park, Paul J.; Fuchs, Robert; Syn, Hannah; Chin, Albert; Townsend, Jared; Benson, Craig C.; Redelman, Doug; Shen, Tsai-wei; Park, Jong Kun; Miano, Joseph M.; Sanders, Kenton M.; Ro, Seungil

2015-01-01

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through expression of specific genes controlled by serum response factor (SRF), a transcription factor that binds to DNA sites known as the CArG boxes. To identify SRF-regulated genes specifically expressed in SMCs, we isolated SMC populations from mouse small intestine and colon, obtained their transcriptomes, and constructed an interactive SMC genome and CArGome browser. To our knowledge, this is the first online resource that provides a comprehensive library of all genetic transcripts expressed in primary SMCs. The browser also serves as the first genome-wide map of SRF binding sites. The browser analysis revealed novel SMC-specific transcriptional variants and SRF target genes, which provided new and unique insights into the cellular and biological functions of the cells in gastrointestinal (GI) physiology. The SRF target genes in SMCs, which were discovered in silico, were confirmed by proteomic analysis of SMC-specific Srf knockout mice. Our genome browser offers a new perspective into the alternative expression of genes in the context of SRF binding sites in SMCs and provides a valuable reference for future functional studies. PMID:26241044

Low functional redundancy among mammalian browsers in regulating an encroaching shrub (Solanum campylacanthum) in African savannah

PubMed Central

Pringle, Robert M.; Goheen, Jacob R.; Palmer, Todd M.; Charles, Grace K.; DeFranco, Elyse; Hohbein, Rhianna; Ford, Adam T.; Tarnita, Corina E.

2014-01-01

Large herbivorous mammals play an important role in structuring African savannahs and are undergoing widespread population declines and local extinctions, with the largest species being the most vulnerable. The impact of these declines on key ecological processes hinges on the degree of functional redundancy within large-herbivore assemblages, a subject that has received little study. We experimentally quantified the effects of three browser species (elephant, impala and dik-dik) on individual- and population-level attributes of Solanum campylacanthum (Solanum incanum sensu lato), an encroaching woody shrub, using semi-permeable exclosures that selectively removed different-sized herbivores. After nearly 5 years, shrub abundance was lowest where all browser species were present and increased with each successive species deletion. Different browsers ate the same plant species in different ways, thereby exerting distinct suites of direct and indirect effects on plant performance and density. Not all of these effects were negative: elephants and impala also dispersed viable seeds and indirectly reduced seed predation by rodents and insects. We integrated these diffuse positive effects with the direct negative effects of folivory using a simple population model, which reinforced the conclusion that different browsers have complementary net effects on plant populations, and further suggested that under some conditions, these net effects may even differ in direction. PMID:24789900

Reaction time effects in lab- versus Web-based research: Experimental evidence.

PubMed

Hilbig, Benjamin E

2016-12-01

Although Web-based research is now commonplace, it continues to spur skepticism from reviewers and editors, especially whenever reaction times are of primary interest. Such persistent preconceptions are based on arguments referring to increased variation, the limits of certain software and technologies, and a noteworthy lack of comparisons (between Web and lab) in fully randomized experiments. To provide a critical test, participants were randomly assigned to complete a lexical decision task either (a) in the lab using standard experimental software (E-Prime), (b) in the lab using a browser-based version (written in HTML and JavaScript), or (c) via the Web using the same browser-based version. The classical word frequency effect was typical in size and corresponded to a very large effect in all three conditions. There was no indication that the Web- or browser-based data collection was in any way inferior. In fact, if anything, a larger effect was obtained in the browser-based conditions than in the condition relying on standard experimental software. No differences between Web and lab (within the browser-based conditions) could be observed, thus disconfirming any substantial influence of increased technical or situational variation. In summary, the present experiment contradicts the still common preconception that reaction time effects of only a few hundred milliseconds cannot be detected in Web experiments.

The Importance of Metadata in System Development and IKM

DTIC Science & Technology

2003-02-01

Defence R& D Canada The Importance of Metadata in System Development and IKM Anthony W. Isenor Technical Memorandum DRDC Atlantic TM 2003-011...Metadata in System Development and IKM Anthony W. Isenor Defence R& D Canada – Atlantic Technical Memorandum DRDC Atlantic TM 2003-011 February... it is important for searches and providing relevant information to the client. A comparison of metadata standards was conducted with emphasis on

The Global Streamflow Indices and Metadata Archive (GSIM) - Part 1: The production of a daily streamflow archive and metadata

NASA Astrophysics Data System (ADS)

Do, Hong Xuan; Gudmundsson, Lukas; Leonard, Michael; Westra, Seth

2018-04-01

This is the first part of a two-paper series presenting the Global Streamflow Indices and Metadata archive (GSIM), a worldwide collection of metadata and indices derived from more than 35 000 daily streamflow time series. This paper focuses on the compilation of the daily streamflow time series based on 12 free-to-access streamflow databases (seven national databases and five international collections). It also describes the development of three metadata products (freely available at https://doi.pangaea.de/10.1594/PANGAEA.887477): (1) a GSIM catalogue collating basic metadata associated with each time series, (2) catchment boundaries for the contributing area of each gauge, and (3) catchment metadata extracted from 12 gridded global data products representing essential properties such as land cover type, soil type, and climate and topographic characteristics. The quality of the delineated catchment boundary is also made available and should be consulted in GSIM application. The second paper in the series then explores production and analysis of streamflow indices. Having collated an unprecedented number of stations and associated metadata, GSIM can be used to advance large-scale hydrological research and improve understanding of the global water cycle.

Design and Implementation of a Metadata-rich File System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ames, S; Gokhale, M B; Maltzahn, C

2010-01-19

Despite continual improvements in the performance and reliability of large scale file systems, the management of user-defined file system metadata has changed little in the past decade. The mismatch between the size and complexity of large scale data stores and their ability to organize and query their metadata has led to a de facto standard in which raw data is stored in traditional file systems, while related, application-specific metadata is stored in relational databases. This separation of data and semantic metadata requires considerable effort to maintain consistency and can result in complex, slow, and inflexible system operation. To address thesemore » problems, we have developed the Quasar File System (QFS), a metadata-rich file system in which files, user-defined attributes, and file relationships are all first class objects. In contrast to hierarchical file systems and relational databases, QFS defines a graph data model composed of files and their relationships. QFS incorporates Quasar, an XPATH-extended query language for searching the file system. Results from our QFS prototype show the effectiveness of this approach. Compared to the de facto standard, the QFS prototype shows superior ingest performance and comparable query performance on user metadata-intensive operations and superior performance on normal file metadata operations.« less

Achieving Sub-Second Search in the CMR

NASA Astrophysics Data System (ADS)

Gilman, J.; Baynes, K.; Pilone, D.; Mitchell, A. E.; Murphy, K. J.

2014-12-01

The Common Metadata Repository (CMR) is the next generation Earth Science Metadata catalog for NASA's Earth Observing data. It joins together the holdings from the EOS Clearing House (ECHO) and the Global Change Master Directory (GCMD), creating a unified, authoritative source for EOSDIS metadata. The CMR allows ingest in many different formats while providing consistent search behavior and retrieval in any supported format. Performance is a critical component of the CMR, ensuring improved data discovery and client interactivity. The CMR delivers sub-second search performance for any of the common query conditions (including spatial) across hundreds of millions of metadata granules. It also allows the addition of new metadata concepts such as visualizations, parameter metadata, and documentation. The CMR's goals presented many challenges. This talk will describe the CMR architecture, design, and innovations that were made to achieve its goals. This includes: * Architectural features like immutability and backpressure. * Data management techniques such as caching and parallel loading that give big performance gains. * Open Source and COTS tools like Elasticsearch search engine. * Adoption of Clojure, a functional programming language for the Java Virtual Machine. * Development of a custom spatial search plugin for Elasticsearch and why it was necessary. * Introduction of a unified model for metadata that maps every supported metadata format to a consistent domain model.

Syntactic and Semantic Validation without a Metadata Management System

NASA Technical Reports Server (NTRS)

Pollack, Janine; Gokey, Christopher D.; Kendig, David; Olsen, Lola; Wharton, Stephen W. (Technical Monitor)

2001-01-01

The ability to maintain quality information is essential to securing the confidence in any system for which the information serves as a data source. NASA's Global Change Master Directory (GCMD), an online Earth science data locator, holds over 9000 data set descriptions and is in a constant state of flux as metadata are created and updated on a daily basis. In such a system, the importance of maintaining the consistency and integrity of these-metadata is crucial. The GCMD has developed a metadata management system utilizing XML, controlled vocabulary, and Java technologies to ensure the metadata not only adhere to valid syntax, but also exhibit proper semantics.

A digital repository with an extensible data model for biobanking and genomic analysis management.

PubMed

Izzo, Massimiliano; Mortola, Francesco; Arnulfo, Gabriele; Fato, Marco M; Varesio, Luigi

2014-01-01

Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid.

A digital repository with an extensible data model for biobanking and genomic analysis management

PubMed Central

2014-01-01

Motivation Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. Results We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Conclusions Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid. PMID:25077808

Evaluating non-relational storage technology for HEP metadata and meta-data catalog

NASA Astrophysics Data System (ADS)

Grigorieva, M. A.; Golosova, M. V.; Gubin, M. Y.; Klimentov, A. A.; Osipova, V. V.; Ryabinkin, E. A.

2016-10-01

Large-scale scientific experiments produce vast volumes of data. These data are stored, processed and analyzed in a distributed computing environment. The life cycle of experiment is managed by specialized software like Distributed Data Management and Workload Management Systems. In order to be interpreted and mined, experimental data must be accompanied by auxiliary metadata, which are recorded at each data processing step. Metadata describes scientific data and represent scientific objects or results of scientific experiments, allowing them to be shared by various applications, to be recorded in databases or published via Web. Processing and analysis of constantly growing volume of auxiliary metadata is a challenging task, not simpler than the management and processing of experimental data itself. Furthermore, metadata sources are often loosely coupled and potentially may lead to an end-user inconsistency in combined information queries. To aggregate and synthesize a range of primary metadata sources, and enhance them with flexible schema-less addition of aggregated data, we are developing the Data Knowledge Base architecture serving as the intelligence behind GUIs and APIs.

Survey data and metadata modelling using document-oriented NoSQL

NASA Astrophysics Data System (ADS)

Rahmatuti Maghfiroh, Lutfi; Gusti Bagus Baskara Nugraha, I.

2018-03-01

Survey data that are collected from year to year have metadata change. However it need to be stored integratedly to get statistical data faster and easier. Data warehouse (DW) can be used to solve this limitation. However there is a change of variables in every period that can not be accommodated by DW. Traditional DW can not handle variable change via Slowly Changing Dimension (SCD). Previous research handle the change of variables in DW to manage metadata by using multiversion DW (MVDW). MVDW is designed using relational model. Some researches also found that developing nonrelational model in NoSQL database has reading time faster than the relational model. Therefore, we propose changes to metadata management by using NoSQL. This study proposes a model DW to manage change and algorithms to retrieve data with metadata changes. Evaluation of the proposed models and algorithms result in that database with the proposed design can retrieve data with metadata changes properly. This paper has contribution in comprehensive data analysis with metadata changes (especially data survey) in integrated storage.

Improving the accessibility and re-use of environmental models through provision of model metadata - a scoping study

NASA Astrophysics Data System (ADS)

Riddick, Andrew; Hughes, Andrew; Harpham, Quillon; Royse, Katherine; Singh, Anubha

2014-05-01

There has been an increasing interest both from academic and commercial organisations over recent years in developing hydrologic and other environmental models in response to some of the major challenges facing the environment, for example environmental change and its effects and ensuring water resource security. This has resulted in a significant investment in modelling by many organisations both in terms of financial resources and intellectual capital. To capitalise on the effort on producing models, then it is necessary for the models to be both discoverable and appropriately described. If this is not undertaken then the effort in producing the models will be wasted. However, whilst there are some recognised metadata standards relating to datasets these may not completely address the needs of modellers regarding input data for example. Also there appears to be a lack of metadata schemes configured to encourage the discovery and re-use of the models themselves. The lack of an established standard for model metadata is considered to be a factor inhibiting the more widespread use of environmental models particularly the use of linked model compositions which fuse together hydrologic models with models from other environmental disciplines. This poster presents the results of a Natural Environment Research Council (NERC) funded scoping study to understand the requirements of modellers and other end users for metadata about data and models. A user consultation exercise using an on-line questionnaire has been undertaken to capture the views of a wide spectrum of stakeholders on how they are currently managing metadata for modelling. This has provided a strong confirmation of our original supposition that there is a lack of systems and facilities to capture metadata about models. A number of specific gaps in current provision for data and model metadata were also identified, including a need for a standard means to record detailed information about the modelling environment and the model code used, to assist the selection of models for linked compositions. Existing best practice, including the use of current metadata standards (e.g. ISO 19110, ISO 19115 and ISO 19119) and the metadata components of WaterML were also evaluated. In addition to commonly used metadata attributes (e.g. spatial reference information) there was significant interest in recording a variety of additional metadata attributes. These included more detailed information about temporal data, and also providing estimates of data accuracy and uncertainty within metadata. This poster describes the key results of this study, including a number of gaps in the provision of metadata for modelling, and outlines how these might be addressed. Overall the scoping study has highlighted significant interest in addressing this issue within the environmental modelling community. There is therefore an impetus for on-going research, and we are seeking to take this forward through collaboration with other interested organisations. Progress towards an internationally recognised model metadata standard is suggested.

HEP Computing

Science.gov Websites

Argonne National Laboratory High Energy Physics Division Windows Desktops Problem Report Service Request Password Help New Users Back to HEP Computing Email on ANL Exchange: See Windows Clients section (Outlook or Thunderbird recommended) Web Browsers: Web Browsers for Windows Desktops Software: Available

Development of a Global Marine Environmental Library

DTIC Science & Technology

2010-06-01

Gulf. Marine Geology , 129, 237- 269. [4] Lerner, S., & Maffei, A. (2001). 4DGeoBrowser: A Web-based data browser and server for accessing and...Digital Library as a Catalyst for Collaboration: Voyages across Disciplinary and Institutional Boundaries with SIO Explorer; Digital Scholarship

South Platte River Basin Data Browser Report

EPA Science Inventory

The purpose of this data browser is to provide a spatial toolkit that delivers primary data that can be used for primary input information for assessments related to environmental endpoints, e.g. surface water hydrology and habitat mapping, related to ecosystem services. A neces...

Are the long-term effects of mesobrowsers on woodland dynamics substitutive or additive to those of elephants?

NASA Astrophysics Data System (ADS)

O'Kane, Christopher A. J.; Duffy, Kevin J.; Page, Bruce R.; Macdonald, David W.

2011-09-01

The large spectrum of existing literature on browser-woodland dynamics, both from savanna and temperate biomes, converges towards concluding that all browsers importantly impact woody plants. In this context a crucial question in the current debate about reintroducing elephant culling, is whether the long-term effects of elephants and mesobrowsers are similar. If the two groups impact the same woody species in the same habitats, sufficiently high biomass-densities of mesobrowsers may, following removal of elephants, continue to heavily impact earlier life-history stages of the same suite of woody plants that elephant impacted, preventing these species from maturing. Thus, as existing mature trees die from natural causes and fade from the system, a similar end-point for woodland structure and composition is achieved. We reviewed 49 years of literature on the savanna browser guild, performing a meta-analysis on the disparate data on the guild's woody plant species use (3677 records) and habitat use (894 records). Mesobrowsers' and elephants' extensive overlap in habitat use and staple woody species diet, together with evidence of their influencing each others' abundance and of their dietary separation increasing with resource depletion, implies that the two groups impact the same core woody species in the same habitats. It therefore seems probable that high biomass-density mesobrowsers may have a long-term substitutive effect to that of elephant on woodland dynamics. Consequently management wanting a particular state of savanna woodland, should consider the biomass-density of both groups, rather than just focus on the system's perceived keystone species. Such principles may also apply to temperate and other systems.

Paleoenvironment of Dryopithecus brancoi at Rudabánya, Hungary: evidence from dental meso- and micro-wear analyses of large vegetarian mammals.

PubMed

Merceron, Gildas; Schulz, Ellen; Kordos, László; Kaiser, Thomas M

2007-10-01

The environment of the hominoid Dryopithecus brancoi at Rudabánya (Late Miocene of Hungary) is reconstructed here using the dietary traits of fossil ruminants and equids. Two independent approaches, dental micro- and meso-wear analyses, are applied to a sample of 73 specimens representing three ruminants: Miotragocerus sp. (Bovidae), Lucentia aff. pierensis (Cervidae), Micromeryx flourensianus (Moschidae), and one equid, Hippotherium intrans (Equidae). The combination of meso- and micro-wear signatures provides both long- and short-term dietary signals, and through comparisons with extant species, the feeding styles of the fossil species are reconstructed. Both approaches categorize the cervid as an intermediate feeder engaged in both browsing and grazing. The bovid Miotragocerus sp. is depicted as a traditional browser. Although the dental meso-wear pattern of the moschid has affinities with intermediate feeders, its dental micro-wear pattern also indicates significant intake of fruits and seeds. Hippotherium intrans was not a grazer and its dental micro-wear pattern significantly differs from that of living browsers, which may suggest that the fossil equid was engaged both in grazing and browsing. However, the lack of extant equids which are pure browsers prevents any definitive judgment on the feeding habits of Hippotherium. Based on these dietary findings, the Rudabánya paleoenvironment is reconstructed as a dense forest. The presence of two intermediate feeders indicates some clearings within this forest; however the absence of grazers suggests that these clearings were most likely confined. To demonstrate the ecological diversity among the late Miocene hominoids in Europe, the diet and habitat of Dryopithecus brancoi and Ouranopithecus macedoniensis (Greece) are compared.

Descriptive Metadata: Emerging Standards.

ERIC Educational Resources Information Center

Ahronheim, Judith R.

1998-01-01

Discusses metadata, digital resources, cross-disciplinary activity, and standards. Highlights include Standard Generalized Markup Language (SGML); Extensible Markup Language (XML); Dublin Core; Resource Description Framework (RDF); Text Encoding Initiative (TEI); Encoded Archival Description (EAD); art and cultural-heritage metadata initiatives;…

Automated Metadata Extraction

DTIC Science & Technology

2008-06-01

provides a means for file owners to add metadata which can then be used by iTunes for cataloging and searching [4]. Metadata can be stored in different...based and contain AAC data formats [3]. Specifically, Apple uses Protected AAC to encode copy-protected music titles purchased from the iTunes Music...Store [4]. The files purchased from the iTunes Music Store include the following metadata. • Name • Email address of purchaser • Year • Album

A Solution to Metadata: Using XML Transformations to Automate Metadata

DTIC Science & Technology

2010-06-01

developed their own metadata standards—Directory Interchange Format (DIF), Ecological Metadata Language ( EML ), and International Organization for...mented all their data using the EML standard. However, when later attempting to publish to a data clearinghouse— such as the Geospatial One-Stop (GOS...construct calls to its transform(s) method by providing the type of the incoming content (e.g., eml ), the type of the resulting content (e.g., fgdc) and

The Department of Defense Net-Centric Data Strategy: Implementation Requires a Joint Community of Interest (COI) Working Group and Joint COI Oversight Council

DTIC Science & Technology

2007-05-17

metadata formats, metadata repositories, enterprise portals and federated search engines that make data visible, available, and usable to users...and provides the metadata formats, metadata repositories, enterprise portals and federated search engines that make data visible, available, and...develop an enterprise- wide data sharing plan, establishment of mission area governance processes for CIOs, DISA development of federated search specifications

FRAMES Metadata Reporting Templates for Ecohydrological Observations, version 1.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christianson, Danielle; Varadharajan, Charuleka; Christoffersen, Brad

FRAMES is a a set of Excel metadata files and package-level descriptive metadata that are designed to facilitate and improve capture of desired metadata for ecohydrological observations. The metadata are bundled with data files into a data package and submitted to a data repository (e.g. the NGEE Tropics Data Repository) via a web form. FRAMES standardizes reporting of diverse ecohydrological and biogeochemical data for synthesis across a range of spatiotemporal scales and incorporates many best data science practices. This version of FRAMES supports observations for primarily automated measurements collected by permanently located sensors, including sap flow (tree water use), leafmore » surface temperature, soil water content, dendrometry (stem diameter growth increment), and solar radiation. Version 1.1 extend the controlled vocabulary and incorporates functionality to facilitate programmatic use of data and FRAMES metadata (R code available at NGEE Tropics Data Repository).« less

Assessing Public Metabolomics Metadata, Towards Improving Quality.

PubMed

Ferreira, João D; Inácio, Bruno; Salek, Reza M; Couto, Francisco M

2017-12-13

Public resources need to be appropriately annotated with metadata in order to make them discoverable, reproducible and traceable, further enabling them to be interoperable or integrated with other datasets. While data-sharing policies exist to promote the annotation process by data owners, these guidelines are still largely ignored. In this manuscript, we analyse automatic measures of metadata quality, and suggest their application as a mean to encourage data owners to increase the metadata quality of their resources and submissions, thereby contributing to higher quality data, improved data sharing, and the overall accountability of scientific publications. We analyse these metadata quality measures in the context of a real-world repository of metabolomics data (i.e. MetaboLights), including a manual validation of the measures, and an analysis of their evolution over time. Our findings suggest that the proposed measures can be used to mimic a manual assessment of metadata quality.

EXIF Custom: Automatic image metadata extraction for Scratchpads and Drupal.

PubMed

Baker, Ed

2013-01-01

Many institutions and individuals use embedded metadata to aid in the management of their image collections. Many deskop image management solutions such as Adobe Bridge and online tools such as Flickr also make use of embedded metadata to describe, categorise and license images. Until now Scratchpads (a data management system and virtual research environment for biodiversity) have not made use of these metadata, and users have had to manually re-enter this information if they have wanted to display it on their Scratchpad site. The Drupal described here allows users to map metadata embedded in their images to the associated field in the Scratchpads image form using one or more customised mappings. The module works seamlessly with the bulk image uploader used on Scratchpads and it is therefore possible to upload hundreds of images easily with automatic metadata (EXIF, XMP and IPTC) extraction and mapping.

Collection Metadata Solutions for Digital Library Applications

NASA Technical Reports Server (NTRS)

Hill, Linda L.; Janee, Greg; Dolin, Ron; Frew, James; Larsgaard, Mary

1999-01-01

Within a digital library, collections may range from an ad hoc set of objects that serve a temporary purpose to established library collections intended to persist through time. The objects in these collections vary widely, from library and data center holdings to pointers to real-world objects, such as geographic places, and the various metadata schemas that describe them. The key to integrated use of such a variety of collections in a digital library is collection metadata that represents the inherent and contextual characteristics of a collection. The Alexandria Digital Library (ADL) Project has designed and implemented collection metadata for several purposes: in XML form, the collection metadata "registers" the collection with the user interface client; in HTML form, it is used for user documentation; eventually, it will be used to describe the collection to network search agents; and it is used for internal collection management, including mapping the object metadata attributes to the common search parameters of the system.

METADATA REGISTRY, ISO/IEC 11179

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pon, R K; Buttler, D J

2008-01-03

ISO/IEC-11179 is an international standard that documents the standardization and registration of metadata to make data understandable and shareable. This standardization and registration allows for easier locating, retrieving, and transmitting data from disparate databases. The standard defines the how metadata are conceptually modeled and how they are shared among parties, but does not define how data is physically represented as bits and bytes. The standard consists of six parts. Part 1 provides a high-level overview of the standard and defines the basic element of a metadata registry - a data element. Part 2 defines the procedures for registering classification schemesmore » and classifying administered items in a metadata registry (MDR). Part 3 specifies the structure of an MDR. Part 4 specifies requirements and recommendations for constructing definitions for data and metadata. Part 5 defines how administered items are named and identified. Part 6 defines how administered items are registered and assigned an identifier.« less

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

EXIF Custom: Automatic image metadata extraction for Scratchpads and Drupal

PubMed Central

2013-01-01

Abstract Many institutions and individuals use embedded metadata to aid in the management of their image collections. Many deskop image management solutions such as Adobe Bridge and online tools such as Flickr also make use of embedded metadata to describe, categorise and license images. Until now Scratchpads (a data management system and virtual research environment for biodiversity) have not made use of these metadata, and users have had to manually re-enter this information if they have wanted to display it on their Scratchpad site. The Drupal described here allows users to map metadata embedded in their images to the associated field in the Scratchpads image form using one or more customised mappings. The module works seamlessly with the bulk image uploader used on Scratchpads and it is therefore possible to upload hundreds of images easily with automatic metadata (EXIF, XMP and IPTC) extraction and mapping. PMID:24723768

The Energy Industry Profile of ISO/DIS 19115-1: Facilitating Discovery and Evaluation of, and Access to Distributed Information Resources

NASA Astrophysics Data System (ADS)

Hills, S. J.; Richard, S. M.; Doniger, A.; Danko, D. M.; Derenthal, L.; Energistics Metadata Work Group

2011-12-01

A diverse group of organizations representative of the international community involved in disciplines relevant to the upstream petroleum industry, - energy companies, - suppliers and publishers of information to the energy industry, - vendors of software applications used by the industry, - partner government and academic organizations, has engaged in the Energy Industry Metadata Standards Initiative. This Initiative envisions the use of standard metadata within the community to enable significant improvements in the efficiency with which users discover, evaluate, and access distributed information resources. The metadata standard needed to realize this vision is the initiative's primary deliverable. In addition to developing the metadata standard, the initiative is promoting its adoption to accelerate realization of the vision, and publishing metadata exemplars conformant with the standard. Implementation of the standard by community members, in the form of published metadata which document the information resources each organization manages, will allow use of tools requiring consistent metadata for efficient discovery and evaluation of, and access to, information resources. While metadata are expected to be widely accessible, access to associated information resources may be more constrained. The initiative is being conducting by Energistics' Metadata Work Group, in collaboration with the USGIN Project. Energistics is a global standards group in the oil and natural gas industry. The Work Group determined early in the initiative, based on input solicited from 40+ organizations and on an assessment of existing metadata standards, to develop the target metadata standard as a profile of a revised version of ISO 19115, formally the "Energy Industry Profile of ISO/DIS 19115-1 v1.0" (EIP). The Work Group is participating on the ISO/TC 211 project team responsible for the revision of ISO 19115, now ready for "Draft International Standard" (DIS) status. With ISO 19115 an established, capability-rich, open standard for geographic metadata, EIP v1 is expected to be widely acceptable within the community and readily sustainable over the long-term. The EIP design, also per community requirements, will enable discovery, evaluation, and access to types of information resources considered important to the community, including structured and unstructured digital resources, and physical assets such as hardcopy documents and material samples. This presentation will briefly review the development of this initiative as well as the current and planned Work Group activities. More time will be spent providing an overview of the EIP v1, including the requirements it prescribes, design efforts made to enable automated metadata capture and processing, and the structure and content of its documentation, which was written to minimize ambiguity and facilitate implementation. The Work Group considers EIP v1 a solid initial design for interoperable metadata, and first step toward the vision of the Initiative.

Using a linked data approach to aid development of a metadata portal to support Marine Strategy Framework Directive (MSFD) implementation

NASA Astrophysics Data System (ADS)

Wood, Chris

2016-04-01

Under the Marine Strategy Framework Directive (MSFD), EU Member States are mandated to achieve or maintain 'Good Environmental Status' (GES) in their marine areas by 2020, through a series of Programme of Measures (PoMs). The Celtic Seas Partnership (CSP), an EU LIFE+ project, aims to support policy makers, special-interest groups, users of the marine environment, and other interested stakeholders on MSFD implementation in the Celtic Seas geographical area. As part of this support, a metadata portal has been built to provide a signposting service to datasets that are relevant to MSFD within the Celtic Seas. To ensure that the metadata has the widest possible reach, a linked data approach was employed to construct the database. Although the metadata are stored in a traditional RDBS, the metadata are exposed as linked data via the D2RQ platform, allowing virtual RDF graphs to be generated. SPARQL queries can be executed against the end-point allowing any user to manipulate the metadata. D2RQ's mapping language, based on turtle, was used to map a wide range of relevant ontologies to the metadata (e.g. The Provenance Ontology (prov-o), Ocean Data Ontology (odo), Dublin Core Elements and Terms (dc & dcterms), Friend of a Friend (foaf), and Geospatial ontologies (geo)) allowing users to browse the metadata, either via SPARQL queries or by using D2RQ's HTML interface. The metadata were further enhanced by mapping relevant parameters to the NERC Vocabulary Server, itself built on a SPARQL endpoint. Additionally, a custom web front-end was built to enable users to browse the metadata and express queries through an intuitive graphical user interface that requires no prior knowledge of SPARQL. As well as providing means to browse the data via MSFD-related parameters (Descriptor, Criteria, and Indicator), the metadata records include the dataset's country of origin, the list of organisations involved in the management of the data, and links to any relevant INSPIRE-compliant services relating to the dataset. The web front-end therefore enables users to effectively filter, sort, or search the metadata. As the MSFD timeline requires Member States to review their progress on achieving or maintaining GES every six years, the timely development of this metadata portal will not only aid interested stakeholders in understanding how member states are meeting their targets, but also shows how linked data can be used effectively to support policy makers and associated legislative bodies.

THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, Ranjeet; Shrestha, Biva; Palanisamy, Giri

Nobody is better suited to describe data than the scientist who created it. This description about a data is called Metadata. In general terms, Metadata represents the who, what, when, where, why and how of the dataset [1]. eXtensible Markup Language (XML) is the preferred output format for metadata, as it makes it portable and, more importantly, suitable for system discoverability. The newly developed ORNL Metadata Editor (OME) is a Web-based tool that allows users to create and maintain XML files containing key information, or metadata, about the research. Metadata include information about the specific projects, parameters, time periods, andmore » locations associated with the data. Such information helps put the research findings in context. In addition, the metadata produced using OME will allow other researchers to find these data via Metadata clearinghouses like Mercury [2][4]. OME is part of ORNL s Mercury software fleet [2][3]. It was jointly developed to support projects funded by the United States Geological Survey (USGS), U.S. Department of Energy (DOE), National Aeronautics and Space Administration (NASA) and National Oceanic and Atmospheric Administration (NOAA). OME s architecture provides a customizable interface to support project-specific requirements. Using this new architecture, the ORNL team developed OME instances for USGS s Core Science Analytics, Synthesis, and Libraries (CSAS&L), DOE s Next Generation Ecosystem Experiments (NGEE) and Atmospheric Radiation Measurement (ARM) Program, and the international Surface Ocean Carbon Dioxide ATlas (SOCAT). Researchers simply use the ORNL Metadata Editor to enter relevant metadata into a Web-based form. From the information on the form, the Metadata Editor can create an XML file on the server that the editor is installed or to the user s personal computer. Researchers can also use the ORNL Metadata Editor to modify existing XML metadata files. As an example, an NGEE Arctic scientist use OME to register their datasets to the NGEE data archive and allows the NGEE archive to publish these datasets via a data search portal (http://ngee.ornl.gov/data). These highly descriptive metadata created using OME allows the Archive to enable advanced data search options using keyword, geo-spatial, temporal and ontology filters. Similarly, ARM OME allows scientists or principal investigators (PIs) to submit their data products to the ARM data archive. How would OME help Big Data Centers like the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC)? The ORNL DAAC is one of NASA s Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of the Earth's environment. Typically data produced, archived and analyzed is at a scale of multiple petabytes, which makes the discoverability of the data very challenging. Without proper metadata associated with the data, it is difficult to find the data you are looking for and equally difficult to use and understand the data. OME will allow data centers like the NGEE and ORNL DAAC to produce meaningful, high quality, standards-based, descriptive information about their data products in-turn helping with the data discoverability and interoperability. Useful Links: USGS OME: http://mercury.ornl.gov/OME/ NGEE OME: http://ngee-arctic.ornl.gov/ngeemetadata/ ARM OME: http://archive2.ornl.gov/armome/ Contact: Ranjeet Devarakonda (devarakondar@ornl.gov) References: [1] Federal Geographic Data Committee. Content standard for digital geospatial metadata. Federal Geographic Data Committee, 1998. [2] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94. [3] Wilson, B. E., Palanisamy, G., Devarakonda, R., Rhyne, B. T., Lindsley, C., & Green, J. (2010). Mercury Toolset for Spatiotemporal Metadata. [4] Pouchard, L. C., Branstetter, M. L., Cook, R. B., Devarakonda, R., Green, J., Palanisamy, G., ... & Noy, N. F. (2013). A Linked Science investigation: enhancing climate change data discovery with semantic technologies. Earth science informatics, 6(3), 175-185.« less

78 FR 30226 - Accessibility Requirements for Internet Browsers

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-22

... products and services with peripheral devices or specialized customer premise equipment commonly used by... the telephone or services that such manufacturer or provider offers is accessible to and usable by... requires certain Internet browsers used for advanced communications services to be accessible to people...

Network Security Risks of Online Social Networking in the Workplace

DTIC Science & Technology

2013-11-01

Facebook explains pornographic shock spam, hints at browser vulnera- bility, nakedsecurity. URL – http://nakedsecurity.sophos.com/2011/11/16/ facebook...explains- pornographic -shock-spam-hints-at-browser-vul nerability/. 22 UNCLASSIFIED UNCLASSIFIED DSTO–GD–0772 44. Blatz, J. (2011) CSRF: attack and

Emissions & Generation Resource Integrated Database (eGRID), eGRID2002 (with years 1996 - 2000 data)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is a comprehensive source of data on the environmental characteristics of almost all electric power generated in the United States. These environmental characteristics include air emissions for nitrogen oxides, sulfur dioxide, carbon dioxide, methane, nitrous oxide, and mercury; emissions rates; net generation; resource mix; and many other attributes. eGRID2002 (years 1996 through 2000 data) contains 16 Excel spreadsheets and the Technical Support Document, as well as the eGRID Data Browser, User's Manual, and Readme file. Archived eGRID data can be viewed as spreadsheets or by using the eGRID Data Browser. The eGRID spreadsheets can be manipulated by data users and enables users to view all the data underlying eGRID. The eGRID Data Browser enables users to view key data using powerful search features. Note that the eGRID Data Browser will not run on a Mac-based machine without Windows emulation.

WEBSLIDE: A "Virtual" Slide Projector Based on World Wide Web

NASA Astrophysics Data System (ADS)

Barra, Maria; Ferrandino, Salvatore; Scarano, Vittorio

1999-03-01

We present here the design key concepts of WEBSLIDE, a software project whose objective is to provide a simple, cheap and efficient solution for showing slides during lessons in computer labs. In fact, WEBSLIDE allows the video monitors of several client machines (the "STUDENTS") to be synchronously updated by the actions of a particular client machine, called the "INSTRUCTOR." The system is based on the World Wide Web and the software components of WEBSLIDE mainly consists in a WWW server, browsers and small Cgi-Bill scripts. What makes WEBSLIDE particularly appealing for small educational institutions is that WEBSLIDE is built with "off the shelf" products: it does not involve using a specifically designed program but any Netscape browser, one of the most popular browsers available on the market, is sufficient. Another possible use is to use our system to implement "guided automatic tours" through several pages or Intranets internal news bulletins: the company Web server can broadcast to all employees relevant information on their browser.

Nessi: An EEG-Controlled Web Browser for Severely Paralyzed Patients

PubMed Central

Bensch, Michael; Karim, Ahmed A.; Mellinger, Jürgen; Hinterberger, Thilo; Tangermann, Michael; Bogdan, Martin; Rosenstiel, Wolfgang; Birbaumer, Niels

2007-01-01

We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs) enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links). Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications. PMID:18350132

A metadata-driven approach to data repository design.

PubMed

Harvey, Matthew J; McLean, Andrew; Rzepa, Henry S

2017-01-01

The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with DataCite in accordance with their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data preview are illustrated, including the demonstration of a method for integration with commercial software that confers rich domain-specific data analytics without introducing customisation into the repository itself.

Stop the Bleeding: the Development of a Tool to Streamline NASA Earth Science Metadata Curation Efforts

NASA Astrophysics Data System (ADS)

le Roux, J.; Baker, A.; Caltagirone, S.; Bugbee, K.

2017-12-01

The Common Metadata Repository (CMR) is a high-performance, high-quality repository for Earth science metadata records, and serves as the primary way to search NASA's growing 17.5 petabytes of Earth science data holdings. Released in 2015, CMR has the capability to support several different metadata standards already being utilized by NASA's combined network of Earth science data providers, or Distributed Active Archive Centers (DAACs). The Analysis and Review of CMR (ARC) Team located at Marshall Space Flight Center is working to improve the quality of records already in CMR with the goal of making records optimal for search and discovery. This effort entails a combination of automated and manual review, where each NASA record in CMR is checked for completeness, accuracy, and consistency. This effort is highly collaborative in nature, requiring communication and transparency of findings amongst NASA personnel, DAACs, the CMR team and other metadata curation teams. Through the evolution of this project it has become apparent that there is a need to document and report findings, as well as track metadata improvements in a more efficient manner. The ARC team has collaborated with Element 84 in order to develop a metadata curation tool to meet these needs. In this presentation, we will provide an overview of this metadata curation tool and its current capabilities. Challenges and future plans for the tool will also be discussed.

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

PubMed

Good, Benjamin M; Tennis, Joseph T; Wilkinson, Mark D

2009-09-25

Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products. We assessed the metadata that users of CiteULike and Connotea associated with citations in PubMed with the following metrics: coverage of the document space, density of metadata (tags) per document, rates of inter-annotator agreement, and rates of agreement with MeSH indexing. CiteULike and Connotea were very similar on all of the measurements. In comparison to PubMed, document coverage and per-document metadata density were much lower for the social tagging systems. Inter-annotator agreement within the social tagging systems and the agreement between the aggregated social tagging metadata and MeSH indexing was low though the latter could be increased through voting. The most promising uses of metadata from current academic social tagging repositories will be those that find ways to utilize the novel relationships between users, tags, and documents exposed through these systems. For more traditional kinds of indexing-based applications (such as keyword-based search) to benefit substantially from socially generated metadata in the life sciences, more documents need to be tagged and more tags are needed for each document. These issues may be addressed both by finding ways to attract more users to current systems and by creating new user interfaces that encourage more collectively useful individual tagging behaviour.

A Metadata Element Set for Project Documentation

NASA Technical Reports Server (NTRS)

Hodge, Gail; Templeton, Clay; Allen, Robert B.

2003-01-01

Abstract NASA Goddard Space Flight Center is a large engineering enterprise with many projects. We describe our efforts to develop standard metadata sets across project documentation which we term the "Goddard Core". We also address broader issues for project management metadata.

The UCSC Genome Browser: What Every Molecular Biologist Should Know

PubMed Central

Mangan, Mary E.; Williams, Jennifer M.; Kuhn, Robert M.; Lathe, Warren C.

2016-01-01

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one’s understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. PMID:19816931

DataForge: Modular platform for data storage and analysis

NASA Astrophysics Data System (ADS)

Nozik, Alexander

2018-04-01

DataForge is a framework for automated data acquisition, storage and analysis based on modern achievements of applied programming. The aim of the DataForge is to automate some standard tasks like parallel data processing, logging, output sorting and distributed computing. Also the framework extensively uses declarative programming principles via meta-data concept which allows a certain degree of meta-programming and improves results reproducibility.

Applying an Archetype-Based Approach to Electroencephalography/Event-Related Potential Experiments in the EEGBase Resource.

PubMed

Papež, Václav; Mouček, Roman

2017-01-01

The purpose of this study is to investigate the feasibility of applying openEHR (an archetype-based approach for electronic health records representation) to modeling data stored in EEGBase, a portal for experimental electroencephalography/event-related potential (EEG/ERP) data management. The study evaluates re-usage of existing openEHR archetypes and proposes a set of new archetypes together with the openEHR templates covering the domain. The main goals of the study are to (i) link existing EEGBase data/metadata and openEHR archetype structures and (ii) propose a new openEHR archetype set describing the EEG/ERP domain since this set of archetypes currently does not exist in public repositories. The main methodology is based on the determination of the concepts obtained from EEGBase experimental data and metadata that are expressible structurally by the openEHR reference model and semantically by openEHR archetypes. In addition, templates as the third openEHR resource allow us to define constraints over archetypes. Clinical Knowledge Manager (CKM), a public openEHR archetype repository, was searched for the archetypes matching the determined concepts. According to the search results, the archetypes already existing in CKM were applied and the archetypes not existing in the CKM were newly developed. openEHR archetypes support linkage to external terminologies. To increase semantic interoperability of the new archetypes, binding with the existing odML electrophysiological terminology was assured. Further, to increase structural interoperability, also other current solutions besides EEGBase were considered during the development phase. Finally, a set of templates using the selected archetypes was created to meet EEGBase requirements. A set of eleven archetypes that encompassed the domain of experimental EEG/ERP measurements were identified. Of these, six were reused without changes, one was extended, and four were newly created. All archetypes were arranged in the templates reflecting the EEGBase metadata structure. A mechanism of odML terminology referencing was proposed to assure semantic interoperability of the archetypes. The openEHR approach was found to be useful not only for clinical purposes but also for experimental data modeling.

Metadata for WIS and WIGOS: GAW Profile of ISO19115 and Draft WIGOS Core Metadata Standard

NASA Astrophysics Data System (ADS)

Klausen, Jörg; Howe, Brian

2014-05-01

The World Meteorological Organization (WMO) Integrated Global Observing System (WIGOS) is a key WMO priority to underpin all WMO Programs and new initiatives such as the Global Framework for Climate Services (GFCS). The development of the WIGOS Operational Information Resource (WIR) is central to the WIGOS Framework Implementation Plan (WIGOS-IP). The WIR shall provide information on WIGOS and its observing components, as well as requirements of WMO application areas. An important aspect is the description of the observational capabilities by way of structured metadata. The Global Atmosphere Watch is the WMO program addressing the chemical composition and selected physical properties of the atmosphere. Observational data are collected and archived by GAW World Data Centres (WDCs) and related data centres. The Task Team on GAW WDCs (ET-WDC) have developed a profile of the ISO19115 metadata standard that is compliant with the WMO Information System (WIS) specification for the WMO Core Metadata Profile v1.3. This profile is intended to harmonize certain aspects of the documentation of observations as well as the interoperability of the WDCs. The Inter-Commission-Group on WIGOS (ICG-WIGOS) has established the Task Team on WIGOS Metadata (TT-WMD) with representation of all WMO Technical Commissions and the objective to define the WIGOS Core Metadata. The result of this effort is a draft semantic standard comprising of a set of metadata classes that are considered to be of critical importance for the interpretation of observations relevant to WIGOS. The purpose of the presentation is to acquaint the audience with the standard and to solicit informal feed-back from experts in the various disciplines of meteorology and climatology. This feed-back will help ET-WDC and TT-WMD to refine the GAW metadata profile and the draft WIGOS metadata standard, thereby increasing their utility and acceptance.

SIPSMetGen: It's Not Just For Aircraft Data and ECS Anymore.

NASA Astrophysics Data System (ADS)

Schwab, M.

2015-12-01

The SIPSMetGen utility, developed for the NASA EOSDIS project, under the EED contract, simplified the creation of file level metadata for the ECS System. The utility has been enhanced for ease of use, efficiency, speed and increased flexibility. The SIPSMetGen utility was originally created as a means of generating file level spatial metadata for Operation IceBridge. The first version created only ODL metadata, specific for ingest into ECS. The core strength of the utility was, and continues to be, its ability to take complex shapes and patterns of data collection point clouds from aircraft flights and simplify them to a relatively simple concave hull geo-polygon. It has been found to be a useful and easy to use tool for creating file level metadata for many other missions, both aircraft and satellite. While the original version was useful it had its limitations. In 2014 Raytheon was tasked to make enhancements to SIPSMetGen, this resulted a new version of SIPSMetGen which can create ISO Compliant XML metadata; provides optimization and streamlining of the algorithm for creating the spatial metadata; a quicker runtime with more consistent results; a utility that can be configured to run multi-threaded on systems with multiple processors. The utility comes with a java based graphical user interface to aid in configuration and running of the utility. The enhanced SIPSMetGen allows more diverse data sets to be archived with file level metadata. The advantage of archiving data with file level metadata is that it makes it easier for data users, and scientists to find relevant data. File level metadata unlocks the power of existing archives and metadata repositories such as ECS and CMR and search and discovery utilities like Reverb and Earth Data Search. Current missions now using SIPSMetGen include: Aquarius, Measures, ARISE, and Nimbus.

Metadata Creation, Management and Search System for your Scientific Data

NASA Astrophysics Data System (ADS)

Devarakonda, R.; Palanisamy, G.

2012-12-01

Mercury Search Systems is a set of tools for creating, searching, and retrieving of biogeochemical metadata. Mercury toolset provides orders of magnitude improvements in search speed, support for any metadata format, integration with Google Maps for spatial queries, multi-facetted type search, search suggestions, support for RSS (Really Simple Syndication) delivery of search results, and enhanced customization to meet the needs of the multiple projects that use Mercury. Mercury's metadata editor provides a easy way for creating metadata and Mercury's search interface provides a single portal to search for data and information contained in disparate data management systems, each of which may use any metadata format including FGDC, ISO-19115, Dublin-Core, Darwin-Core, DIF, ECHO, and EML. Mercury harvests metadata and key data from contributing project servers distributed around the world and builds a centralized index. The search interfaces then allow the users to perform a variety of fielded, spatial, and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury is being used more than 14 different projects across 4 federal agencies. It was originally developed for NASA, with continuing development funded by NASA, USGS, and DOE for a consortium of projects. Mercury search won the NASA's Earth Science Data Systems Software Reuse Award in 2008. References: R. Devarakonda, G. Palanisamy, B.E. Wilson, and J.M. Green, "Mercury: reusable metadata management data discovery and access system", Earth Science Informatics, vol. 3, no. 1, pp. 87-94, May 2010. R. Devarakonda, G. Palanisamy, J.M. Green, B.E. Wilson, "Data sharing and retrieval using OAI-PMH", Earth Science Informatics DOI: 10.1007/s12145-010-0073-0, (2010);

[Design of the image browser for PACS image workstation].

PubMed

Li, Feng; Zhou, He-Qin

2006-09-01

The design of PACS image workstation based on DICOM3.0 is introduced in the paper, then the designing method of the PACS image browser based on the control system theory is presented,focusing on two main units:DICOM analyzer and the information mapping transformer.

NATIONAL LANDSCAPE METRICS BROWSER (V1.0)

EPA Science Inventory

This metric browser website describes and displays wall-to-wall landscape metrics that have been calculated for the entire conterminous U.S. The intent is to provide the user with an overview of the nature and utility of this landscape metric data set. The land cover and pattern ...

International Portal

EIA Publications

The International Energy Portal includes a powerful data browser that provides country-level energy data; many countries have at least 30 years of historical data. The data browser provides users the ability to view and download complete datasets for consumption, production, trade, reserves, and carbon dioxide emissions for different fuels and energy sources.

Introduction to the fathead minnow genome browser and opportunities for collaborative development

EPA Science Inventory

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

Master Metadata Repository and Metadata-Management System

NASA Technical Reports Server (NTRS)

Armstrong, Edward; Reed, Nate; Zhang, Wen

2007-01-01

A master metadata repository (MMR) software system manages the storage and searching of metadata pertaining to data from national and international satellite sources of the Global Ocean Data Assimilation Experiment (GODAE) High Resolution Sea Surface Temperature Pilot Project [GHRSSTPP]. These sources produce a total of hundreds of data files daily, each file classified as one of more than ten data products representing global sea-surface temperatures. The MMR is a relational database wherein the metadata are divided into granulelevel records [denoted file records (FRs)] for individual satellite files and collection-level records [denoted data set descriptions (DSDs)] that describe metadata common to all the files from a specific data product. FRs and DSDs adhere to the NASA Directory Interchange Format (DIF). The FRs and DSDs are contained in separate subdatabases linked by a common field. The MMR is configured in MySQL database software with custom Practical Extraction and Reporting Language (PERL) programs to validate and ingest the metadata records. The database contents are converted into the Federal Geographic Data Committee (FGDC) standard format by use of the Extensible Markup Language (XML). A Web interface enables users to search for availability of data from all sources.

Brady's Geothermal Field Nodal Seismometers Metadata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lesley Parker

Metadata for the nodal seismometer array deployed at the POROTOMO's Natural Laboratory in Brady Hot Spring, Nevada during the March 2016 testing. Metadata includes location and timing for each instrument as well as file lists of data to be uploaded in a separate submission.

Extraction of CT dose information from DICOM metadata: automated Matlab-based approach.

PubMed

Dave, Jaydev K; Gingold, Eric L

2013-01-01

The purpose of this study was to extract exposure parameters and dose-relevant indexes of CT examinations from information embedded in DICOM metadata. DICOM dose report files were identified and retrieved from a PACS. An automated software program was used to extract from these files information from the structured elements in the DICOM metadata relevant to exposure. Extracting information from DICOM metadata eliminated potential errors inherent in techniques based on optical character recognition, yielding 100% accuracy.

Trends in the Evolution of the Public Web, 1998-2002; The Fedora Project: An Open-source Digital Object Repository Management System; State of the Dublin Core Metadata Initiative, April 2003; Preservation Metadata; How Many People Search the ERIC Database Each Day?

ERIC Educational Resources Information Center

O'Neill, Edward T.; Lavoie, Brian F.; Bennett, Rick; Staples, Thornton; Wayland, Ross; Payette, Sandra; Dekkers, Makx; Weibel, Stuart; Searle, Sam; Thompson, Dave; Rudner, Lawrence M.

2003-01-01

Includes five articles that examine key trends in the development of the public Web: size and growth, internationalization, and metadata usage; Flexible Extensible Digital Object and Repository Architecture (Fedora) for use in digital libraries; developments in the Dublin Core Metadata Initiative (DCMI); the National Library of New Zealand Te Puna…

Heuristics for Relevancy Ranking of Earth Dataset Search Results

NASA Astrophysics Data System (ADS)

Lynnes, C.; Quinn, P.; Norton, J.

2016-12-01

As the Variety of Earth science datasets increases, science researchers find it more challenging to discover and select the datasets that best fit their needs. The most common way of search providers to address this problem is to rank the datasets returned for a query by their likely relevance to the user. Large web page search engines typically use text matching supplemented with reverse link counts, semantic annotations and user intent modeling. However, this produces uneven results when applied to dataset metadata records simply externalized as a web page. Fortunately, data and search provides have decades of experience in serving data user communities, allowing them to form heuristics that leverage the structure in the metadata together with knowledge about the user community. Some of these heuristics include specific ways of matching the user input to the essential measurements in the dataset and determining overlaps of time range and spatial areas. Heuristics based on the novelty of the datasets can prioritize later, better versions of data over similar predecessors. And knowledge of how different user types and communities use data can be brought to bear in cases where characteristics of the user (discipline, expertise) or their intent (applications, research) can be divined. The Earth Observing System Data and Information System has begun implementing some of these heuristics in the relevancy algorithm of its Common Metadata Repository search engine.

Heuristics for Relevancy Ranking of Earth Dataset Search Results

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Quinn, Patrick; Norton, James

2016-01-01

As the Variety of Earth science datasets increases, science researchers find it more challenging to discover and select the datasets that best fit their needs. The most common way of search providers to address this problem is to rank the datasets returned for a query by their likely relevance to the user. Large web page search engines typically use text matching supplemented with reverse link counts, semantic annotations and user intent modeling. However, this produces uneven results when applied to dataset metadata records simply externalized as a web page. Fortunately, data and search provides have decades of experience in serving data user communities, allowing them to form heuristics that leverage the structure in the metadata together with knowledge about the user community. Some of these heuristics include specific ways of matching the user input to the essential measurements in the dataset and determining overlaps of time range and spatial areas. Heuristics based on the novelty of the datasets can prioritize later, better versions of data over similar predecessors. And knowledge of how different user types and communities use data can be brought to bear in cases where characteristics of the user (discipline, expertise) or their intent (applications, research) can be divined. The Earth Observing System Data and Information System has begun implementing some of these heuristics in the relevancy algorithm of its Common Metadata Repository search engine.

Relevancy Ranking of Satellite Dataset Search Results

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Quinn, Patrick; Norton, James

2017-01-01

As the Variety of Earth science datasets increases, science researchers find it more challenging to discover and select the datasets that best fit their needs. The most common way of search providers to address this problem is to rank the datasets returned for a query by their likely relevance to the user. Large web page search engines typically use text matching supplemented with reverse link counts, semantic annotations and user intent modeling. However, this produces uneven results when applied to dataset metadata records simply externalized as a web page. Fortunately, data and search provides have decades of experience in serving data user communities, allowing them to form heuristics that leverage the structure in the metadata together with knowledge about the user community. Some of these heuristics include specific ways of matching the user input to the essential measurements in the dataset and determining overlaps of time range and spatial areas. Heuristics based on the novelty of the datasets can prioritize later, better versions of data over similar predecessors. And knowledge of how different user types and communities use data can be brought to bear in cases where characteristics of the user (discipline, expertise) or their intent (applications, research) can be divined. The Earth Observing System Data and Information System has begun implementing some of these heuristics in the relevancy algorithm of its Common Metadata Repository search engine.

The RBV metadata catalog

NASA Astrophysics Data System (ADS)

Andre, Francois; Fleury, Laurence; Gaillardet, Jerome; Nord, Guillaume

2015-04-01

RBV (Réseau des Bassins Versants) is a French initiative to consolidate the national efforts made by more than 15 elementary observatories funded by various research institutions (CNRS, INRA, IRD, IRSTEA, Universities) that study river and drainage basins. The RBV Metadata Catalogue aims at giving an unified vision of the work produced by every observatory to both the members of the RBV network and any external person interested by this domain of research. Another goal is to share this information with other existing metadata portals. Metadata management is heterogeneous among observatories ranging from absence to mature harvestable catalogues. Here, we would like to explain the strategy used to design a state of the art catalogue facing this situation. Main features are as follows : - Multiple input methods: Metadata records in the catalog can either be entered with the graphical user interface, harvested from an existing catalogue or imported from information system through simplified web services. - Hierarchical levels: Metadata records may describe either an observatory, one of its experimental site or a single dataset produced by one instrument. - Multilingualism: Metadata can be easily entered in several configurable languages. - Compliance to standards : the backoffice part of the catalogue is based on a CSW metadata server (Geosource) which ensures ISO19115 compatibility and the ability of being harvested (globally or partially). On going tasks focus on the use of SKOS thesaurus and SensorML description of the sensors. - Ergonomy : The user interface is built with the GWT Framework to offer a rich client application with a fully ajaxified navigation. - Source code sharing : The work has led to the development of reusable components which can be used to quickly create new metadata forms in other GWT applications You can visit the catalogue (http://portailrbv.sedoo.fr/) or contact us by email rbv@sedoo.fr.

OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research.

PubMed

Uciteli, Alexandr; Herre, Heinrich

2015-01-01

The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct representation of their metadata. In various research organizations, which are planning and coordinating studies, the required metadata are specified differently, depending on many conditions, e.g., on the used study management software. The latter does not always meet the needs of a particular research organization, e.g., with respect to the relevant metadata attributes and structuring possibilities. The objective of the research, set forth in this paper, is the development of a new approach for ontology-based representation and management of metadata. The basic features of this approach are demonstrated by the software tool OntoStudyEdit (OSE). The OSE is designed and developed according to the three ontology method. This method for developing software is based on the interactions of three different kinds of ontologies: a task ontology, a domain ontology and a top-level ontology. The OSE can be easily adapted to different requirements, and it supports an ontologically founded representation and efficient management of metadata. The metadata specifications can by imported from various sources; they can be edited with the OSE, and they can be exported in/to several formats, which are used, e.g., by different study management software. Advantages of this approach are the adaptability of the OSE by integrating suitable domain ontologies, the ontological specification of mappings between the import/export formats and the DO, the specification of the study metadata in a uniform manner and its reuse in different research projects, and an intuitive data entry for non-expert users.

EarthCube Data Discovery Hub: Enhancing, Curating and Finding Data across Multiple Geoscience Data Sources.

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Valentine, D.; Richard, S. M.; Gupta, A.; Meier, O.; Peucker-Ehrenbrink, B.; Hudman, G.; Stocks, K. I.; Hsu, L.; Whitenack, T.; Grethe, J. S.; Ozyurt, I. B.

2017-12-01

EarthCube Data Discovery Hub (DDH) is an EarthCube Building Block project using technologies developed in CINERGI (Community Inventory of EarthCube Resources for Geoscience Interoperability) to enable geoscience users to explore a growing portfolio of EarthCube-created and other geoscience-related resources. Over 1 million metadata records are available for discovery through the project portal (cinergi.sdsc.edu). These records are retrieved from data facilities, including federal, state and academic sources, or contributed by geoscientists through workshops, surveys, or other channels. CINERGI metadata augmentation pipeline components 1) provide semantic enhancement based on a large ontology of geoscience terms, using text analytics to generate keywords with references to ontology classes, 2) add spatial extents based on place names found in the metadata record, and 3) add organization identifiers to the metadata. The records are indexed and can be searched via a web portal and standard search APIs. The added metadata content improves discoverability and interoperability of the registered resources. Specifically, the addition of ontology-anchored keywords enables faceted browsing and lets users navigate to datasets related by variables measured, equipment used, science domain, processes described, geospatial features studied, and other dataset characteristics that are generated by the pipeline. DDH also lets data curators access and edit the automatically generated metadata records using the CINERGI metadata editor, accept or reject the enhanced metadata content, and consider it in updating their metadata descriptions. We consider several complex data discovery workflows, in environmental seismology (quantifying sediment and water fluxes using seismic data), marine biology (determining available temperature, location, weather and bleaching characteristics of coral reefs related to measurements in a given coral reef survey), and river geochemistry (discovering observations relevant to geochemical measurements outside the tidal zone, given specific discharge conditions).

Efficiently Communicating Rich Heterogeneous Geospatial Data from the FeMO2008 Dive Cruise with FlashMap on EarthRef.org

NASA Astrophysics Data System (ADS)

Minnett, R. C.; Koppers, A. A.; Staudigel, D.; Staudigel, H.

2008-12-01

EarthRef.org is comprehensive and convenient resource for Earth Science reference data and models. It encompasses four main portals: the Geochemical Earth Reference Model (GERM), the Magnetics Information Consortium (MagIC), the Seamount Biogeosciences Network (SBN), and the Enduring Resources for Earth Science Education (ERESE). Their underlying databases are publically available and the scientific community has contributed widely and is urged to continue to do so. However, the net result is a vast and largely heterogeneous warehouse of geospatial data ranging from carefully prepared maps of seamounts to geochemical data/metadata, daily reports from seagoing expeditions, large volumes of raw and processed multibeam data, images of paleomagnetic sampling sites, etc. This presents a considerable obstacle for integrating other rich media content, such as videos, images, data files, cruise tracks, and interoperable database results, without overwhelming the web user. The four EarthRef.org portals clearly lend themselves to a more intuitive user interface and has, therefore, been an invaluable test bed for the design and implementation of FlashMap, a versatile KML-driven geospatial browser written for reliability and speed in Adobe Flash. FlashMap allows layers of content to be loaded and displayed over a streaming high-resolution map which can be zoomed and panned similarly to Google Maps and Google Earth. Many organizations, from National Geographic to the USGS, have begun using Google Earth software to display geospatial content. However, Google Earth, as a desktop application, does not integrate cleanly with existing websites requiring the user to navigate away from the browser and focus on a separate application and Google Maps, written in Java Script, does not scale up reliably to large datasets. FlashMap remedies these problems as a web-based application that allows for seamless integration of the real-time display power of Google Earth and the flexibility of the web without losing scalability and control of the base maps. Our Flash-based application is fully compatible with KML (Keyhole Markup Language) 2.2, the most recent iteration of KML, allowing users with existing Google Earth KML files to effortlessly display their geospatial content embedded in a web page. As a test case for FlashMap, the annual Iron-Oxidizing Microbial Observatory (FeMO) dive cruise to the Loihi Seamount, in conjunction with data available from ongoing and published FeMO laboratory studies, showcases the flexibility of this single web-based application. With a KML 2.2 compatible web-service providing the content, any database can display results in FlashMap. The user can then hide and show multiple layers of content, potentially from several data sources, and rapidly digest a vast quantity of information to narrow the search results. This flexibility gives experienced users the ability to drill down to exactly the record they are looking for (SERC at Carleton College's educational application of FlashMap at http://serc.carleton.edu/sp/erese/activities/22223.html) and allows users familiar with Google Earth the ability to load and view geospatial data content within a browser from any computer with an internet connection.

JSXGraph--Dynamic Mathematics with JavaScript

ERIC Educational Resources Information Center

Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

2010-01-01

Since Java applets seem to be on the retreat in web application, other approaches for displaying interactive mathematics in the web browser are needed. One such alternative could be our open-source project JSXGraph. It is a cross-browser library for displaying interactive geometry, function plotting, graphs, and data visualization in a web…

Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

Vulnerability Assessment of Open Source Wireshark and Chrome Browser

DTIC Science & Technology

2013-08-01

UNLIMITED 5 We spent much of the initial time learning about the logical model that modern HTML5 web browsers support, including how users interact with...are supposed to protect users of that site against cross-site scripting) and the new powerful an all-encompassing HTML5 standard. This vulnerability

Airborne Hazards and Open Burn Pit Registry

MedlinePlus

... Burn Pit Registry requires a common web browser technology to guide you through the registry questionnaire. You may try a different browser, or you may try from a different computer. You may also see this problem if you are in a high security environment where this is disabled by a network policy. ...

75 FR 4689 - Electronic Tariff Filings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-29

... collaborative process relies upon the use of metadata (or information) about the tariff filing, including such... code.\\5\\ Because the Commission is using the electronic metadata to establish statutory action dates... code, as well as accurately providing any other metadata. 6. Similarly, the Commission will be using...

The center for expanded data annotation and retrieval

PubMed Central

Bean, Carol A; Cheung, Kei-Hoi; Dumontier, Michel; Durante, Kim A; Gevaert, Olivier; Gonzalez-Beltran, Alejandra; Khatri, Purvesh; Kleinstein, Steven H; O’Connor, Martin J; Pouliot, Yannick; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Wiser, Jeffrey A

2015-01-01

The Center for Expanded Data Annotation and Retrieval is studying the creation of comprehensive and expressive metadata for biomedical datasets to facilitate data discovery, data interpretation, and data reuse. We take advantage of emerging community-based standard templates for describing different kinds of biomedical datasets, and we investigate the use of computational techniques to help investigators to assemble templates and to fill in their values. We are creating a repository of metadata from which we plan to identify metadata patterns that will drive predictive data entry when filling in metadata templates. The metadata repository not only will capture annotations specified when experimental datasets are initially created, but also will incorporate links to the published literature, including secondary analyses and possible refinements or retractions of experimental interpretations. By working initially with the Human Immunology Project Consortium and the developers of the ImmPort data repository, we are developing and evaluating an end-to-end solution to the problems of metadata authoring and management that will generalize to other data-management environments. PMID:26112029

Establishing semantic interoperability of biomedical metadata registries using extended semantic relationships.

PubMed

Park, Yu Rang; Yoon, Young Jo; Kim, Hye Hyeon; Kim, Ju Han

2013-01-01

Achieving semantic interoperability is critical for biomedical data sharing between individuals, organizations and systems. The ISO/IEC 11179 MetaData Registry (MDR) standard has been recognized as one of the solutions for this purpose. The standard model, however, is limited. Representing concepts consist of two or more values, for instance, are not allowed including blood pressure with systolic and diastolic values. We addressed the structural limitations of ISO/IEC 11179 by an integrated metadata object model in our previous research. In the present study, we introduce semantic extensions for the model by defining three new types of semantic relationships; dependency, composite and variable relationships. To evaluate our extensions in a real world setting, we measured the efficiency of metadata reduction by means of mapping to existing others. We extracted metadata from the College of American Pathologist Cancer Protocols and then evaluated our extensions. With no semantic loss, one third of the extracted metadata could be successfully eliminated, suggesting better strategy for implementing clinical MDRs with improved efficiency and utility.

What Information Does Your EHR Contain? Automatic Generation of a Clinical Metadata Warehouse (CMDW) to Support Identification and Data Access Within Distributed Clinical Research Networks.

PubMed

Bruland, Philipp; Doods, Justin; Storck, Michael; Dugas, Martin

2017-01-01

Data dictionaries provide structural meta-information about data definitions in health information technology (HIT) systems. In this regard, reusing healthcare data for secondary purposes offers several advantages (e.g. reduce documentation times or increased data quality). Prerequisites for data reuse are its quality, availability and identical meaning of data. In diverse projects, research data warehouses serve as core components between heterogeneous clinical databases and various research applications. Given the complexity (high number of data elements) and dynamics (regular updates) of electronic health record (EHR) data structures, we propose a clinical metadata warehouse (CMDW) based on a metadata registry standard. Metadata of two large hospitals were automatically inserted into two CMDWs containing 16,230 forms and 310,519 data elements. Automatic updates of metadata are possible as well as semantic annotations. A CMDW allows metadata discovery, data quality assessment and similarity analyses. Common data models for distributed research networks can be established based on similarity analyses.

Separation of metadata and pixel data to speed DICOM tag morphing.

PubMed

Ismail, Mahmoud; Philbin, James

2013-01-01

The DICOM information model combines pixel data and metadata in single DICOM object. It is not possible to access the metadata separately from the pixel data. There are use cases where only metadata is accessed. The current DICOM object format increases the running time of those use cases. Tag morphing is one of those use cases. Tag morphing includes deletion, insertion or manipulation of one or more of the metadata attributes. It is typically used for order reconciliation on study acquisition or to localize the issuer of patient ID (IPID) and the patient ID attributes when data from one domain is transferred to a different domain. In this work, we propose using Multi-Series DICOM (MSD) objects, which separate metadata from pixel data and remove duplicate attributes, to reduce the time required for Tag Morphing. The time required to update a set of study attributes in each format is compared. The results show that the MSD format significantly reduces the time required for tag morphing.

A Generic Metadata Editor Supporting System Using Drupal CMS

NASA Astrophysics Data System (ADS)

Pan, J.; Banks, N. G.; Leggott, M.

2011-12-01

Metadata handling is a key factor in preserving and reusing scientific data. In recent years, standardized structural metadata has become widely used in Geoscience communities. However, there exist many different standards in Geosciences, such as the current version of the Federal Geographic Data Committee's Content Standard for Digital Geospatial Metadata (FGDC CSDGM), the Ecological Markup Language (EML), the Geography Markup Language (GML), and the emerging ISO 19115 and related standards. In addition, there are many different subsets within the Geoscience subdomain such as the Biological Profile of the FGDC (CSDGM), or for geopolitical regions, such as the European Profile or the North American Profile in the ISO standards. It is therefore desirable to have a software foundation to support metadata creation and editing for multiple standards and profiles, without re-inventing the wheels. We have developed a software module as a generic, flexible software system to do just that: to facilitate the support for multiple metadata standards and profiles. The software consists of a set of modules for the Drupal Content Management System (CMS), with minimal inter-dependencies to other Drupal modules. There are two steps in using the system's metadata functions. First, an administrator can use the system to design a user form, based on an XML schema and its instances. The form definition is named and stored in the Drupal database as a XML blob content. Second, users in an editor role can then use the persisted XML definition to render an actual metadata entry form, for creating or editing a metadata record. Behind the scenes, the form definition XML is transformed into a PHP array, which is then rendered via Drupal Form API. When the form is submitted the posted values are used to modify a metadata record. Drupal hooks can be used to perform custom processing on metadata record before and after submission. It is trivial to store the metadata record as an actual XML file or in a storage/archive system. We are working on adding many features to help editor users, such as auto completion, pre-populating of forms, partial saving, as well as automatic schema validation. In this presentation we will demonstrate a few sample editors, including an FGDC editor and a bare bone editor for ISO 19115/19139. We will also demonstrate the use of templates during the definition phase, with the support of export and import functions. Form pre-population and input validation will also be covered. Theses modules are available as open-source software from the Islandora software foundation, as a component of a larger Drupal-based data archive system. They can be easily installed as stand-alone system, or to be plugged into other existing metadata platforms.

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.

PubMed

Horridge, Matthew; Tudorache, Tania; Nuylas, Csongor; Vendetti, Jennifer; Noy, Natalya F; Musen, Mark A

2014-08-15

WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project. WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

PubMed

Foster, Joseph M; Moreno, Pablo; Fabregat, Antonio; Hermjakob, Henning; Steinbeck, Christoph; Apweiler, Rolf; Wakelam, Michael J O; Vizcaíno, Juan Antonio

2013-01-01

Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age (Invited)

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Langenberg, M.; Pagel, S.; Dau, A.; Nuhn, M.; Garcia Ortiz, J. P.; Dietert, H.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2010-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is bound to be accessible only from a few repositories and users will have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community.

Research of marine sensor web based on SOA and EDA

NASA Astrophysics Data System (ADS)

Jiang, Yongguo; Dou, Jinfeng; Guo, Zhongwen; Hu, Keyong

2015-04-01

A great deal of ocean sensor observation data exists, for a wide range of marine disciplines, derived from in situ and remote observing platforms, in real-time, near-real-time and delayed mode. Ocean monitoring is routinely completed using sensors and instruments. Standardization is the key requirement for exchanging information about ocean sensors and sensor data and for comparing and combining information from different sensor networks. One or more sensors are often physically integrated into a single ocean `instrument' device, which often brings in many challenges related to diverse sensor data formats, parameters units, different spatiotemporal resolution, application domains, data quality and sensors protocols. To face these challenges requires the standardization efforts aiming at facilitating the so-called Sensor Web, which making it easy to provide public access to sensor data and metadata information. In this paper, a Marine Sensor Web, based on SOA and EDA and integrating the MBARI's PUCK protocol, IEEE 1451 and OGC SWE 2.0, is illustrated with a five-layer architecture. The Web Service layer and Event Process layer are illustrated in detail with an actual example. The demo study has demonstrated that a standard-based system can be built to access sensors and marine instruments distributed globally using common Web browsers for monitoring the environment and oceanic conditions besides marine sensor data on the Web, this framework of Marine Sensor Web can also play an important role in many other domains' information integration.

MiMiR – an integrated platform for microarray data sharing, mining and analysis

PubMed Central

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-01-01

Background Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. Results A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. Conclusion The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies. PMID:18801157

Visualization of seismic tomography on Google Earth: Improvement of KML generator and its web application to accept the data file in European standard format

NASA Astrophysics Data System (ADS)

Yamagishi, Y.; Yanaka, H.; Tsuboi, S.

2009-12-01

We have developed a conversion tool for the data of seismic tomography into KML, called KML generator, and made it available on the web site (http://www.jamstec.go.jp/pacific21/google_earth). The KML generator enables us to display vertical and horizontal cross sections of the model on Google Earth in three-dimensional manner, which would be useful to understand the Earth's interior. The previous generator accepts text files of grid-point data having longitude, latitude, and seismic velocity anomaly. Each data file contains the data for each depth. Metadata, such as bibliographic reference, grid-point interval, depth, are described in other information file. We did not allow users to upload their own tomographic model to the web application, because there is not standard format to represent tomographic model. Recently European seismology research project, NEIRES (Network of Research Infrastructures for European Seismology), advocates that the data of seismic tomography should be standardized. They propose a new format based on JSON (JavaScript Object Notation), which is one of the data-interchange formats, as a standard one for the tomography. This format consists of two parts, which are metadata and grid-point data values. The JSON format seems to be powerful to handle and to analyze the tomographic model, because the structure of the format is fully defined by JavaScript objects, thus the elements are directly accessible by a script. In addition, there exist JSON libraries for several programming languages. The International Federation of Digital Seismograph Network (FDSN) adapted this format as a FDSN standard format for seismic tomographic model. There might be a possibility that this format would not only be accepted by European seismologists but also be accepted as the world standard. Therefore we improve our KML generator for seismic tomography to accept the data file having also JSON format. We also improve the web application of the generator so that the JSON formatted data file can be uploaded. Users can convert any tomographic model data to KML. The KML obtained through the new generator should provide an arena to compare various tomographic models and other geophysical observations on Google Earth, which may act as a common platform for geoscience browser.

MiMiR--an integrated platform for microarray data sharing, mining and analysis.

PubMed

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-09-18

Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

WGE: a CRISPR database for genome engineering.

PubMed

Hodgkins, Alex; Farne, Anna; Perera, Sajith; Grego, Tiago; Parry-Smith, David J; Skarnes, William C; Iyer, Vivek

2015-09-15

The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome. The WGE database is freely available at www.sanger.ac.uk/htgt/wge : vvi@sanger.ac.uk or skarnes@sanger.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

A metadata reporting framework (FRAMES) for synthesis of ecohydrological observations

DOE PAGES

Christianson, Danielle S.; Varadharajan, Charuleka; Christoffersen, Bradley; ...

2017-06-20

Metadata describe the ancillary information needed for data interpretation, comparison across heterogeneous datasets, and quality control and quality assessment (QA/QC). Metadata enable the synthesis of diverse ecohydrological and biogeochemical observations, an essential step in advancing a predictive understanding of earth systems. Environmental observations can be taken across a wide range of spatiotemporal scales in a variety of measurement settings and approaches, and saved in multiple formats. Thus, well-organized, consistent metadata are required to produce usable data products from diverse observations collected in disparate field sites. However, existing metadata reporting protocols do not support the complex data synthesis needs of interdisciplinarymore » earth system research. We developed a metadata reporting framework (FRAMES) to enable predictive understanding of carbon cycling in tropical forests under global change. FRAMES adheres to best practices for data and metadata organization, enabling consistent data reporting and thus compatibility with a variety of standardized data protocols. We used an iterative scientist-centered design process to develop FRAMES. The resulting modular organization streamlines metadata reporting and can be expanded to incorporate additional data types. The flexible data reporting format incorporates existing field practices to maximize data-entry efficiency. With FRAMES’s multi-scale measurement position hierarchy, data can be reported at observed spatial resolutions and then easily aggregated and linked across measurement types to support model-data integration. FRAMES is in early use by both data providers and users. Here in this article, we describe FRAMES, identify lessons learned, and discuss areas of future development.« less

A metadata reporting framework (FRAMES) for synthesis of ecohydrological observations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christianson, Danielle S.; Varadharajan, Charuleka; Christoffersen, Bradley

Metadata describe the ancillary information needed for data interpretation, comparison across heterogeneous datasets, and quality control and quality assessment (QA/QC). Metadata enable the synthesis of diverse ecohydrological and biogeochemical observations, an essential step in advancing a predictive understanding of earth systems. Environmental observations can be taken across a wide range of spatiotemporal scales in a variety of measurement settings and approaches, and saved in multiple formats. Thus, well-organized, consistent metadata are required to produce usable data products from diverse observations collected in disparate field sites. However, existing metadata reporting protocols do not support the complex data synthesis needs of interdisciplinarymore » earth system research. We developed a metadata reporting framework (FRAMES) to enable predictive understanding of carbon cycling in tropical forests under global change. FRAMES adheres to best practices for data and metadata organization, enabling consistent data reporting and thus compatibility with a variety of standardized data protocols. We used an iterative scientist-centered design process to develop FRAMES. The resulting modular organization streamlines metadata reporting and can be expanded to incorporate additional data types. The flexible data reporting format incorporates existing field practices to maximize data-entry efficiency. With FRAMES’s multi-scale measurement position hierarchy, data can be reported at observed spatial resolutions and then easily aggregated and linked across measurement types to support model-data integration. FRAMES is in early use by both data providers and users. Here in this article, we describe FRAMES, identify lessons learned, and discuss areas of future development.« less

Streamlining geospatial metadata in the Semantic Web

NASA Astrophysics Data System (ADS)

Fugazza, Cristiano; Pepe, Monica; Oggioni, Alessandro; Tagliolato, Paolo; Carrara, Paola

2016-04-01

In the geospatial realm, data annotation and discovery rely on a number of ad-hoc formats and protocols. These have been created to enable domain-specific use cases generalized search is not feasible for. Metadata are at the heart of the discovery process and nevertheless they are often neglected or encoded in formats that either are not aimed at efficient retrieval of resources or are plainly outdated. Particularly, the quantum leap represented by the Linked Open Data (LOD) movement did not induce so far a consistent, interlinked baseline in the geospatial domain. In a nutshell, datasets, scientific literature related to them, and ultimately the researchers behind these products are only loosely connected; the corresponding metadata intelligible only to humans, duplicated on different systems, seldom consistently. Instead, our workflow for metadata management envisages i) editing via customizable web- based forms, ii) encoding of records in any XML application profile, iii) translation into RDF (involving the semantic lift of metadata records), and finally iv) storage of the metadata as RDF and back-translation into the original XML format with added semantics-aware features. Phase iii) hinges on relating resource metadata to RDF data structures that represent keywords from code lists and controlled vocabularies, toponyms, researchers, institutes, and virtually any description one can retrieve (or directly publish) in the LOD Cloud. In the context of a distributed Spatial Data Infrastructure (SDI) built on free and open-source software, we detail phases iii) and iv) of our workflow for the semantics-aware management of geospatial metadata.

78 FR 67352 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-12

...-75-001. Applicants: Entergy Arkansas, Inc. Description: Metadata Correction--Sec. 1.01 Amendment to.... Description: Metadata Correction--Section 1.01 Amendment to be effective 12/31/9998. Filed Date: 10/25/13...: Entergy Louisiana, LLC. Description: Metadata Correction--Section 1.01 Amendment to be effective 12/31...

Organizing Scientific Data Sets: Studying Similarities and Differences in Metadata and Subject Term Creation

ERIC Educational Resources Information Center

White, Hollie C.

2012-01-01

Background: According to Salo (2010), the metadata entered into repositories are "disorganized" and metadata schemes underlying repositories are "arcane". This creates a challenging repository environment in regards to personal information management (PIM) and knowledge organization systems (KOSs). This dissertation research is…

International Metadata Initiatives: Lessons in Bibliographic Control.

ERIC Educational Resources Information Center

Caplan, Priscilla

This paper looks at a subset of metadata schemes, including the Text Encoding Initiative (TEI) header, the Encoded Archival Description (EAD), the Dublin Core Metadata Element Set (DCMES), and the Visual Resources Association (VRA) Core Categories for visual resources. It examines why they developed as they did, major point of difference from…

36 CFR 1235.48 - What documentation must agencies transfer with electronic records?

Code of Federal Regulations, 2010 CFR

2010-07-01

... digital geospatial data files can include metadata that conforms to the Federal Geographic Data Committee's Content Standards for Digital Geospatial Metadata, as specified in Executive Order 12906 of April... number (301) 837-2903 for digital photographs and metadata, or the National Archives and Records...

36 CFR 1235.48 - What documentation must agencies transfer with electronic records?

Code of Federal Regulations, 2012 CFR

2012-07-01

... digital geospatial data files can include metadata that conforms to the Federal Geographic Data Committee's Content Standards for Digital Geospatial Metadata, as specified in Executive Order 12906 of April... number (301) 837-2903 for digital photographs and metadata, or the National Archives and Records...

Leveraging Metadata to Create Better Web Services

ERIC Educational Resources Information Center

Mitchell, Erik

2012-01-01

Libraries have been increasingly concerned with data creation, management, and publication. This increase is partly driven by shifting metadata standards in libraries and partly by the growth of data and metadata repositories being managed by libraries. In order to manage these data sets, libraries are looking for new preservation and discovery…

36 CFR § 1235.48 - What documentation must agencies transfer with electronic records?

Code of Federal Regulations, 2013 CFR

2013-07-01

... digital geospatial data files can include metadata that conforms to the Federal Geographic Data Committee's Content Standards for Digital Geospatial Metadata, as specified in Executive Order 12906 of April... number (301) 837-2903 for digital photographs and metadata, or the National Archives and Records...

36 CFR 1235.48 - What documentation must agencies transfer with electronic records?

Code of Federal Regulations, 2011 CFR

2011-07-01

... digital geospatial data files can include metadata that conforms to the Federal Geographic Data Committee's Content Standards for Digital Geospatial Metadata, as specified in Executive Order 12906 of April... number (301) 837-2903 for digital photographs and metadata, or the National Archives and Records...

36 CFR 1235.48 - What documentation must agencies transfer with electronic records?

Code of Federal Regulations, 2014 CFR

2014-07-01

... digital geospatial data files can include metadata that conforms to the Federal Geographic Data Committee's Content Standards for Digital Geospatial Metadata, as specified in Executive Order 12906 of April... number (301) 837-2903 for digital photographs and metadata, or the National Archives and Records...

Shared Geospatial Metadata Repository for Ontario University Libraries: Collaborative Approaches

ERIC Educational Resources Information Center

Forward, Erin; Leahey, Amber; Trimble, Leanne

2015-01-01

Successfully providing access to special collections of digital geospatial data in academic libraries relies upon complete and accurate metadata. Creating and maintaining metadata using specialized standards is a formidable challenge for libraries. The Ontario Council of University Libraries' Scholars GeoPortal project, which created a shared…

106-17 Telemetry Standards Metadata Configuration Chapter 23

DTIC Science & Technology

2017-07-01

23-1 23.2 Metadata Description Language ...Chapter 23, July 2017 iii Acronyms HTML Hypertext Markup Language MDL Metadata Description Language PCM pulse code modulation TMATS Telemetry...Attributes Transfer Standard W3C World Wide Web Consortium XML eXtensible Markup Language XSD XML schema document Telemetry Network Standard

Digital Initiatives and Metadata Use in Thailand

ERIC Educational Resources Information Center

SuKantarat, Wichada

2008-01-01

Purpose: This paper aims to provide information about various digital initiatives in libraries in Thailand and especially use of Dublin Core metadata in cataloguing digitized objects in academic and government digital databases. Design/methodology/approach: The author began researching metadata use in Thailand in 2003 and 2004 while on sabbatical…

Normalized Metadata Generation for Human Retrieval Using Multiple Video Surveillance Cameras.

PubMed

Jung, Jaehoon; Yoon, Inhye; Lee, Seungwon; Paik, Joonki

2016-06-24

Since it is impossible for surveillance personnel to keep monitoring videos from a multiple camera-based surveillance system, an efficient technique is needed to help recognize important situations by retrieving the metadata of an object-of-interest. In a multiple camera-based surveillance system, an object detected in a camera has a different shape in another camera, which is a critical issue of wide-range, real-time surveillance systems. In order to address the problem, this paper presents an object retrieval method by extracting the normalized metadata of an object-of-interest from multiple, heterogeneous cameras. The proposed metadata generation algorithm consists of three steps: (i) generation of a three-dimensional (3D) human model; (ii) human object-based automatic scene calibration; and (iii) metadata generation. More specifically, an appropriately-generated 3D human model provides the foot-to-head direction information that is used as the input of the automatic calibration of each camera. The normalized object information is used to retrieve an object-of-interest in a wide-range, multiple-camera surveillance system in the form of metadata. Experimental results show that the 3D human model matches the ground truth, and automatic calibration-based normalization of metadata enables a successful retrieval and tracking of a human object in the multiple-camera video surveillance system.

Normalized Metadata Generation for Human Retrieval Using Multiple Video Surveillance Cameras

PubMed Central

Jung, Jaehoon; Yoon, Inhye; Lee, Seungwon; Paik, Joonki

2016-01-01

Since it is impossible for surveillance personnel to keep monitoring videos from a multiple camera-based surveillance system, an efficient technique is needed to help recognize important situations by retrieving the metadata of an object-of-interest. In a multiple camera-based surveillance system, an object detected in a camera has a different shape in another camera, which is a critical issue of wide-range, real-time surveillance systems. In order to address the problem, this paper presents an object retrieval method by extracting the normalized metadata of an object-of-interest from multiple, heterogeneous cameras. The proposed metadata generation algorithm consists of three steps: (i) generation of a three-dimensional (3D) human model; (ii) human object-based automatic scene calibration; and (iii) metadata generation. More specifically, an appropriately-generated 3D human model provides the foot-to-head direction information that is used as the input of the automatic calibration of each camera. The normalized object information is used to retrieve an object-of-interest in a wide-range, multiple-camera surveillance system in the form of metadata. Experimental results show that the 3D human model matches the ground truth, and automatic calibration-based normalization of metadata enables a successful retrieval and tracking of a human object in the multiple-camera video surveillance system. PMID:27347961

Evaluating and Improving Metadata for Data Use and Understanding

NASA Astrophysics Data System (ADS)

Habermann, T.

2013-12-01

The last several decades have seen an extraordinary increase in the number and breadth of environmental data available to the scientific community and the general public. These increases have focused the environmental data community on creating metadata for discovering data and on the creation and population of catalogs and portals for facilitating discovery. This focus is reflected in the fields required by commonly used metadata standards and has resulted in collections populated with metadata that meet, but don't go far beyond, minimal discovery requirements. Discovery is the first step towards addressing scientific questions using data. As more data are discovered and accessed, users need metadata that 1) automates use and integration of these data in tools and 2) facilitates understanding the data when it is compared to similar datasets or as internal variations are observed. When data discovery is the primary goal, it is important to create records for as many datasets as possible. The content of these records is controlled by minimum requirements, and evaluation is generally limited to testing for required fields and counting records. As the use and understanding needs become more important, more comprehensive evaluation tools are needed. An approach is described for evaluating existing metadata in the light of these new requirements and for improving the metadata to meet them.

Collaborative Sharing of Multidimensional Space-time Data Using HydroShare

NASA Astrophysics Data System (ADS)

Gan, T.; Tarboton, D. G.; Horsburgh, J. S.; Dash, P. K.; Idaszak, R.; Yi, H.; Blanton, B.

2015-12-01

HydroShare is a collaborative environment being developed for sharing hydrological data and models. It includes capability to upload data in many formats as resources that can be shared. The HydroShare data model for resources uses a specific format for the representation of each type of data and specifies metadata common to all resource types as well as metadata unique to specific resource types. The Network Common Data Form (NetCDF) was chosen as the format for multidimensional space-time data in HydroShare. NetCDF is widely used in hydrological and other geoscience modeling because it contains self-describing metadata and supports the creation of array-oriented datasets that may include three spatial dimensions, a time dimension and other user defined dimensions. For example, NetCDF may be used to represent precipitation or surface air temperature fields that have two dimensions in space and one dimension in time. This presentation will illustrate how NetCDF files are used in HydroShare. When a NetCDF file is loaded into HydroShare, header information is extracted using the "ncdump" utility. Python functions developed for the Django web framework on which HydroShare is based, extract science metadata present in the NetCDF file, saving the user from having to enter it. Where the file follows Climate Forecast (CF) convention and Attribute Convention for Dataset Discovery (ACDD) standards, metadata is thus automatically populated. Users also have the ability to add metadata to the resource that may not have been present in the original NetCDF file. HydroShare's metadata editing functionality then writes this science metadata back into the NetCDF file to maintain consistency between the science metadata in HydroShare and the metadata in the NetCDF file. This further helps researchers easily add metadata information following the CF and ACDD conventions. Additional data inspection and subsetting functions were developed, taking advantage of Python and command line libraries for working with NetCDF files. We describe the design and implementation of these features and illustrate how NetCDF files from a modeling application may be curated in HydroShare and thus enhance reproducibility of the associated research. We also discuss future development planned for multidimensional space-time data in HydroShare.

EUDAT B2FIND : A Cross-Discipline Metadata Service and Discovery Portal

NASA Astrophysics Data System (ADS)

Widmann, Heinrich; Thiemann, Hannes

2016-04-01

The European Data Infrastructure (EUDAT) project aims at a pan-European environment that supports a variety of multiple research communities and individuals to manage the rising tide of scientific data by advanced data management technologies. This led to the establishment of the community-driven Collaborative Data Infrastructure that implements common data services and storage resources to tackle the basic requirements and the specific challenges of international and interdisciplinary research data management. The metadata service B2FIND plays a central role in this context by providing a simple and user-friendly discovery portal to find research data collections stored in EUDAT data centers or in other repositories. For this we store the diverse metadata collected from heterogeneous sources in a comprehensive joint metadata catalogue and make them searchable in an open data portal. The implemented metadata ingestion workflow consists of three steps. First the metadata records - provided either by various research communities or via other EUDAT services - are harvested. Afterwards the raw metadata records are converted and mapped to unified key-value dictionaries as specified by the B2FIND schema. The semantic mapping of the non-uniform, community specific metadata to homogenous structured datasets is hereby the most subtle and challenging task. To assure and improve the quality of the metadata this mapping process is accompanied by • iterative and intense exchange with the community representatives, • usage of controlled vocabularies and community specific ontologies and • formal and semantic validation. Finally the mapped and checked records are uploaded as datasets to the catalogue, which is based on the open source data portal software CKAN. CKAN provides a rich RESTful JSON API and uses SOLR for dataset indexing that enables users to query and search in the catalogue. The homogenization of the community specific data models and vocabularies enables not only the unique presentation of these datasets as tables of field-value pairs but also the faceted, spatial and temporal search in the B2FIND metadata portal. Furthermore the service provides transparent access to the scientific data objects through the given references and identifiers in the metadata. B2FIND offers support for new communities interested in publishing their data within EUDAT. We present here the functionality and the features of the B2FIND service and give an outlook of further developments as interfaces to external libraries and use of Linked Data.

Keeping Research Data from the Continental Deep Drilling Programme (KTB) Accessible and Taking First Steps Towards Digital Preservation

NASA Astrophysics Data System (ADS)

Klump, J. F.; Ulbricht, D.; Conze, R.

2014-12-01

The Continental Deep Drilling Programme (KTB) was a scientific drilling project from 1987 to 1995 near Windischeschenbach, Bavaria. The main super-deep borehole reached a depth of 9,101 meters into the Earth's continental crust. The project used the most current equipment for data capture and processing. After the end of the project key data were disseminated through the web portal of the International Continental Scientific Drilling Program (ICDP). The scientific reports were published as printed volumes. As similar projects have also experienced, it becomes increasingly difficult to maintain a data portal over a long time. Changes in software and underlying hardware make a migration of the entire system inevitable. Around 2009 the data presented on the ICDP web portal were migrated to the Scientific Drilling Database (SDDB) and published through DataCite using Digital Object Identifiers (DOI) as persistent identifiers. The SDDB portal used a relational database with a complex data model to store data and metadata. A PHP-based Content Management System with custom modifications made it possible to navigate and browse datasets using the metadata and then download datasets. The data repository software eSciDoc allows storing self-contained packages consistent with the OAIS reference model. Each package consists of binary data files and XML-metadata. Using a REST-API the packages can be stored in the eSciDoc repository and can be searched using the XML-metadata. During the last maintenance cycle of the SDDB the data and metadata were migrated into the eSciDoc repository. Discovery metadata was generated following the GCMD-DIF, ISO19115 and DataCite schemas. The eSciDoc repository allows to store an arbitrary number of XML-metadata records with each data object. In addition to descriptive metadata each data object may contain pointers to related materials, such as IGSN-metadata to link datasets to physical specimens, or identifiers of literature interpreting the data. Datasets are presented by XSLT-stylesheet transformation using the stored metadata. The presentation shows several migration cycles of data and metadata, which were driven by aging software systems. Currently the datasets reside as self-contained entities in a repository system that is ready for digital preservation.

GNU Radio Sandia Utilities v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilbert, Jacob; Knee, Peter

This software adds a data handling module to the GNU Radio (GR) software defined radio (SDR) framework as well as some general-purpose function blocks (filters, metadata control, etc). This software is useful for processing bursty RF transmissions with GR, and serves as a base for applying SDR signal processing techniques to a whole burst of data at a time, as opposed to streaming data which GR has been primarily focused around.

76 FR 10628 - Self-Regulatory Organizations; the Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Change Regarding Providing Participants With a New Optional Settlement Web Interface February 22, 2011... Rule Change The proposed rule change will establish a new browser-based interface, the ``Settlement Web... Browser System (``PBS'').\\4\\ Based on request from its Participants, DTC has created a more user-friendly...

On the Nets. Comparing Web Browsers: Mosaic, Cello, Netscape, WinWeb and InternetWorks Life.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

World Wide Web browsers are compared by speed, setup, hypertext transport protocol (HTTP) handling, management of file transfer protocol (FTP), telnet, gopher, and wide area information server (WAIS); bookmark options; and communication functions. Netscape has the most features, the fastest retrieval, sophisticated bookmark capabilities. (JMV)

Baby Steps: Starting Out on the World Wide Web.

ERIC Educational Resources Information Center

Simpson, Carol; McElmeel, Sharron L.

1997-01-01

While the Internet is the physical medium used to transport data, the World Wide Web is the collection of protocols and standards used to access the information. This article provides a basic explanation of what the Web is and describes common browser commands. Discusses graphic Web browsers; universal resource locators (URLs); file, message,…

The ranking algorithm of the Coach browser for the UMLS metathesaurus.

PubMed Central

Harbourt, A. M.; Syed, E. J.; Hole, W. T.; Kingsland, L. C.

1993-01-01

This paper presents the novel ranking algorithm of the Coach Metathesaurus browser which is a major module of the Coach expert search refinement program. An example shows how the ranking algorithm can assist in creating a list of candidate terms useful in augmenting a suboptimal Grateful Med search of MEDLINE. PMID:8130570

World-Wide Web: Adding Multimedia to Cyberspace.

ERIC Educational Resources Information Center

Descy, Don E.

1994-01-01

Describes the World-Wide Web (WWW), a network information resource based on hypertext. How to access WWW browsers through remote login (telnet) or though free browser software, such as Mosaic, is provided. Eight information sources that can be accessed through the WWW are listed. The address of a listserv reporting on Internet developments is…

Visits, Hits, Caching and Counting on the World Wide Web: Old Wine in New Bottles?

ERIC Educational Resources Information Center

Berthon, Pierre; Pitt, Leyland; Prendergast, Gerard

1997-01-01

Although web browser caching speeds up retrieval, reduces network traffic, and decreases the load on servers and browser's computers, an unintended consequence for marketing research is that Web servers undercount hits. This article explores counting problems, caching, proxy servers, trawler software and presents a series of correction factors…

Decoding Technology: Web Browsers

ERIC Educational Resources Information Center

Walker, Tim; Donohue, Chip

2007-01-01

More than ever, early childhood administrators are relying on the Internet for information. A key to becoming an exceptional Web "surfer" is getting to know the ins and outs of the Web browser being used. There are several options available, and almost all can be downloaded for free. However, many of the functions and features they offer are very…

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software

PubMed Central

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong

2017-01-01

Abstract Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. PMID:28327936

STAR: an integrated solution to management and visualization of sequencing data.

PubMed

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei

2013-12-15

Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

GWIPS-viz: development of a ribo-seq genome browser

PubMed Central

Michel, Audrey M.; Fox, Gearoid; M. Kiran, Anmol; De Bo, Christof; O’Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.

2014-01-01

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing. PMID:24185699

Multi-Sector Sustainability Browser (MSSB) User Manual: A ...

EPA Pesticide Factsheets

EPA’s Sustainable and Healthy Communities (SHC) Research Program is developing methodologies, resources, and tools to assist community members and local decision makers in implementing policy choices that facilitate sustainable approaches in managing their resources affecting the built environment, natural environment, and human health. In order to assist communities and decision makers in implementing sustainable practices, EPA is developing computer-based systems including models, databases, web tools, and web browsers to help communities decide upon approaches that support their desired outcomes. Communities need access to resources that will allow them to achieve their sustainability objectives through intelligent decisions in four key sustainability areas: • Land Use • Buildings and Infrastructure • Transportation • Materials Management (i.e., Municipal Solid Waste [MSW] processing and disposal) The Multi-Sector Sustainability Browser (MSSB) is designed to support sustainable decision-making for communities, local and regional planners, and policy and decision makers. Document is an EPA Technical Report, which is the user manual for the Multi-Sector Sustainability Browser (MSSB) tool. The purpose of the document is to provide basic guidance on use of the tool for users

Winning by a neck: tall giraffes avoid competing with shorter browsers.

PubMed

Cameron, Elissa Z; du Toit, Johan T

2007-01-01

With their vertically elongated body form, giraffes generally feed above the level of other browsers within the savanna browsing guild, despite having access to foliage at lower levels. They ingest more leaf mass per bite when foraging high in the tree, perhaps because smaller, more selective browsers deplete shoots at lower levels or because trees differentially allocate resources to promote shoot growth in the upper canopy. We erected exclosures around individual Acacia nigrescens trees in the greater Kruger ecosystem, South Africa. After a complete growing season, we found no differences in leaf biomass per shoot across height zones in excluded trees but significant differences in control trees. We conclude that giraffes preferentially browse at high levels in the canopy to avoid competition with smaller browsers. Our findings are analogous with those from studies of grazing guilds and demonstrate that resource partitioning can be driven by competition when smaller foragers displace larger foragers from shared resources. This provides the first experimental support for the classic evolutionary hypothesis that vertical elongation of the giraffe body is an outcome of competition within the browsing ungulate guild.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2002-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth s radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth s Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2005-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth's radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth's Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

The UCSC Genome Browser database: extensions and updates 2013.

PubMed

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Raney, Brian J; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Lee, Brian T; Learned, Katrina; Kirkup, Vanessa; Hsu, Fan; Heitner, Steve; Harte, Rachel A; Haeussler, Maximilian; Guruvadoo, Luvina; Goldman, Mary; Giardine, Belinda M; Fujita, Pauline A; Dreszer, Timothy R; Diekhans, Mark; Cline, Melissa S; Clawson, Hiram; Barber, Galt P; Haussler, David; Kent, W James

2013-01-01

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

PubMed

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2017-04-01

Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line-based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. © The Authors 2017. Published by Oxford University Press.

Seeking the Path to Metadata Nirvana

NASA Astrophysics Data System (ADS)

Graybeal, J.

2008-12-01

Scientists have always found reusing other scientists' data challenging. Computers did not fundamentally change the problem, but enabled more and larger instances of it. In fact, by removing human mediation and time delays from the data sharing process, computers emphasize the contextual information that must be exchanged in order to exchange and reuse data. This requirement for contextual information has two faces: "interoperability" when talking about systems, and "the metadata problem" when talking about data. As much as any single organization, the Marine Metadata Interoperability (MMI) project has been tagged with the mission "Solve the metadata problem." Of course, if that goal is achieved, then sustained, interoperable data systems for interdisciplinary observing networks can be easily built -- pesky metadata differences, like which protocol to use for data exchange, or what the data actually measures, will be a thing of the past. Alas, as you might imagine, there will always be complexities and incompatibilities that are not addressed, and data systems that are not interoperable, even within a science discipline. So should we throw up our hands and surrender to the inevitable? Not at all. Rather, we try to minimize metadata problems as much as we can. In this we increasingly progress, despite natural forces that pull in the other direction. Computer systems let us work with more complexity, build community knowledge and collaborations, and preserve and publish our progress and (dis-)agreements. Funding organizations, science communities, and technologists see the importance interoperable systems and metadata, and direct resources toward them. With the new approaches and resources, projects like IPY and MMI can simultaneously define, display, and promote effective strategies for sustainable, interoperable data systems. This presentation will outline the role metadata plays in durable interoperable data systems, for better or worse. It will describe times when "just choosing a standard" can work, and when it probably won't work. And it will point out signs that suggest a metadata storm is coming to your community project, and how you might avoid it. From these lessons we will seek a path to producing interoperable, interdisciplinary, metadata-enlightened environment observing systems.

A browser-based event display for the CMS Experiment at the LHC using WebGL

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

Modern web browsers are powerful and sophisticated applications that support an ever-wider range of uses. One such use is rendering high-quality, GPU-accelerated, interactive 2D and 3D graphics in an HTML canvas. This can be done via WebGL, a JavaScript API based on OpenGL ES. Applications delivered via the browser have several distinct benefits for the developer and user. For example, they can be implemented using well-known and well-developed technologies, while distribution and use via a browser allows for rapid prototyping and deployment and ease of installation. In addition, delivery of applications via the browser allows for easy use on mobile, touch-enabled devices such as phones and tablets. iSpy WebGL is an application for visualization of events detected and reconstructed by the CMS Experiment at the Large Hadron Collider at CERN. The first event display developed for an LHC experiment to use WebGL, iSpy WebGL is a client-side application written in JavaScript, HTML, and CSS and uses the WebGL API three.js. iSpy WebGL is used for monitoring of CMS detector performance, for production of images and animations of CMS collisions events for the public, as a virtual reality application using Google Cardboard, and asa tool available for public education and outreach such as in the CERN Open Data Portal and the CMS masterclasses. We describe here its design, development, and usage as well as future plans.

Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies.

PubMed

Sharma, Deepak K; Solbrig, Harold R; Tao, Cui; Weng, Chunhua; Chute, Christopher G; Jiang, Guoqian

2017-06-05

Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains. We leveraged a Semantic Web-based metadata repository enhanced with both ISO11179 metadata standard and Clinical Information Modeling Initiative (CIMI) Reference Model. We used the common data elements (CDEs) defined in The Cancer Genome Atlas (TCGA) data dictionary, and extracted the metadata of the CDEs using the NCI Cancer Data Standards Repository (caDSR) CDE dataset rendered in the Resource Description Framework (RDF). The ITEM/ITEM_GROUP pattern defined in the latest CIMI Reference Model is used to represent reusable model elements (mini-Archetypes). We produced a metadata repository with 38 clinical cancer genome study domains, comprising a rich collection of mini-Archetype pattern instances. We performed a case study of the domain "clinical pharmaceutical" in the TCGA data dictionary and demonstrated enriched data elements in the metadata repository are very useful in support of building detailed clinical models. Our informatics approach leveraging Semantic Web technologies provides an effective way to build a CIMI-compliant metadata repository that would facilitate the detailed clinical modeling to support use cases beyond TCGA in clinical cancer study domains.

Incorporating clinical metadata with digital image features for automated identification of cutaneous melanoma.

PubMed

Liu, Z; Sun, J; Smith, M; Smith, L; Warr, R

2013-11-01

Computer-assisted diagnosis (CAD) of malignant melanoma (MM) has been advocated to help clinicians to achieve a more objective and reliable assessment. However, conventional CAD systems examine only the features extracted from digital photographs of lesions. Failure to incorporate patients' personal information constrains the applicability in clinical settings. To develop a new CAD system to improve the performance of automatic diagnosis of melanoma, which, for the first time, incorporates digital features of lesions with important patient metadata into a learning process. Thirty-two features were extracted from digital photographs to characterize skin lesions. Patients' personal information, such as age, gender and, lesion site, and their combinations, was quantified as metadata. The integration of digital features and metadata was realized through an extended Laplacian eigenmap, a dimensionality-reduction method grouping lesions with similar digital features and metadata into the same classes. The diagnosis reached 82.1% sensitivity and 86.1% specificity when only multidimensional digital features were used, but improved to 95.2% sensitivity and 91.0% specificity after metadata were incorporated appropriately. The proposed system achieves a level of sensitivity comparable with experienced dermatologists aided by conventional dermoscopes. This demonstrates the potential of our method for assisting clinicians in diagnosing melanoma, and the benefit it could provide to patients and hospitals by greatly reducing unnecessary excisions of benign naevi. This paper proposes an enhanced CAD system incorporating clinical metadata into the learning process for automatic classification of melanoma. Results demonstrate that the additional metadata and the mechanism to incorporate them are useful for improving CAD of melanoma. © 2013 British Association of Dermatologists.

SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript.

PubMed

Bakhtiari, M

2012-06-01

Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems. The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation. The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers. HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox). © 2012 American Association of Physicists in Medicine.

System for Earth Sample Registration SESAR: Services for IGSN Registration and Sample Metadata Management

NASA Astrophysics Data System (ADS)

Chan, S.; Lehnert, K. A.; Coleman, R. J.

2011-12-01

SESAR, the System for Earth Sample Registration, is an online registry for physical samples collected for Earth and environmental studies. SESAR generates and administers the International Geo Sample Number IGSN, a unique identifier for samples that is dramatically advancing interoperability amongst information systems for sample-based data. SESAR was developed to provide the complete range of registry services, including definition of IGSN syntax and metadata profiles, registration and validation of name spaces requested by users, tools for users to submit and manage sample metadata, validation of submitted metadata, generation and validation of the unique identifiers, archiving of sample metadata, and public or private access to the sample metadata catalog. With the development of SESAR v3, we placed particular emphasis on creating enhanced tools that make metadata submission easier and more efficient for users, and that provide superior functionality for users to manage metadata of their samples in their private workspace MySESAR. For example, SESAR v3 includes a module where users can generate custom spreadsheet templates to enter metadata for their samples, then upload these templates online for sample registration. Once the content of the template is uploaded, it is displayed online in an editable grid format. Validation rules are executed in real-time on the grid data to ensure data integrity. Other new features of SESAR v3 include the capability to transfer ownership of samples to other SESAR users, the ability to upload and store images and other files in a sample metadata profile, and the tracking of changes to sample metadata profiles. In the next version of SESAR (v3.5), we will further improve the discovery, sharing, registration of samples. For example, we are developing a more comprehensive suite of web services that will allow discovery and registration access to SESAR from external systems. Both batch and individual registrations will be possible through web services. Based on valuable feedback from the user community, we will introduce enhancements that add greater flexibility to the system to accommodate the vast diversity of metadata that users want to store. Users will be able to create custom metadata fields and use these for the samples they register. Users will also be able to group samples into 'collections' to make retrieval for research projects or publications easier. An improved interface design will allow for better workflow transition and navigation throughout the application. In keeping up with the demands of a growing community, SESAR has also made process changes to ensure efficiency in system development. For example, we have implemented a release cycle to better track enhancements and fixes to the system, and an API library that facilitates reusability of code. Usage tracking, metrics and surveys capture information to guide the direction of future developments. A new set of administrative tools allows greater control of system management.

77 FR 33739 - Announcement of Requirements and Registration for “Health Data Platform Metadata Challenge”

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-07

... Information Technology. SUMMARY: As part of the HHS Open Government Plan, the HealthData.gov Platform (HDP) is... application of existing voluntary consensus standards for metadata common to all open government data, and... vocabulary recommendations for Linked Data publishers, defining cross domain semantic metadata of open...

Inferring Metadata for a Semantic Web Peer-to-Peer Environment

ERIC Educational Resources Information Center

Brase, Jan; Painter, Mark

2004-01-01

Learning Objects Metadata (LOM) aims at describing educational resources in order to allow better reusability and retrieval. In this article we show how additional inference rules allows us to derive additional metadata from existing ones. Additionally, using these rules as integrity constraints helps us to define the constraints on LOM elements,…