A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

Chesapeake Bay Program Water Quality Database

EPA Pesticide Factsheets

The Chesapeake Information Management System (CIMS), designed in 1996, is an integrated, accessible information management system for the Chesapeake Bay Region. CIMS is an organized, distributed library of information and software tools designed to increase basin-wide public access to Chesapeake Bay information. The information delivered by CIMS includes technical and public information, educational material, environmental indicators, policy documents, and scientific data. Through the use of relational databases, web-based programming, and web-based GIS a large number of Internet resources have been established. These resources include multiple distributed on-line databases, on-demand graphing and mapping of environmental data, and geographic searching tools for environmental information. Baseline monitoring data, summarized data and environmental indicators that document ecosystem status and trends, confirm linkages between water quality, habitat quality and abundance, and the distribution and integrity of biological populations are also available. One of the major features of the CIMS network is the Chesapeake Bay Program's Data Hub, providing users access to a suite of long- term water quality and living resources databases. Chesapeake Bay mainstem and tidal tributary water quality, benthic macroinvertebrates, toxics, plankton, and fluorescence data can be obtained for a network of over 800 monitoring stations.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

PubMed

Weirick, Tyler; John, David; Uchida, Shizuka

2017-03-01

Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' sequence from one reference annotation could be annotated in another. Furthermore, relationships to nearby or overlapping annotated transcripts are even more complicated when using different genome assemblies. To better understand these problems, we surveyed current and previous versions of genomic assemblies and annotations across a number of public databases containing long noncoding RNA. We identified numerous discrepancies of transcripts regarding their genomic locations, transcript lengths and identifiers. Further investigation showed that the positional differences between reference annotations of essentially the same transcript could lead to differences in its measured expression at the RNA level. To aid in resolving these problems, we present the algorithm 'Universal Genomic Accession Hash (UGAHash)' and created an open source web tool to encourage the usage of the UGAHash algorithm. The UGAHash web tool (http://ugahash.uni-frankfurt.de) can be accessed freely without registration. The web tool allows researchers to generate Universal Genomic Accessions for genomic features or to explore annotations deposited in the public databases of the past and present versions. We anticipate that the UGAHash web tool will be a valuable tool to check for the existence of transcripts before judging the newly discovered transcripts as novel. © The Author 2016. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

A Web-Based Database for Nurse Led Outreach Teams (NLOT) in Toronto.

PubMed

Li, Shirley; Kuo, Mu-Hsing; Ryan, David

2016-01-01

A web-based system can provide access to real-time data and information. Healthcare is moving towards digitizing patients' medical information and securely exchanging it through web-based systems. In one of Ontario's health regions, Nurse Led Outreach Teams (NLOT) provide emergency mobile nursing services to help reduce unnecessary transfers from long-term care homes to emergency departments. Currently the NLOT team uses a Microsoft Access database to keep track of the health information on the residents that they serve. The Access database lacks scalability, portability, and interoperability. The objective of this study is the development of a web-based database using Oracle Application Express that is easily accessible from mobile devices. The web-based database will allow NLOT nurses to enter and access resident information anytime and from anywhere.

WheatGenome.info: an integrated database and portal for wheat genome information.

PubMed

Lai, Kaitao; Berkman, Paul J; Lorenc, Michal Tadeusz; Duran, Chris; Smits, Lars; Manoli, Sahana; Stiller, Jiri; Edwards, David

2012-02-01

Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

Lynx: a database and knowledge extraction engine for integrative medicine.

PubMed

Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T Conrad; Maltsev, Natalia

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)--a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces.

Web Based Data Access to the World Data Center for Climate

NASA Astrophysics Data System (ADS)

Toussaint, F.; Lautenschlager, M.

2006-12-01

The World Data Center for Climate (WDC-Climate, www.wdc-climate.de) is hosted by the Model &Data Group (M&D) of the Max Planck Institute for Meteorology. The M&D department is financed by the German government and uses the computers and mass storage facilities of the German Climate Computing Centre (Deutsches Klimarechenzentrum, DKRZ). The WDC-Climate provides web access to 200 Terabytes of climate data; the total mass storage archive contains nearly 4 Petabytes. Although the majority of the datasets concern model output data, some satellite and observational data are accessible as well. The underlying relational database is distributed on five servers. The CERA relational data model is used to integrate catalogue data and mass data. The flexibility of the model allows to store and access very different types of data and metadata. The CERA metadata catalogue provides easy access to the content of the CERA database as well as to other data in the web. Visit ceramodel.wdc-climate.de for additional information on the CERA data model. The majority of the users access data via the CERA metadata catalogue, which is open without registration. However, prior to retrieving data user are required to check in and apply for a userid and password. The CERA metadata catalogue is servlet based. So it is accessible worldwide through any web browser at cera.wdc-climate.de. In addition to data and metadata access by the web catalogue, WDC-Climate offers a number of other forms of web based data access. All metadata are available via http request as xml files in various metadata formats (ISO, DC, etc., see wini.wdc-climate.de) which allows for easy data interchange with other catalogues. Model data can be retrieved in GRIB, ASCII, NetCDF, and binary (IEEE) format. WDC-Climate serves as data centre for various projects. Since xml files are accessible by http, the integration of data into applications of different projects is very easy. Projects supported by WDC-Climate are e.g. CEOP, IPCC, and CARIBIC. A script tool for data download (jblob) is offered on the web page, to make retrieval of huge data quantities more comfortable.

Analysis Tool Web Services from the EMBL-EBI.

PubMed

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-07-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.

Analysis Tool Web Services from the EMBL-EBI

PubMed Central

McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Cowley, Andrew Peter; Lopez, Rodrigo

2013-01-01

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods. PMID:23671338

Designing a data portal for synthesis modeling

NASA Astrophysics Data System (ADS)

Holmes, M. A.

2006-12-01

Processing of field and model data in multi-disciplinary integrated science studies is a vital part of synthesis modeling. Collection and storage techniques for field data vary greatly between the participating scientific disciplines due to the nature of the data being collected, whether it be in situ, remotely sensed, or recorded by automated data logging equipment. Spreadsheets, personal databases, text files and binary files are used in the initial storage and processing of the raw data. In order to be useful to scientists, engineers and modelers the data need to be stored in a format that is easily identifiable, accessible and transparent to a variety of computing environments. The Model Operations and Synthesis (MOAS) database and associated web portal were created to provide such capabilities. The industry standard relational database is comprised of spatial and temporal data tables, shape files and supporting metadata accessible over the network, through a menu driven web-based portal or spatially accessible through ArcSDE connections from the user's local GIS desktop software. A separate server provides public access to spatial data and model output in the form of attributed shape files through an ArcIMS web-based graphical user interface.

Bringing it all together: A Web-based Database for Chemical and Biological Data to Support Environmental Toxicology (ACS Fall meeting 8 of 12)

EPA Science Inventory

The EPA Comptox Chemistry Dashboard is a web-based application providing access to a set of data resources provided by the National Center of Computational Toxicology. Sitting on a foundation of chemistry data for ~750,000 chemical substances the application integrates bioassay s...

Optimizing Libraries’ Content Findability Using Simple Object Access Protocol (SOAP) With Multi-Tier Architecture

NASA Astrophysics Data System (ADS)

Lahinta, A.; Haris, I.; Abdillah, T.

2017-03-01

The aim of this paper is to describe a developed application of Simple Object Access Protocol (SOAP) as a model for improving libraries’ digital content findability on the library web. The study applies XML text-based protocol tools in the collection of data about libraries’ visibility performance in the search results of the book. Model from the integrated Web Service Document Language (WSDL) and Universal Description, Discovery and Integration (UDDI) are applied to analyse SOAP as element within the system. The results showed that the developed application of SOAP with multi-tier architecture can help people simply access the website in the library server Gorontalo Province and support access to digital collections, subscription databases, and library catalogs in each library in Regency or City in Gorontalo Province.

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.

VaProS: a database-integration approach for protein/genome information retrieval.

PubMed

Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

2016-12-01

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts' knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/ .

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

PubMed

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Gelpí, Josep Lluís

2012-05-01

MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb). http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

Lynx: a database and knowledge extraction engine for integrative medicine

PubMed Central

Sulakhe, Dinanath; Balasubramanian, Sandhya; Xie, Bingqing; Feng, Bo; Taylor, Andrew; Wang, Sheng; Berrocal, Eduardo; Dave, Utpal; Xu, Jinbo; Börnigen, Daniela; Gilliam, T. Conrad; Maltsev, Natalia

2014-01-01

We have developed Lynx (http://lynx.ci.uchicago.edu)—a web-based database and a knowledge extraction engine, supporting annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Its underlying knowledge base (LynxKB) integrates various classes of information from >35 public databases and private collections, as well as manually curated data from our group and collaborators. Lynx provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization to assist the user in extracting meaningful knowledge from LynxKB and experimental data, whereas its service-oriented architecture provides public access to LynxKB and its analytical tools via user-friendly web services and interfaces. PMID:24270788

Casimage project: a digital teaching files authoring environment.

PubMed

Rosset, Antoine; Muller, Henning; Martins, Martina; Dfouni, Natalia; Vallée, Jean-Paul; Ratib, Osman

2004-04-01

The goal of the Casimage project is to offer an authoring and editing environment integrated with the Picture Archiving and Communication Systems (PACS) for creating image-based electronic teaching files. This software is based on a client/server architecture allowing remote access of users to a central database. This authoring environment allows radiologists to create reference databases and collection of digital images for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The environment includes all tools to create teaching files, including textual description, annotations, and image manipulation. The software also allows users to generate stand-alone CD-ROMs and web-based teaching files to easily share their collections. The system includes a web server compatible with the Medical Imaging Resource Center standard (MIRC, http://mirc.rsna.org) to easily integrate collections in the RSNA web network dedicated to teaching files. This software could be installed on any PACS workstation to allow users to add new cases at any time and anywhere during clinical operations. Several images collections were created with this tool, including thoracic imaging that was subsequently made available on a CD-Rom and on our web site and through the MIRC network for public access.

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

Hermes, the Information Messenger, Integrating Information Services and Delivering Them to the End User.

ERIC Educational Resources Information Center

Coello-Coutino, Gerardo; Ainsworth, Shirley; Escalante-Gonzalbo, Ana Marie

2002-01-01

Describes Hermes, a research tool that uses specially designed acquisition, parsing and presentation methods to integrate information resources on the Internet, from searching in disparate bibliographic databases, to accessing full text articles online, and developing a web of information associated with each reference via one common interface.…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Enhancing UCSF Chimera through web services

PubMed Central

Huang, Conrad C.; Meng, Elaine C.; Morris, John H.; Pettersen, Eric F.; Ferrin, Thomas E.

2014-01-01

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. PMID:24861624

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

A service-based framework for pharmacogenomics data integration

NASA Astrophysics Data System (ADS)

Wang, Kun; Bai, Xiaoying; Li, Jing; Ding, Cong

2010-08-01

Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

IntegratedMap: a Web interface for integrating genetic map data.

PubMed

Yang, Hongyu; Wang, Hongyu; Gingle, Alan R

2005-05-01

IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources. IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp

G6PDdb, an integrated database of glucose-6-phosphate dehydrogenase (G6PD) mutations.

PubMed

Kwok, Colin J; Martin, Andrew C R; Au, Shannon W N; Lam, Veronica M S

2002-03-01

G6PDdb (http://www.rubic.rdg.ac.uk/g6pd/ or http://www.bioinf.org.uk/g6pd/) is a newly created web-accessible locus-specific mutation database for the human Glucose-6-phosphate dehydrogenase (G6PD) gene. The relational database integrates up-to-date mutational and structural data from various databanks (GenBank, Protein Data Bank, etc.) with biochemically characterized variants and their associated phenotypes obtained from published literature and the Favism website. An automated analysis of the mutations likely to have a significant impact on the structure of the protein has been performed using a recently developed procedure. The database may be queried online and the full results of the analysis of the structural impact of mutations are available. The web page provides a form for submitting additional mutation data and is linked to resources such as the Favism website, OMIM, HGMD, HGVBASE, and the PDB. This database provides insights into the molecular aspects and clinical significance of G6PD deficiency for researchers and clinicians and the web page functions as a knowledge base relevant to the understanding of G6PD deficiency and its management. Copyright 2002 Wiley-Liss, Inc.

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

SIDECACHE: Information access, management and dissemination framework for web services.

PubMed

Doderer, Mark S; Burkhardt, Cory; Robbins, Kay A

2011-06-14

Many bioinformatics algorithms and data sets are deployed using web services so that the results can be explored via the Internet and easily integrated into other tools and services. These services often include data from other sites that is accessed either dynamically or through file downloads. Developers of these services face several problems because of the dynamic nature of the information from the upstream services. Many publicly available repositories of bioinformatics data frequently update their information. When such an update occurs, the developers of the downstream service may also need to update. For file downloads, this process is typically performed manually followed by web service restart. Requests for information obtained by dynamic access of upstream sources is sometimes subject to rate restrictions. SideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating. We have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.

Storage and distribution of pathology digital images using integrated web-based viewing systems.

PubMed

Marchevsky, Alberto M; Dulbandzhyan, Ronda; Seely, Kevin; Carey, Steve; Duncan, Raymond G

2002-05-01

Health care providers have expressed increasing interest in incorporating digital images of gross pathology specimens and photomicrographs in routine pathology reports. To describe the multiple technical and logistical challenges involved in the integration of the various components needed for the development of a system for integrated Web-based viewing, storage, and distribution of digital images in a large health system. An Oracle version 8.1.6 database was developed to store, index, and deploy pathology digital photographs via our Intranet. The database allows for retrieval of images by patient demographics or by SNOMED code information. The Intranet of a large health system accessible from multiple computers located within the medical center and at distant private physician offices. The images can be viewed using any of the workstations of the health system that have authorized access to our Intranet, using a standard browser or a browser configured with an external viewer or inexpensive plug-in software, such as Prizm 2.0. The images can be printed on paper or transferred to film using a digital film recorder. Digital images can also be displayed at pathology conferences by using wireless local area network (LAN) and secure remote technologies. The standardization of technologies and the adoption of a Web interface for all our computer systems allows us to distribute digital images from a pathology database to a potentially large group of users distributed in multiple locations throughout a large medical center.

CHOmine: an integrated data warehouse for CHO systems biology and modeling

PubMed Central

Hanscho, Michael; Ruckerbauer, David E.; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

Abstract The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. Database URL: http://www.chogenome.org PMID:28605771

Enhancing UCSF Chimera through web services.

PubMed

Huang, Conrad C; Meng, Elaine C; Morris, John H; Pettersen, Eric F; Ferrin, Thomas E

2014-07-01

Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (http://www.rbvi.ucsf.edu/chimera/docs/webservices.html). By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. Web server availability: http://webservices.rbvi.ucsf.edu/opal2/dashboard?command=serviceList. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Combining data from multiple sources using the CUAHSI Hydrologic Information System

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Ames, D. P.; Horsburgh, J. S.; Goodall, J. L.

2012-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) has developed a Hydrologic Information System (HIS) to provide better access to data by enabling the publication, cataloging, discovery, retrieval, and analysis of hydrologic data using web services. The CUAHSI HIS is an Internet based system comprised of hydrologic databases and servers connected through web services as well as software for data publication, discovery and access. The HIS metadata catalog lists close to 100 web services registered to provide data through this system, ranging from large federal agency data sets to experimental watersheds managed by University investigators. The system's flexibility in storing and enabling public access to similarly formatted data and metadata has created a community data resource from governmental and academic data that might otherwise remain private or analyzed only in isolation. Comprehensive understanding of hydrology requires integration of this information from multiple sources. HydroDesktop is the client application developed as part of HIS to support data discovery and access through this system. HydroDesktop is founded on an open source GIS client and has a plug-in architecture that has enabled the integration of modeling and analysis capability with the functionality for data discovery and access. Model integration is possible through a plug-in built on the OpenMI standard and data visualization and analysis is supported by an R plug-in. This presentation will demonstrate HydroDesktop, showing how it provides an analysis environment within which data from multiple sources can be discovered, accessed and integrated.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

PubMed

Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

2016-10-01

We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct aggregate data analysis that will inform the next generation of epilepsy self-management studies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A Community Data Model for Hydrologic Observations

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Zaslavsky, I.; Maidment, D. R.; Valentine, D.; Jennings, B.

2006-12-01

The CUAHSI Hydrologic Information System project is developing information technology infrastructure to support hydrologic science. Hydrologic information science involves the description of hydrologic environments in a consistent way, using data models for information integration. This includes a hydrologic observations data model for the storage and retrieval of hydrologic observations in a relational database designed to facilitate data retrieval for integrated analysis of information collected by multiple investigators. It is intended to provide a standard format to facilitate the effective sharing of information between investigators and to facilitate analysis of information within a single study area or hydrologic observatory, or across hydrologic observatories and regions. The observations data model is designed to store hydrologic observations and sufficient ancillary information (metadata) about the observations to allow them to be unambiguously interpreted and used and provide traceable heritage from raw measurements to usable information. The design is based on the premise that a relational database at the single observation level is most effective for providing querying capability and cross dimension data retrieval and analysis. This premise is being tested through the implementation of a prototype hydrologic observations database, and the development of web services for the retrieval of data from and ingestion of data into the database. These web services hosted by the San Diego Supercomputer center make data in the database accessible both through a Hydrologic Data Access System portal and directly from applications software such as Excel, Matlab and ArcGIS that have Standard Object Access Protocol (SOAP) capability. This paper will (1) describe the data model; (2) demonstrate the capability for representing diverse data in the same database; (3) demonstrate the use of the database from applications software for the performance of hydrologic analysis across different observation types.

The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

PubMed Central

Hyam, Roger; Hagedorn, Gregor; Chagnoux, Simon; Röpert, Dominik; Casino, Ana; Droege, Gabi; Glöckler, Falko; Gödderz, Karsten; Groom, Quentin; Hoffmann, Jana; Holleman, Ayco; Kempa, Matúš; Koivula, Hanna; Marhold, Karol; Nicolson, Nicky; Smith, Vincent S.; Triebel, Dagmar

2017-01-01

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: http://cetaf.org/cetaf-stable-identifiers PMID:28365724

On Building a Search Interface Discovery System

NASA Astrophysics Data System (ADS)

Shestakov, Denis

A huge portion of the Web known as the deep Web is accessible via search interfaces to myriads of databases on the Web. While relatively good approaches for querying the contents of web databases have been recently proposed, one cannot fully utilize them having most search interfaces unlocated. Thus, the automatic recognition of search interfaces to online databases is crucial for any application accessing the deep Web. This paper describes the architecture of the I-Crawler, a system for finding and classifying search interfaces. The I-Crawler is intentionally designed to be used in the deep web characterization surveys and for constructing directories of deep web resources.

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

PubMed Central

Baumbach, Jan

2007-01-01

Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at . PMID:17986320

DECADE web portal: toward the integration of MaGa, EarthChem and VOTW data systems to further the knowledge on Earth degassing

NASA Astrophysics Data System (ADS)

Cardellini, Carlo; Frigeri, Alessandro; Lehnert, Kerstin; Ash, Jason; McCormick, Brendan; Chiodini, Giovanni; Fischer, Tobias; Cottrell, Elizabeth

2015-04-01

The release of volatiles from the Earth's interior takes place in both volcanic and non-volcanic areas of the planet. The comprehension of such complex process and the improvement of the current estimates of global carbon emissions, will greatly benefit from the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing interoperability between three data systems that will make their data accessible via the DECADE portal: (1) the Smithsonian Institutionian's Global Volcanism Program database (VOTW) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. The DECADE web portal will create a powerful search engine of these databases from a single entry point and will return comprehensive multi-component datasets. A user will be able, for example, to obtain data relating to compositions of emitted gases, compositions and age of the erupted products and coincident activity, of a specific volcano. This level of capability requires a complete synergy between the databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process allowing to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

NNDC Data Services

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

Tuli, J.K.; Sonzogni,A.

The National Nuclear Data Center has provided remote access to some of its resources since 1986. The major databases and other resources available currently through NNDC Web site are summarized. The National Nuclear Data Center (NNDC) has provided remote access to the nuclear physics databases it maintains and to other resources since 1986. With considerable innovation access is now mostly through the Web. The NNDC Web pages have been modernized to provide a consistent state-of-the-art style. The improved database services and other resources available from the NNOC site at www.nndc.bnl.govwill be described.

Sharing mutants and experimental information prepublication using FgMutantDB

USDA-ARS?s Scientific Manuscript database

There has been no central location for storing generated mutants of Fusarium graminearum or for data associated with these mutants. Instead researchers relied on several independent, non-integrated databases. FgMutantDB was designed as a simple spreadsheet that is accessible globally on the web th...

ExPASy: SIB bioinformatics resource portal.

PubMed

Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz

2012-07-01

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Ionic Liquids Database- (ILThermo)

National Institute of Standards and Technology Data Gateway

SRD 147 NIST Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

FirstSearch and NetFirst--Web and Dial-up Access: Plus Ca Change, Plus C'est la Meme Chose?

ERIC Educational Resources Information Center

Koehler, Wallace; Mincey, Danielle

1996-01-01

Compares and evaluates the differences between OCLC's dial-up and World Wide Web FirstSearch access methods and their interfaces with the underlying databases. Also examines NetFirst, OCLC's new Internet catalog, the only Internet tracking database from a "traditional" database service. (Author/PEN)

Ocean Drilling Program: Web Site Access Statistics

Science.gov Websites

and products Drilling services and tools Online Janus database Search the ODP/TAMU web site ODP's main See statistics for JOIDES members. See statistics for Janus database. 1997 October November December accessible only on www-odp.tamu.edu. ** End of ODP, start of IODP. Privacy Policy ODP | Search | Database

Improving Land Cover Mapping: a Mobile Application Based on ESA Sentinel 2 Imagery

NASA Astrophysics Data System (ADS)

Melis, M. T.; Dessì, F.; Loddo, P.; La Mantia, C.; Da Pelo, S.; Deflorio, A. M.; Ghiglieri, G.; Hailu, B. T.; Kalegele, K.; Mwasi, B. N.

2018-04-01

The increasing availability of satellite data is a real value for the enhancement of environmental knowledge and land management. Possibilities to integrate different source of geo-data are growing and methodologies to create thematic database are becoming very sophisticated. Moreover, the access to internet services and, in particular, to web mapping services is well developed and spread either between expert users than the citizens. Web map services, like Google Maps or Open Street Maps, give the access to updated optical imagery or topographic maps but information on land cover/use - are not still provided. Therefore, there are many failings in the general utilization -non-specialized users- and access to those maps. This issue is particularly felt where the digital (web) maps could form the basis for land use management as they are more economic and accessible than the paper maps. These conditions are well known in many African countries where, while the internet access is becoming open to all, the local map agencies and their products are not widespread.

Recent advances in the Lesser Antilles observatories Part 2 : WebObs - an integrated web-based system for monitoring and networks management

NASA Astrophysics Data System (ADS)

Beauducel, François; Bosson, Alexis; Randriamora, Frédéric; Anténor-Habazac, Christian; Lemarchand, Arnaud; Saurel, Jean-Marie; Nercessian, Alexandre; Bouin, Marie-Paule; de Chabalier, Jean-Bernard; Clouard, Valérie

2010-05-01

Seismological and Volcanological observatories have common needs and often common practical problems for multi disciplinary data monitoring applications. In fact, access to integrated data in real-time and estimation of measurements uncertainties are keys for an efficient interpretation, but instruments variety, heterogeneity of data sampling and acquisition systems lead to difficulties that may hinder crisis management. In Guadeloupe observatory, we have developed in the last years an operational system that attempts to answer the questions in the context of a pluri-instrumental observatory. Based on a single computer server, open source scripts (Matlab, Perl, Bash, Nagios) and a Web interface, the system proposes: an extended database for networks management, stations and sensors (maps, station file with log history, technical characteristics, meta-data, photos and associated documents); a web-form interfaces for manual data input/editing and export (like geochemical analysis, some of the deformation measurements, ...); routine data processing with dedicated automatic scripts for each technique, production of validated data outputs, static graphs on preset moving time intervals, and possible e-mail alarms; computers, acquisition processes, stations and individual sensors status automatic check with simple criteria (files update and signal quality), displayed as synthetic pages for technical control. In the special case of seismology, WebObs includes a digital stripchart multichannel continuous seismogram associated with EarthWorm acquisition chain (see companion paper Part 1), event classification database, location scripts, automatic shakemaps and regional catalog with associated hypocenter maps accessed through a user request form. This system leads to a real-time Internet access for integrated monitoring and becomes a strong support for scientists and technicians exchange, and is widely open to interdisciplinary real-time modeling. It has been set up at Martinique observatory and installation is planned this year at Montserrat Volcanological Observatory. It also in production at the geomagnetic observatory of Addis Abeba in Ethiopia.

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (). PMID:17202161

Federated or cached searches: Providing expected performance from multiple invasive species databases

NASA Astrophysics Data System (ADS)

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-06-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Federated or cached searches: providing expected performance from multiple invasive species databases

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-01-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

FlyMine: an integrated database for Drosophila and Anopheles genomics

PubMed Central

Lyne, Rachel; Smith, Richard; Rutherford, Kim; Wakeling, Matthew; Varley, Andrew; Guillier, Francois; Janssens, Hilde; Ji, Wenyan; Mclaren, Peter; North, Philip; Rana, Debashis; Riley, Tom; Sullivan, Julie; Watkins, Xavier; Woodbridge, Mark; Lilley, Kathryn; Russell, Steve; Ashburner, Michael; Mizuguchi, Kenji; Micklem, Gos

2007-01-01

FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists. PMID:17615057

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

PubMed Central

Simonyan, Vahan; Chumakov, Konstantin; Dingerdissen, Hayley; Faison, William; Goldweber, Scott; Golikov, Anton; Gulzar, Naila; Karagiannis, Konstantinos; Vinh Nguyen Lam, Phuc; Maudru, Thomas; Muravitskaja, Olesja; Osipova, Ekaterina; Pan, Yang; Pschenichnov, Alexey; Rostovtsev, Alexandre; Santana-Quintero, Luis; Smith, Krista; Thompson, Elaine E.; Tkachenko, Valery; Torcivia-Rodriguez, John; Wan, Quan; Wang, Jing; Wu, Tsung-Jung; Wilson, Carolyn; Mazumder, Raja

2016-01-01

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure. The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu PMID:26989153

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

PubMed

Simonyan, Vahan; Chumakov, Konstantin; Dingerdissen, Hayley; Faison, William; Goldweber, Scott; Golikov, Anton; Gulzar, Naila; Karagiannis, Konstantinos; Vinh Nguyen Lam, Phuc; Maudru, Thomas; Muravitskaja, Olesja; Osipova, Ekaterina; Pan, Yang; Pschenichnov, Alexey; Rostovtsev, Alexandre; Santana-Quintero, Luis; Smith, Krista; Thompson, Elaine E; Tkachenko, Valery; Torcivia-Rodriguez, John; Voskanian, Alin; Wan, Quan; Wang, Jing; Wu, Tsung-Jung; Wilson, Carolyn; Mazumder, Raja

2016-01-01

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure.The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu. © The Author(s) 2016. Published by Oxford University Press.

EuroPhenome and EMPReSS: online mouse phenotyping resource

PubMed Central

Mallon, Ann-Marie; Hancock, John M.

2008-01-01

EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC). PMID:17905814

EuroPhenome and EMPReSS: online mouse phenotyping resource.

PubMed

Mallon, Ann-Marie; Blake, Andrew; Hancock, John M

2008-01-01

EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC).

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

PubMed Central

Juty, Nick; Blomberg, Niklas; Burdett, Tony; Conlin, Tom; Conte, Nathalie; Courtot, Mélanie; Deck, John; Dumontier, Michel; Fellows, Donal K.; Gonzalez-Beltran, Alejandra; Gormanns, Philipp; Grethe, Jeffrey; Hastings, Janna; Hériché, Jean-Karim; Hermjakob, Henning; Ison, Jon C.; Jimenez, Rafael C.; Jupp, Simon; Kunze, John; Laibe, Camille; Le Novère, Nicolas; Malone, James; Martin, Maria Jesus; McEntyre, Johanna R.; Morris, Chris; Muilu, Juha; Müller, Wolfgang; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Sariyar, Murat; Snoep, Jacky L.; Soiland-Reyes, Stian; Stanford, Natalie J.; Swainston, Neil; Washington, Nicole; Williams, Alan R.; Wimalaratne, Sarala M.; Winfree, Lilly M.; Wolstencroft, Katherine; Goble, Carole; Mungall, Christopher J.; Haendel, Melissa A.; Parkinson, Helen

2017-01-01

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines. PMID:28662064

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

PubMed

McMurry, Julie A; Juty, Nick; Blomberg, Niklas; Burdett, Tony; Conlin, Tom; Conte, Nathalie; Courtot, Mélanie; Deck, John; Dumontier, Michel; Fellows, Donal K; Gonzalez-Beltran, Alejandra; Gormanns, Philipp; Grethe, Jeffrey; Hastings, Janna; Hériché, Jean-Karim; Hermjakob, Henning; Ison, Jon C; Jimenez, Rafael C; Jupp, Simon; Kunze, John; Laibe, Camille; Le Novère, Nicolas; Malone, James; Martin, Maria Jesus; McEntyre, Johanna R; Morris, Chris; Muilu, Juha; Müller, Wolfgang; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Sariyar, Murat; Snoep, Jacky L; Soiland-Reyes, Stian; Stanford, Natalie J; Swainston, Neil; Washington, Nicole; Williams, Alan R; Wimalaratne, Sarala M; Winfree, Lilly M; Wolstencroft, Katherine; Goble, Carole; Mungall, Christopher J; Haendel, Melissa A; Parkinson, Helen

2017-06-01

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

The comparative effectiveness of conventional and digital image libraries.

PubMed

McColl, R I; Johnson, A

2001-03-01

Before introducing a hospital-wide image database to improve access, navigation and retrieval speed, a comparative study between a conventional slide library and a matching image database was undertaken to assess its relative benefits. Paired time trials and personal questionnaires revealed faster retrieval rates, higher image quality, and easier viewing for the pilot digital image database. Analysis of confidentiality, copyright and data protection exposed similar issues for both systems, thus concluding that the digital image database is a more effective library system. The authors suggest that in the future, medical images will be stored on large, professionally administered, centrally located file servers, allowing specialist image libraries to be tailored locally for individual users. The further integration of the database with web technology will enable cheap and efficient remote access for a wide range of users.

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

PubMed Central

Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F. X.

2004-01-01

Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db. PMID:14681437

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

Computational knowledge integration in biopharmaceutical research.

PubMed

Ficenec, David; Osborne, Mark; Pradines, Joel; Richards, Dan; Felciano, Ramon; Cho, Raymond J; Chen, Richard O; Liefeld, Ted; Owen, James; Ruttenberg, Alan; Reich, Christian; Horvath, Joseph; Clark, Tim

2003-09-01

An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.

Building an Integrated Environment for Multimedia

NASA Technical Reports Server (NTRS)

1997-01-01

Multimedia courseware on the solar system and earth science suitable for use in elementary, middle, and high schools was developed under this grant. The courseware runs on Silicon Graphics, Incorporated (SGI) workstations and personal computers (PCs). There is also a version of the courseware accessible via the World Wide Web. Accompanying multimedia database systems were also developed to enhance the multimedia courseware. The database systems accompanying the PC software are based on the relational model, while the database systems accompanying the SGI software are based on the object-oriented model.

Earth System Model Development and Analysis using FRE-Curator and Live Access Servers: On-demand analysis of climate model output with data provenance.

NASA Astrophysics Data System (ADS)

Radhakrishnan, A.; Balaji, V.; Schweitzer, R.; Nikonov, S.; O'Brien, K.; Vahlenkamp, H.; Burger, E. F.

2016-12-01

There are distinct phases in the development cycle of an Earth system model. During the model development phase, scientists make changes to code and parameters and require rapid access to results for evaluation. During the production phase, scientists may make an ensemble of runs with different settings, and produce large quantities of output, that must be further analyzed and quality controlled for scientific papers and submission to international projects such as the Climate Model Intercomparison Project (CMIP). During this phase, provenance is a key concern:being able to track back from outputs to inputs. We will discuss one of the paths taken at GFDL in delivering tools across this lifecycle, offering on-demand analysis of data by integrating the use of GFDL's in-house FRE-Curator, Unidata's THREDDS and NOAA PMEL's Live Access Servers (LAS).Experience over this lifecycle suggests that a major difficulty in developing analysis capabilities is only partially the scientific content, but often devoted to answering the questions "where is the data?" and "how do I get to it?". "FRE-Curator" is the name of a database-centric paradigm used at NOAA GFDL to ingest information about the model runs into an RDBMS (Curator database). The components of FRE-Curator are integrated into Flexible Runtime Environment workflow and can be invoked during climate model simulation. The front end to FRE-Curator, known as the Model Development Database Interface (MDBI) provides an in-house web-based access to GFDL experiments: metadata, analysis output and more. In order to provide on-demand visualization, MDBI uses Live Access Servers which is a highly configurable web server designed to provide flexible access to geo-referenced scientific data, that makes use of OPeNDAP. Model output saved in GFDL's tape archive, the size of the database and experiments, continuous model development initiatives with more dynamic configurations add complexity and challenges in providing an on-demand visualization experience to our GFDL users.

The Virtual Watershed Observatory: Cyberinfrastructure for Model-Data Integration and Access

NASA Astrophysics Data System (ADS)

Duffy, C.; Leonard, L. N.; Giles, L.; Bhatt, G.; Yu, X.

2011-12-01

The Virtual Watershed Observatory (VWO) is a concept where scientists, water managers, educators and the general public can create a virtual observatory from integrated hydrologic model results, national databases and historical or real-time observations via web services. In this paper, we propose a prototype for automated and virtualized web services software using national data products for climate reanalysis, soils, geology, terrain and land cover. The VWO has the broad purpose of making accessible water resource simulations, real-time data assimilation, calibration and archival at the scale of HUC 12 watersheds (Hydrologic Unit Code) anywhere in the continental US. Our prototype for model-data integration focuses on creating tools for fast data storage from selected national databases, as well as the computational resources necessary for a dynamic, distributed watershed simulation. The paper will describe cyberinfrastructure tools and workflow that attempts to resolve the problem of model-data accessibility and scalability such that individuals, research teams, managers and educators can create a WVO in a desired context. Examples are given for the NSF-funded Shale Hills Critical Zone Observatory and the European Critical Zone Observatories within the SoilTrEC project. In the future implementation of WVO services will benefit from the development of a cloud cyber infrastructure as the prototype evolves to data and model intensive computation for continental scale water resource predictions.

Geoinformatics in the public service: building a cyberinfrastructure across the geological surveys

USGS Publications Warehouse

Allison, M. Lee; Gundersen, Linda C.; Richard, Stephen M.; Keller, G. Randy; Baru, Chaitanya

2011-01-01

Advanced information technology infrastructure is increasingly being employed in the Earth sciences to provide researchers with efficient access to massive central databases and to integrate diversely formatted information from a variety of sources. These geoinformatics initiatives enable manipulation, modeling and visualization of data in a consistent way, and are helping to develop integrated Earth models at various scales, and from the near surface to the deep interior. This book uses a series of case studies to demonstrate computer and database use across the geosciences. Chapters are thematically grouped into sections that cover data collection and management; modeling and community computational codes; visualization and data representation; knowledge management and data integration; and web services and scientific workflows. Geoinformatics is a fascinating and accessible introduction to this emerging field for readers across the solid Earth sciences and an invaluable reference for researchers interested in initiating new cyberinfrastructure projects of their own.

Web tools for predictive toxicology model building.

PubMed

Jeliazkova, Nina

2012-07-01

The development and use of web tools in chemistry has accumulated more than 15 years of history already. Powered by the advances in the Internet technologies, the current generation of web systems are starting to expand into areas, traditional for desktop applications. The web platforms integrate data storage, cheminformatics and data analysis tools. The ease of use and the collaborative potential of the web is compelling, despite the challenges. The topic of this review is a set of recently published web tools that facilitate predictive toxicology model building. The focus is on software platforms, offering web access to chemical structure-based methods, although some of the frameworks could also provide bioinformatics or hybrid data analysis functionalities. A number of historical and current developments are cited. In order to provide comparable assessment, the following characteristics are considered: support for workflows, descriptor calculations, visualization, modeling algorithms, data management and data sharing capabilities, availability of GUI or programmatic access and implementation details. The success of the Web is largely due to its highly decentralized, yet sufficiently interoperable model for information access. The expected future convergence between cheminformatics and bioinformatics databases provides new challenges toward management and analysis of large data sets. The web tools in predictive toxicology will likely continue to evolve toward the right mix of flexibility, performance, scalability, interoperability, sets of unique features offered, friendly user interfaces, programmatic access for advanced users, platform independence, results reproducibility, curation and crowdsourcing utilities, collaborative sharing and secure access.

U.S. Army Research Laboratory (ARL) multimodal signatures database

NASA Astrophysics Data System (ADS)

Bennett, Kelly

2008-04-01

The U.S. Army Research Laboratory (ARL) Multimodal Signatures Database (MMSDB) is a centralized collection of sensor data of various modalities that are co-located and co-registered. The signatures include ground and air vehicles, personnel, mortar, artillery, small arms gunfire from potential sniper weapons, explosives, and many other high value targets. This data is made available to Department of Defense (DoD) and DoD contractors, Intel agencies, other government agencies (OGA), and academia for use in developing target detection, tracking, and classification algorithms and systems to protect our Soldiers. A platform independent Web interface disseminates the signatures to researchers and engineers within the scientific community. Hierarchical Data Format 5 (HDF5) signature models provide an excellent solution for the sharing of complex multimodal signature data for algorithmic development and database requirements. Many open source tools for viewing and plotting HDF5 signatures are available over the Web. Seamless integration of HDF5 signatures is possible in both proprietary computational environments, such as MATLAB, and Free and Open Source Software (FOSS) computational environments, such as Octave and Python, for performing signal processing, analysis, and algorithm development. Future developments include extending the Web interface into a portal system for accessing ARL algorithms and signatures, High Performance Computing (HPC) resources, and integrating existing database and signature architectures into sensor networking environments.

Village Green Project: Web-accessible Database

EPA Science Inventory

The purpose of this web-accessible database is for the public to be able to view instantaneous readings from a solar-powered air monitoring station located in a public location (prototype pilot test is outside of a library in Durham County, NC). The data are wirelessly transmitte...

Genomics Portals: integrative web-platform for mining genomics data.

PubMed

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

A Semantic Sensor Web for Environmental Decision Support Applications

PubMed Central

Gray, Alasdair J. G.; Sadler, Jason; Kit, Oles; Kyzirakos, Kostis; Karpathiotakis, Manos; Calbimonte, Jean-Paul; Page, Kevin; García-Castro, Raúl; Frazer, Alex; Galpin, Ixent; Fernandes, Alvaro A. A.; Paton, Norman W.; Corcho, Oscar; Koubarakis, Manolis; De Roure, David; Martinez, Kirk; Gómez-Pérez, Asunción

2011-01-01

Sensing devices are increasingly being deployed to monitor the physical world around us. One class of application for which sensor data is pertinent is environmental decision support systems, e.g., flood emergency response. For these applications, the sensor readings need to be put in context by integrating them with other sources of data about the surrounding environment. Traditional systems for predicting and detecting floods rely on methods that need significant human resources. In this paper we describe a semantic sensor web architecture for integrating multiple heterogeneous datasets, including live and historic sensor data, databases, and map layers. The architecture provides mechanisms for discovering datasets, defining integrated views over them, continuously receiving data in real-time, and visualising on screen and interacting with the data. Our approach makes extensive use of web service standards for querying and accessing data, and semantic technologies to discover and integrate datasets. We demonstrate the use of our semantic sensor web architecture in the context of a flood response planning web application that uses data from sensor networks monitoring the sea-state around the coast of England. PMID:22164110

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov PMID:18073190

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

PubMed

Chiba, Hirokazu; Uchiyama, Ikuo

2017-02-08

Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary. We developed SPANG, a SPARQL client that has unique features for querying RDF datasets. SPANG dynamically generates typical SPARQL queries according to specified arguments. It can also call SPARQL template libraries constructed in a local system or published on the Web. Further, it enables combinatorial execution of multiple queries, each with a distinct target database. These features facilitate easy and effective access to RDF datasets and integrative analysis of distributed data. SPANG helps users to exploit RDF datasets by generation and reuse of SPARQL queries through a simple interface. This client will enhance integrative exploitation of biological RDF datasets distributed across the Web. This software package is freely available at http://purl.org/net/spang .

Content and Accessibility of Shoulder and Elbow Fellowship Web Sites in the United States.

PubMed

Young, Bradley L; Oladeji, Lasun O; Cichos, Kyle; Ponce, Brent

2016-01-01

Increasing numbers of training physicians are using the Internet to gather information about graduate medical education programs. The content and accessibility of web sites that provide this information have been demonstrated to influence applicants' decisions. Assessments of orthopedic fellowship web sites including sports medicine, pediatrics, hand and spine have found varying degrees of accessibility and material. The purpose of this study was to evaluate the accessibility and content of the American Shoulder and Elbow Surgeons (ASES) fellowship web sites (SEFWs). A complete list of ASES programs was obtained from a database on the ASES web site. The accessibility of each SEFWs was assessed by the existence of a functioning link found in the database and through Google®. Then, the following content areas of each SEFWs were evaluated: fellow education, faculty/previous fellow information, and recruitment. At the time of the study, 17 of the 28 (60.7%) ASES programs had web sites accessible through Google®, and only five (17.9%) had functioning links in the ASES database. Nine programs lacked a web site. Concerning web site content, the majority of SEFWs contained information regarding research opportunities, research requirements, case descriptions, meetings and conferences, teaching responsibilities, attending faculty, the application process, and a program description. Fewer than half of the SEFWs provided information regarding rotation schedules, current fellows, previous fellows, on-call expectations, journal clubs, medical school of current fellows, residency of current fellows, employment of previous fellows, current research, and previous research. A large portion of ASES fellowship programs lacked functioning web sites, and even fewer provided functioning links through the ASES database. Valuable information for potential applicants was largely inadequate across present SEFWs.

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

PubMed

D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

2017-01-01

Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

Evaluation of the content and accessibility of web sites for accredited orthopaedic sports medicine fellowships.

PubMed

Mulcahey, Mary K; Gosselin, Michelle M; Fadale, Paul D

2013-06-19

The Internet is a common source of information for orthopaedic residents applying for sports medicine fellowships, with the web sites of the American Orthopaedic Society for Sports Medicine (AOSSM) and the San Francisco Match serving as central databases. We sought to evaluate the web sites for accredited orthopaedic sports medicine fellowships with regard to content and accessibility. We reviewed the existing web sites of the ninety-five accredited orthopaedic sports medicine fellowships included in the AOSSM and San Francisco Match databases from February to March 2012. A Google search was performed to determine the overall accessibility of program web sites and to supplement information obtained from the AOSSM and San Francisco Match web sites. The study sample consisted of the eighty-seven programs whose web sites connected to information about the fellowship. Each web site was evaluated for its informational value. Of the ninety-five programs, fifty-one (54%) had links listed in the AOSSM database. Three (3%) of all accredited programs had web sites that were linked directly to information about the fellowship. Eighty-eight (93%) had links listed in the San Francisco Match database; however, only five (5%) had links that connected directly to information about the fellowship. Of the eighty-seven programs analyzed in our study, all eighty-seven web sites (100%) provided a description of the program and seventy-six web sites (87%) included information about the application process. Twenty-one web sites (24%) included a list of current fellows. Fifty-six web sites (64%) described the didactic instruction, seventy (80%) described team coverage responsibilities, forty-seven (54%) included a description of cases routinely performed by fellows, forty-one (47%) described the role of the fellow in seeing patients in the office, eleven (13%) included call responsibilities, and seventeen (20%) described a rotation schedule. Two Google searches identified direct links for 67% to 71% of all accredited programs. Most accredited orthopaedic sports medicine fellowships lack easily accessible or complete web sites in the AOSSM or San Francisco Match databases. Improvement in the accessibility and quality of information on orthopaedic sports medicine fellowship web sites would facilitate the ability of applicants to obtain useful information.

SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

High Temperature Superconducting Materials Database

National Institute of Standards and Technology Data Gateway

SRD 62 NIST High Temperature Superconducting Materials Database (Web, free access)   The NIST High Temperature Superconducting Materials Database (WebHTS) provides evaluated thermal, mechanical, and superconducting property data for oxides and other nonconventional superconductors.

Development and implementation of an Integrated Water Resources Management System (IWRMS)

NASA Astrophysics Data System (ADS)

Flügel, W.-A.; Busch, C.

2011-04-01

One of the innovative objectives in the EC project BRAHMATWINN was the development of a stakeholder oriented Integrated Water Resources Management System (IWRMS). The toolset integrates the findings of the project and presents it in a user friendly way for decision support in sustainable integrated water resources management (IWRM) in river basins. IWRMS is a framework, which integrates different types of basin information and which supports the development of IWRM options for climate change mitigation. It is based on the River Basin Information System (RBIS) data models and delivers a graphical user interface for stakeholders. A special interface was developed for the integration of the enhanced DANUBIA model input and the NetSyMod model with its Mulino decision support system (mulino mDss) component. The web based IWRMS contains and combines different types of data and methods to provide river basin data and information for decision support. IWRMS is based on a three tier software framework which uses (i) html/javascript at the client tier, (ii) PHP programming language to realize the application tier, and (iii) a postgresql/postgis database tier to manage and storage all data, except the DANUBIA modelling raw data, which are file based and registered in the database tier. All three tiers can reside on one or different computers and are adapted to the local hardware infrastructure. IWRMS as well as RBIS are based on Open Source Software (OSS) components and flexible and time saving access to that database is guaranteed by web-based interfaces for data visualization and retrieval. The IWRMS is accessible via the BRAHMATWINN homepage: http://www.brahmatwinn.uni-jena.de and a user manual for the RBIS is available for download as well.

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

The climate4impact platform: Providing, tailoring and facilitating climate model data access

NASA Astrophysics Data System (ADS)

Pagé, Christian; Pagani, Andrea; Plieger, Maarten; Som de Cerff, Wim; Mihajlovski, Andrej; de Vreede, Ernst; Spinuso, Alessandro; Hutjes, Ronald; de Jong, Fokke; Bärring, Lars; Vega, Manuel; Cofiño, Antonio; d'Anca, Alessandro; Fiore, Sandro; Kolax, Michael

2017-04-01

One of the main objectives of climate4impact is to provide standardized web services and tools that are reusable in other portals. These services include web processing services, web coverage services and web mapping services (WPS, WCS and WMS). Tailored portals can be targeted to specific communities and/or countries/regions while making use of those services. Easier access to climate data is very important for the climate change impact communities. To fulfill this objective, the climate4impact (http://climate4impact.eu/) web portal and services has been developed, targeting climate change impact modellers, impact and adaptation consultants, as well as other experts using climate change data. It provides to users harmonized access to climate model data through tailored services. It features static and dynamic documentation, Use Cases and best practice examples, an advanced search interface, an integrated authentication and authorization system with the Earth System Grid Federation (ESGF), a visualization interface with ADAGUC web mapping tools. In the latest version, statistical downscaling services, provided by the Santander Meteorology Group Downscaling Portal, were integrated. An innovative interface to integrate statistical downscaling services will be released in the upcoming version. The latter will be a big step in bridging the gap between climate scientists and the climate change impact communities. The climate4impact portal builds on the infrastructure of an international distributed database that has been set to disseminate the results from the global climate model results of the Coupled Model Intercomparison project Phase 5 (CMIP5). This database, the ESGF, is an international collaboration that develops, deploys and maintains software infrastructure for the management, dissemination, and analysis of climate model data. The European FP7 project IS-ENES, Infrastructure for the European Network for Earth System modelling, supports the European contribution to ESGF and contributes to the ESGF open source effort, notably through the development of search, monitoring, quality control, and metadata services. In its second phase, IS-ENES2 supports the implementation of regional climate model results from the international Coordinated Regional Downscaling Experiments (CORDEX). These services were extended within the European FP7 Climate Information Portal for Copernicus (CLIPC) project, and some could be later integrated into the European Copernicus platform.

Structural Ceramics Database

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

Integrating geo web services for a user driven exploratory analysis

NASA Astrophysics Data System (ADS)

Moncrieff, Simon; Turdukulov, Ulanbek; Gulland, Elizabeth-Kate

2016-04-01

In data exploration, several online data sources may need to be dynamically aggregated or summarised over spatial region, time interval, or set of attributes. With respect to thematic data, web services are mainly used to present results leading to a supplier driven service model limiting the exploration of the data. In this paper we propose a user need driven service model based on geo web processing services. The aim of the framework is to provide a method for the scalable and interactive access to various geographic data sources on the web. The architecture combines a data query, processing technique and visualisation methodology to rapidly integrate and visually summarise properties of a dataset. We illustrate the environment on a health related use case that derives Age Standardised Rate - a dynamic index that needs integration of the existing interoperable web services of demographic data in conjunction with standalone non-spatial secure database servers used in health research. Although the example is specific to the health field, the architecture and the proposed approach are relevant and applicable to other fields that require integration and visualisation of geo datasets from various web services and thus, we believe is generic in its approach.

Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

PubMed Central

Jiao, Xiaoli; Sherman, Brad T.; Huang, Da Wei; Stephens, Robert; Baseler, Michael W.; Lane, H. Clifford; Lempicki, Richard A.

2012-01-01

Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. Availability: The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html. Contact: xiaoli.jiao@nih.gov; rlempicki@nih.gov PMID:22543366

DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

PubMed

Jiao, Xiaoli; Sherman, Brad T; Huang, Da Wei; Stephens, Robert; Baseler, Michael W; Lane, H Clifford; Lempicki, Richard A

2012-07-01

The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html.

Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

Web client and ODBC access to legacy database information: a low cost approach.

PubMed Central

Sanders, N. W.; Mann, N. H.; Spengler, D. M.

1997-01-01

A new method has been developed for the Department of Orthopaedics of Vanderbilt University Medical Center to access departmental clinical data. Previously this data was stored only in the medical center's mainframe DB2 database, it is now additionally stored in a departmental SQL database. Access to this data is available via any ODBC compliant front-end or a web client. With a small budget and no full time staff, we were able to give our department on-line access to many years worth of patient data that was previously inaccessible. PMID:9357735

Digging Deeper: The Deep Web.

ERIC Educational Resources Information Center

Turner, Laura

2001-01-01

Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

Do-It-Yourself: A Special Library's Approach to Creating Dynamic Web Pages Using Commercial Off-The-Shelf Applications

NASA Technical Reports Server (NTRS)

Steeman, Gerald; Connell, Christopher

2000-01-01

Many librarians may feel that dynamic Web pages are out of their reach, financially and technically. Yet we are reminded in library and Web design literature that static home pages are a thing of the past. This paper describes how librarians at the Institute for Defense Analyses (IDA) library developed a database-driven, dynamic intranet site using commercial off-the-shelf applications. Administrative issues include surveying a library users group for interest and needs evaluation; outlining metadata elements; and, committing resources from managing time to populate the database and training in Microsoft FrontPage and Web-to-database design. Technical issues covered include Microsoft Access database fundamentals, lessons learned in the Web-to-database process (including setting up Database Source Names (DSNs), redesigning queries to accommodate the Web interface, and understanding Access 97 query language vs. Standard Query Language (SQL)). This paper also offers tips on editing Active Server Pages (ASP) scripting to create desired results. A how-to annotated resource list closes out the paper.

The EMBL nucleotide sequence database

PubMed Central

Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Lombard, Vincent; Lopez, Rodrigo; Parkinson, Helen; Redaschi, Nicole; Sterk, Peter; Stoehr, Peter; Tuli, Mary Ann

2001-01-01

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. PMID:11125039

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Sharing and executing linked data queries in a collaborative environment.

PubMed

García Godoy, María Jesús; López-Camacho, Esteban; Navas-Delgado, Ismael; Aldana-Montes, José F

2013-07-01

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. The Bioqueries portal is freely accessible at http://bioqueries.uma.es. Supplementary data are available at Bioinformatics online.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (www.ncbi.nlm.nih.gov).

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2005-01-01

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2006-01-01

GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience

PubMed Central

Akil, Huda; Ascoli, Giorgio A.; Bowden, Douglas M.; Bug, William; Donohue, Duncan E.; Goldberg, David H.; Grafstein, Bernice; Grethe, Jeffrey S.; Gupta, Amarnath; Halavi, Maryam; Kennedy, David N.; Marenco, Luis; Martone, Maryann E.; Miller, Perry L.; Müller, Hans-Michael; Robert, Adrian; Shepherd, Gordon M.; Sternberg, Paul W.; Van Essen, David C.; Williams, Robert W.

2009-01-01

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience’s Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line. PMID:18946742

The neuroscience information framework: a data and knowledge environment for neuroscience.

PubMed

Gardner, Daniel; Akil, Huda; Ascoli, Giorgio A; Bowden, Douglas M; Bug, William; Donohue, Duncan E; Goldberg, David H; Grafstein, Bernice; Grethe, Jeffrey S; Gupta, Amarnath; Halavi, Maryam; Kennedy, David N; Marenco, Luis; Martone, Maryann E; Miller, Perry L; Müller, Hans-Michael; Robert, Adrian; Shepherd, Gordon M; Sternberg, Paul W; Van Essen, David C; Williams, Robert W

2008-09-01

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience's Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultant-collaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov , http://neurogateway.org , and other sites as they come on line.

Solution Kinetics Database on the Web

National Institute of Standards and Technology Data Gateway

SRD 40 NDRL/NIST Solution Kinetics Database on the Web (Web, free access)   Data for free radical processes involving primary radicals from water, inorganic radicals and carbon-centered radicals in solution, and singlet oxygen and organic peroxyl radicals in various solvents.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

PubMed Central

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

CHOmine: an integrated data warehouse for CHO systems biology and modeling.

PubMed

Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

DICOM image integration into an electronic medical record using thin viewing clients

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Taira, Ricky K.

1998-07-01

Purpose -- To integrate radiological DICOM images into our currently existing web-browsable Electronic Medical Record (MINDscape). Over the last five years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A text-based view of this data called the Mini Medical Record (MMR) has been available for three years. MINDscape, unlike the text based MMR, provides a platform independent, web browser view of the MIND dataset that can easily be linked to other information resources on the network. We have now added the integration of radiological images into MINDscape through a DICOM webserver. Methods/New Work -- we have integrated a commercial webserver that acts as a DICOM Storage Class Provider to our, computed radiography (CR), computed tomography (CT), digital fluoroscopy (DF), magnetic resonance (MR) and ultrasound (US) scanning devices. These images can be accessed through CGI queries or by linking the image server database using ODBC or SQL gateways. This allows the use of dynamic HTML links to the images on the DICOM webserver from MINDscape, so that the radiology reports already resident in the MIND repository can be married with the associated images through the unique examination accession number generated by our Radiology Information System (RIS). The web browser plug-in used provides a wavelet decompression engine (up to 16-bits per pixel) and performs the following image manipulation functions: window/level, flip, invert, sort, rotate, zoom, cine-loop and save as JPEG. Results -- Radiological DICOM image sets (CR, CT, MR and US) are displayed with associated exam reports for referring physician and clinicians anywhere within the widespread academic medical center on PCs, Macs, X-terminals and Unix computers. This system is also being used for home teleradiology application. Conclusion -- Radiological DICOM images can be made available medical center wide to physicians quickly using low-cost and ubiquitous, thin client browsing technology and wavelet compression.

Remote visual analysis of large turbulence databases at multiple scales

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

Pulido, Jesus; Livescu, Daniel; Kanov, Kalin

The remote analysis and visualization of raw large turbulence datasets is challenging. Current accurate direct numerical simulations (DNS) of turbulent flows generate datasets with billions of points per time-step and several thousand time-steps per simulation. Until recently, the analysis and visualization of such datasets was restricted to scientists with access to large supercomputers. The public Johns Hopkins Turbulence database simplifies access to multi-terabyte turbulence datasets and facilitates the computation of statistics and extraction of features through the use of commodity hardware. In this paper, we present a framework designed around wavelet-based compression for high-speed visualization of large datasets and methodsmore » supporting multi-resolution analysis of turbulence. By integrating common technologies, this framework enables remote access to tools available on supercomputers and over 230 terabytes of DNS data over the Web. Finally, the database toolset is expanded by providing access to exploratory data analysis tools, such as wavelet decomposition capabilities and coherent feature extraction.« less

Remote visual analysis of large turbulence databases at multiple scales

DOE PAGES

Pulido, Jesus; Livescu, Daniel; Kanov, Kalin; ...

2018-06-15

The remote analysis and visualization of raw large turbulence datasets is challenging. Current accurate direct numerical simulations (DNS) of turbulent flows generate datasets with billions of points per time-step and several thousand time-steps per simulation. Until recently, the analysis and visualization of such datasets was restricted to scientists with access to large supercomputers. The public Johns Hopkins Turbulence database simplifies access to multi-terabyte turbulence datasets and facilitates the computation of statistics and extraction of features through the use of commodity hardware. In this paper, we present a framework designed around wavelet-based compression for high-speed visualization of large datasets and methodsmore » supporting multi-resolution analysis of turbulence. By integrating common technologies, this framework enables remote access to tools available on supercomputers and over 230 terabytes of DNS data over the Web. Finally, the database toolset is expanded by providing access to exploratory data analysis tools, such as wavelet decomposition capabilities and coherent feature extraction.« less

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

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

McMurry, Julie A.; Juty, Nick; Blomberg, Niklas

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline themore » important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.« less

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

DOE PAGES

McMurry, Julie A.; Juty, Nick; Blomberg, Niklas; ...

2017-06-29

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline themore » important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.« less

DECADE Web Portal: Integrating MaGa, EarthChem and GVP Will Further Our Knowledge on Earth Degassing

NASA Astrophysics Data System (ADS)

Cardellini, C.; Frigeri, A.; Lehnert, K. A.; Ash, J.; McCormick, B.; Chiodini, G.; Fischer, T. P.; Cottrell, E.

2014-12-01

The release of gases from the Earth's interior to the exosphere takes place in both volcanic and non-volcanic areas of the planet. Fully understanding this complex process requires the integration of geochemical, petrological and volcanological data. At present, major online data repositories relevant to studies of degassing are not linked and interoperable. We are developing interoperability between three of those, which will support more powerful synoptic studies of degassing. The three data systems that will make their data accessible via the DECADE portal are: (1) the Smithsonian Institution's Global Volcanism Program database (GVP) of volcanic activity data, (2) EarthChem databases for geochemical and geochronological data of rocks and melt inclusions, and (3) the MaGa database (Mapping Gas emissions) which contains compositional and flux data of gases released at volcanic and non-volcanic degassing sites. These databases are developed and maintained by institutions or groups of experts in a specific field, and data are archived in formats specific to these databases. In the framework of the Deep Earth Carbon Degassing (DECADE) initiative of the Deep Carbon Observatory (DCO), we are developing a web portal that will create a powerful search engine of these databases from a single entry point. The portal will return comprehensive multi-component datasets, based on the search criteria selected by the user. For example, a single geographic or temporal search will return data relating to compositions of emitted gases and erupted products, the age of the erupted products, and coincident activity at the volcano. The development of this level of capability for the DECADE Portal requires complete synergy between these databases, including availability of standard-based web services (WMS, WFS) at all data systems. Data and metadata can thus be extracted from each system without interfering with each database's local schema or being replicated to achieve integration at the DECADE web portal. The DECADE portal will enable new synoptic perspectives on the Earth degassing process. Other data systems can be easily plugged in using the existing framework. Our vision is to explore Earth degassing related datasets over previously unexplored spatial or temporal ranges.

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

PubMed Central

Blenda, Anna; Scheffler, Jodi; Scheffler, Brian; Palmer, Michael; Lacape, Jean-Marc; Yu, John Z; Jesudurai, Christopher; Jung, Sook; Muthukumar, Sriram; Yellambalase, Preetham; Ficklin, Stephen; Staton, Margaret; Eshelman, Robert; Ulloa, Mauricio; Saha, Sukumar; Burr, Ben; Liu, Shaolin; Zhang, Tianzhen; Fang, Deqiu; Pepper, Alan; Kumpatla, Siva; Jacobs, John; Tomkins, Jeff; Cantrell, Roy; Main, Dorrie

2006-01-01

Background The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. Description At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. Conclusion The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp. PMID:16737546

Managing Large Scale Project Analysis Teams through a Web Accessible Database

NASA Technical Reports Server (NTRS)

O'Neil, Daniel A.

2008-01-01

Large scale space programs analyze thousands of requirements while mitigating safety, performance, schedule, and cost risks. These efforts involve a variety of roles with interdependent use cases and goals. For example, study managers and facilitators identify ground-rules and assumptions for a collection of studies required for a program or project milestone. Task leaders derive product requirements from the ground rules and assumptions and describe activities to produce needed analytical products. Disciplined specialists produce the specified products and load results into a file management system. Organizational and project managers provide the personnel and funds to conduct the tasks. Each role has responsibilities to establish information linkages and provide status reports to management. Projects conduct design and analysis cycles to refine designs to meet the requirements and implement risk mitigation plans. At the program level, integrated design and analysis cycles studies are conducted to eliminate every 'to-be-determined' and develop plans to mitigate every risk. At the agency level, strategic studies analyze different approaches to exploration architectures and campaigns. This paper describes a web-accessible database developed by NASA to coordinate and manage tasks at three organizational levels. Other topics in this paper cover integration technologies and techniques for process modeling and enterprise architectures.

A new relational database structure and online interface for the HITRAN database

NASA Astrophysics Data System (ADS)

Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

2013-11-01

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Secure, web-accessible call rosters for academic radiology departments.

PubMed

Nguyen, A V; Tellis, W M; Avrin, D E

2000-05-01

Traditionally, radiology department call rosters have been posted via paper and bulletin boards. Frequently, changes to these lists are made by multiple people independently, but often not synchronized, resulting in confusion among the house staff and technical staff as to who is on call and when. In addition, multiple and disparate copies exist in different sections of the department, and changes made would not be propagated to all the schedules. To eliminate such difficulties, a paperless call scheduling application was developed. Our call scheduling program allowed Java-enabled web access to a database by designated personnel from each radiology section who have privileges to make the necessary changes. Once a person made a change, everyone accessing the database would see the modification. This eliminates the chaos resulting from people swapping shifts at the last minute and not having the time to record or broadcast the change. Furthermore, all changes to the database were logged. Users are given a log-in name and password and can only edit their section; however, all personnel have access to all sections' schedules. Our applet was written in Java 2 using the latest technology in database access. We access our Interbase database through the DataExpress and DB Swing (Borland, Scotts Valley, CA) components. The result is secure access to the call rosters via the web. There are many advantages to the web-enabled access, mainly the ability for people to make changes and have the changes recorded and propagated in a single virtual location and available to all who need to know.

Advancements in web-database applications for rabies surveillance.

PubMed

Rees, Erin E; Gendron, Bruno; Lelièvre, Frédérick; Coté, Nathalie; Bélanger, Denise

2011-08-02

Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include (1) automatic integration of multi-agency data and diagnostic results on a daily basis; (2) a web-based data editing interface that enables authorized users to add, edit and extract data; and (3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response.

Advancements in web-database applications for rabies surveillance

PubMed Central

2011-01-01

Background Protection of public health from rabies is informed by the analysis of surveillance data from human and animal populations. In Canada, public health, agricultural and wildlife agencies at the provincial and federal level are responsible for rabies disease control, and this has led to multiple agency-specific data repositories. Aggregation of agency-specific data into one database application would enable more comprehensive data analyses and effective communication among participating agencies. In Québec, RageDB was developed to house surveillance data for the raccoon rabies variant, representing the next generation in web-based database applications that provide a key resource for the protection of public health. Results RageDB incorporates data from, and grants access to, all agencies responsible for the surveillance of raccoon rabies in Québec. Technological advancements of RageDB to rabies surveillance databases include 1) automatic integration of multi-agency data and diagnostic results on a daily basis; 2) a web-based data editing interface that enables authorized users to add, edit and extract data; and 3) an interactive dashboard to help visualize data simply and efficiently, in table, chart, and cartographic formats. Furthermore, RageDB stores data from citizens who voluntarily report sightings of rabies suspect animals. We also discuss how sightings data can indicate public perception to the risk of racoon rabies and thus aid in directing the allocation of disease control resources for protecting public health. Conclusions RageDB provides an example in the evolution of spatio-temporal database applications for the storage, analysis and communication of disease surveillance data. The database was fast and inexpensive to develop by using open-source technologies, simple and efficient design strategies, and shared web hosting. The database increases communication among agencies collaborating to protect human health from raccoon rabies. Furthermore, health agencies have real-time access to a wide assortment of data documenting new developments in the raccoon rabies epidemic and this enables a more timely and appropriate response. PMID:21810215

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool; Part 5 - WW3 Database

DTIC Science & Technology

2015-02-01

Program ( CDIP ); and Part 4 for the Great Lakes Observing System/Coastal Forecasting System (GLOS/GLCFS). Using step-by-step instructions, this Part 5...Demirbilek, Z., L. Lin, and D. Wilson. 2014a. WaveNet: A web-based metocean data access, processing, and analysis tool; part 3– CDIP database

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2010-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2009-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank(R) staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

AlzPharm: integration of neurodegeneration data using RDF.

PubMed

Lam, Hugo Y K; Marenco, Luis; Clark, Tim; Gao, Yong; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi

2007-05-09

Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.

AlzPharm: integration of neurodegeneration data using RDF

PubMed Central

Lam, Hugo YK; Marenco, Luis; Clark, Tim; Gao, Yong; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi

2007-01-01

Background Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. Results We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Conclusion Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields. PMID:17493287

EST-PAC a web package for EST annotation and protein sequence prediction

PubMed Central

Strahm, Yvan; Powell, David; Lefèvre, Christophe

2006-01-01

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics. PMID:17147782

Fermilab Security Site Access Request Database

Science.gov Websites

Fermilab Security Site Access Request Database Use of the online version of the Fermilab Security Site Access Request Database requires that you login into the ESH&Q Web Site. Note: Only Fermilab generated from the ESH&Q Section's Oracle database on May 27, 2018 05:48 AM. If you have a question

JAX Colony Management System (JCMS): an extensible colony and phenotype data management system.

PubMed

Donnelly, Chuck J; McFarland, Mike; Ames, Abigail; Sundberg, Beth; Springer, Dave; Blauth, Peter; Bult, Carol J

2010-04-01

The Jackson Laboratory Colony Management System (JCMS) is a software application for managing data and information related to research mouse colonies, associated biospecimens, and experimental protocols. JCMS runs directly on computers that run one of the PC Windows operating systems, but can be accessed via web browser interfaces from any computer running a Windows, Macintosh, or Linux operating system. JCMS can be configured for a single user or multiple users in small- to medium-size work groups. The target audience for JCMS includes laboratory technicians, animal colony managers, and principal investigators. The application provides operational support for colony management and experimental workflows, sample and data tracking through transaction-based data entry forms, and date-driven work reports. Flexible query forms allow researchers to retrieve database records based on user-defined criteria. Recent advances in handheld computers with integrated barcode readers, middleware technologies, web browsers, and wireless networks add to the utility of JCMS by allowing real-time access to the database from any networked computer.

PlantRGDB: A Database of Plant Retrocopied Genes.

PubMed

Wang, Yi

2017-01-01

RNA-based gene duplication, known as retrocopy, plays important roles in gene origination and genome evolution. The genomes of many plants have been sequenced, offering an opportunity to annotate and mine the retrocopies in plant genomes. However, comprehensive and unified annotation of retrocopies in these plants is still lacking. In this study I constructed the PlantRGDB (Plant Retrocopied Gene DataBase), the first database of plant retrocopies, to provide a putatively complete centralized list of retrocopies in plant genomes. The database is freely accessible at http://probes.pw.usda.gov/plantrgdb or http://aegilops.wheat.ucdavis.edu/plantrgdb. It currently integrates 49 plant species and 38,997 retrocopies along with characterization information. PlantRGDB provides a user-friendly web interface for searching, browsing and downloading the retrocopies in the database. PlantRGDB also offers graphical viewer-integrated sequence information for displaying the structure of each retrocopy. The attributes of the retrocopies of each species are reported using a browse function. In addition, useful tools, such as an advanced search and BLAST, are available to search the database more conveniently. In conclusion, the database will provide a web platform for obtaining valuable insight into the generation of retrocopies and will supplement research on gene duplication and genome evolution in plants. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Latest developments for the IAGOS database: Interoperability and metadata

NASA Astrophysics Data System (ADS)

Boulanger, Damien; Gautron, Benoit; Thouret, Valérie; Schultz, Martin; van Velthoven, Peter; Broetz, Bjoern; Rauthe-Schöch, Armin; Brissebrat, Guillaume

2014-05-01

In-service Aircraft for a Global Observing System (IAGOS, http://www.iagos.org) aims at the provision of long-term, frequent, regular, accurate, and spatially resolved in situ observations of the atmospheric composition. IAGOS observation systems are deployed on a fleet of commercial aircraft. The IAGOS database is an essential part of the global atmospheric monitoring network. Data access is handled by open access policy based on the submission of research requests which are reviewed by the PIs. Users can access the data through the following web sites: http://www.iagos.fr or http://www.pole-ether.fr as the IAGOS database is part of the French atmospheric chemistry data centre ETHER (CNES and CNRS). The database is in continuous development and improvement. In the framework of the IGAS project (IAGOS for GMES/COPERNICUS Atmospheric Service), major achievements will be reached, such as metadata and format standardisation in order to interoperate with international portals and other databases, QA/QC procedures and traceability, CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) data integration within the central database, and the real-time data transmission. IGAS work package 2 aims at providing the IAGOS data to users in a standardized format including the necessary metadata and information on data processing, data quality and uncertainties. We are currently redefining and standardizing the IAGOS metadata for interoperable use within GMES/Copernicus. The metadata are compliant with the ISO 19115, INSPIRE and NetCDF-CF conventions. IAGOS data will be provided to users in NetCDF or NASA Ames format. We also are implementing interoperability between all the involved IAGOS data services, including the central IAGOS database, the former MOZAIC and CARIBIC databases, Aircraft Research DLR database and the Jülich WCS web application JOIN (Jülich OWS Interface) which combines model outputs with in situ data for intercomparison. The optimal data transfer protocol is being investigated to insure the interoperability. To facilitate satellite and model validation, tools will be made available for co-location and comparison with IAGOS. We will enhance the JOIN application in order to properly display aircraft data as vertical profiles and along individual flight tracks and to allow for graphical comparison to model results that are accessible through interoperable web services, such as the daily products from the GMES/Copernicus atmospheric service.

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

PubMed

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B; Almon, Richard R; DuBois, Debra C; Jusko, William J; Hoffman, Eric P

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp).

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface

PubMed Central

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B.; Almon, Richard R.; DuBois, Debra C.; Jusko, William J.; Hoffman, Eric P.

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp). PMID:14681485

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

PubMed

Li, Chen; Courtot, Mélanie; Le Novère, Nicolas; Laibe, Camille

2010-05-01

Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.

Development of a web-based video management and application processing system

NASA Astrophysics Data System (ADS)

Chan, Shermann S.; Wu, Yi; Li, Qing; Zhuang, Yueting

2001-07-01

How to facilitate efficient video manipulation and access in a web-based environment is becoming a popular trend for video applications. In this paper, we present a web-oriented video management and application processing system, based on our previous work on multimedia database and content-based retrieval. In particular, we extend the VideoMAP architecture with specific web-oriented mechanisms, which include: (1) Concurrency control facilities for the editing of video data among different types of users, such as Video Administrator, Video Producer, Video Editor, and Video Query Client; different users are assigned various priority levels for different operations on the database. (2) Versatile video retrieval mechanism which employs a hybrid approach by integrating a query-based (database) mechanism with content- based retrieval (CBR) functions; its specific language (CAROL/ST with CBR) supports spatio-temporal semantics of video objects, and also offers an improved mechanism to describe visual content of videos by content-based analysis method. (3) Query profiling database which records the `histories' of various clients' query activities; such profiles can be used to provide the default query template when a similar query is encountered by the same kind of users. An experimental prototype system is being developed based on the existing VideoMAP prototype system, using Java and VC++ on the PC platform.

Teaching resources for dermatology on the WWW--quiz system and dynamic lecture scripts using a HTTP-database demon.

PubMed Central

Bittorf, A.; Diepgen, T. L.

1996-01-01

The World Wide Web (WWW) is becoming the major way of acquiring information in all scientific disciplines as well as in business. It is very well suitable for fast distribution and exchange of up to date teaching resources. However, to date most teaching applications on the Web do not use its full power by integrating interactive components. We have set up a computer based training (CBT) framework for Dermatology, which consists of dynamic lecture scripts, case reports, an atlas and a quiz system. All these components heavily rely on an underlying image database that permits the creation of dynamic documents. We used a demon process that keeps the database open and can be accessed using HTTP to achieve better performance and avoid the overhead involved by starting CGI-processes. The result of our evaluation was very encouraging. Images Figure 3 PMID:8947625

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

The article describes the developed database designed as comprehensive data storage of the fixed target experiment BM@N [1] at Joint Institute for Nuclear Research (JINR) in Dubna. The structure and purposes of the BM@N facility will be briefly presented. The scheme of the unified database and its parameters will be described in detail. The use of the BM@N database implemented on the PostgreSQL database management system (DBMS) allows one to provide user access to the actual information of the experiment. Also the interfaces developed for the access to the database will be presented. One was implemented as the set of C++ classes to access the data without SQL statements, the other-Web-interface being available on the Web page of the BM@N experiment.

RAIN: RNA–protein Association and Interaction Networks

PubMed Central

Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan

2017-01-01

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain PMID:28077569

WebCN: A web-based computation tool for in situ-produced cosmogenic nuclides

NASA Astrophysics Data System (ADS)

Ma, Xiuzeng; Li, Yingkui; Bourgeois, Mike; Caffee, Marc; Elmore, David; Granger, Darryl; Muzikar, Paul; Smith, Preston

2007-06-01

Cosmogenic nuclide techniques are increasingly being utilized in geoscience research. For this it is critical to establish an effective, easily accessible and well defined tool for cosmogenic nuclide computations. We have been developing a web-based tool (WebCN) to calculate surface exposure ages and erosion rates based on the nuclide concentrations measured by the accelerator mass spectrometry. WebCN for 10Be and 26Al has been finished and published at http://www.physics.purdue.edu/primelab/for_users/rockage.html. WebCN for 36Cl is under construction. WebCN is designed as a three-tier client/server model and uses the open source PostgreSQL for the database management and PHP for the interface design and calculations. On the client side, an internet browser and Microsoft Access are used as application interfaces to access the system. Open Database Connectivity is used to link PostgreSQL and Microsoft Access. WebCN accounts for both spatial and temporal distributions of the cosmic ray flux to calculate the production rates of in situ-produced cosmogenic nuclides at the Earth's surface.

The Web-Database Connection Tools for Sharing Information on the Campus Intranet.

ERIC Educational Resources Information Center

Thibeault, Nancy E.

This paper evaluates four tools for creating World Wide Web pages that interface with Microsoft Access databases: DB Gateway, Internet Database Assistant (IDBA), Microsoft Internet Database Connector (IDC), and Cold Fusion. The system requirements and features of each tool are discussed. A sample application, "The Virtual Help Desk"…

An evaluation of the availability, accessibility, and quality of online content of vascular surgery training program websites for residency and fellowship applicants.

PubMed

Huang, Bryant Y; Hicks, Taylor D; Haidar, Georges M; Pounds, Lori L; Davies, Mark G

2017-12-01

Vascular surgery residency and fellowship applicants commonly seek information about programs from the Internet. Lack of an effective web presence curtails the ability of programs to attract applicants, and in turn applicants may be unable to ascertain which programs are the best fit for their career aspirations. This study was designed to evaluate the presence, accessibility, comprehensiveness, and quality of vascular surgery training websites (VSTW). A list of accredited vascular surgery training programs (integrated residencies and fellowships) was obtained from four databases for vascular surgery education: the Accreditation Council for Graduate Medical Education, Electronic Residency Application Service, Fellowship and Residency Electronic Interactive Database, and Society for Vascular Surgery. Programs participating in the 2016 National Resident Matching Program were eligible for study inclusion. Accessibility of VSTW was determined by surveying the Accreditation Council for Graduate Medical Education, Electronic Residency Application Service, and Fellowship and Residency Electronic Interactive Database for the total number of programs listed and for the presence or absence of website links. VSTW were analyzed for the availability of recruitment and education content items. The quality of VSTW was determined as a composite of four dimensions: content, design, organization, and user friendliness. Percent agreements and kappa statistics were calculated for inter-rater reliability. Eighty-nine of the 94 fellowship (95%) and 45 of the 48 integrated residencies (94%) programs participating in the 2016 Match had a VSTW. For program recruitment, evaluators found an average of 12 of 32 content items (35.0%) for fellowship programs and an average of 12 of 32 (37%) for integrated residencies. Only 47.1% of fellowship programs (53% integrated residencies) specified the number of positions available for the 2016 Match, 20% (13% integrated residencies) indicated alumni career placement, 34% (38% integrated residencies) supplied interview dates, and merely 17% (18% integrated residencies) detailed the selection process. For program education, fellowship websites provided an average of 5.1 of 15 content items (34.0%), and integrated residency websites provided 5 of 14 items (34%). Of the fellowship programs, 66% (84.4% integrated residencies) provided a rotation schedule, 65% (56% integrated residencies) detailed operative experiences, 38% (38% integrated residencies) posted conference schedules, and just 16% (28.9% integrated residencies) included simulation training. The web presence of vascular surgery training programs lacks sufficient accessibility, content, organization, design, and user friendliness to allow applicants to access information that informs them sufficiently. There are opportunities to more effectively use VSTW for the benefit of training programs and prospective applicants. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

An end-to-end secure patient information access card system.

PubMed

Alkhateeb, A; Singer, H; Yakami, M; Takahashi, T

2000-03-01

The rapid development of the Internet and the increasing interest in Internet-based solutions has promoted the idea of creating Internet-based health information applications. This will force a change in the role of IC cards in healthcare card systems from a data carrier to an access key medium. At the Medical Informatics Department of Kyoto University Hospital we are developing a smart card patient information project where patient databases are accessed via the Internet. Strong end-to-end data encryption is performed via Secure Socket Layers, transparent to transmit patient information. The smart card is playing the crucial role of access key to the database: user authentication is performed internally without ever revealing the actual key. For easy acceptance by healthcare professionals, the user interface is integrated as a plug-in for two familiar Web browsers, Netscape Navigator and MS Internet Explorer.

Turning Access into a web-enabled secure information system for clinical trials.

PubMed

Dongquan Chen; Chen, Wei-Bang; Soong, Mayhue; Soong, Seng-Jaw; Orthner, Helmuth F

2009-08-01

Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. We report a working procedure to transform and develop a standalone Access database into a secure Web-based secure information system. For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. The system lacks audit trails. The cost of development and maintenance may hinder its wide application. The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

PubMed

Katayama, Toshiaki; Wilkinson, Mark D; Micklem, Gos; Kawashima, Shuichi; Yamaguchi, Atsuko; Nakao, Mitsuteru; Yamamoto, Yasunori; Okamoto, Shinobu; Oouchida, Kenta; Chun, Hong-Woo; Aerts, Jan; Afzal, Hammad; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Belleau, Francois; Bolleman, Jerven; Bonnal, Raoul Jp; Chapman, Brad; Cock, Peter Ja; Eriksson, Tore; Gordon, Paul Mk; Goto, Naohisa; Hayashi, Kazuhiro; Horn, Heiko; Ishiwata, Ryosuke; Kaminuma, Eli; Kasprzyk, Arek; Kawaji, Hideya; Kido, Nobuhiro; Kim, Young Joo; Kinjo, Akira R; Konishi, Fumikazu; Kwon, Kyung-Hoon; Labarga, Alberto; Lamprecht, Anna-Lena; Lin, Yu; Lindenbaum, Pierre; McCarthy, Luke; Morita, Hideyuki; Murakami, Katsuhiko; Nagao, Koji; Nishida, Kozo; Nishimura, Kunihiro; Nishizawa, Tatsuya; Ogishima, Soichi; Ono, Keiichiro; Oshita, Kazuki; Park, Keun-Joon; Prins, Pjotr; Saito, Taro L; Samwald, Matthias; Satagopam, Venkata P; Shigemoto, Yasumasa; Smith, Richard; Splendiani, Andrea; Sugawara, Hideaki; Taylor, James; Vos, Rutger A; Withers, David; Yamasaki, Chisato; Zmasek, Christian M; Kawamoto, Shoko; Okubo, Kosaku; Asai, Kiyoshi; Takagi, Toshihisa

2013-02-11

BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

PubMed Central

2013-01-01

Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer. PMID:23398680

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

PubMed

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

NUREBASE: database of nuclear hormone receptors.

PubMed

Duarte, Jorge; Perrière, Guy; Laudet, Vincent; Robinson-Rechavi, Marc

2002-01-01

Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature of nuclear receptors, we have developed NUREBASE, a database containing protein and DNA sequences, reviewed protein alignments and phylogenies, taxonomy and annotations for all nuclear receptors. The reviewed NUREBASE is completed by NUREBASE_DAILY, automatically updated every 24 h. Both databases are organized under a client/server architecture, with a client written in Java which runs on any platform. This client, named FamFetch, integrates a graphical interface allowing selection of families, and manipulation of phylogenies and alignments. NUREBASE sequence data is also accessible through a World Wide Web server, allowing complex queries. All information on accessing and installing NUREBASE may be found at http://www.ens-lyon.fr/LBMC/laudet/nurebase.html.

Accident/Mishap Investigation System

NASA Technical Reports Server (NTRS)

Keller, Richard; Wolfe, Shawn; Gawdiak, Yuri; Carvalho, Robert; Panontin, Tina; Williams, James; Sturken, Ian

2007-01-01

InvestigationOrganizer (IO) is a Web-based collaborative information system that integrates the generic functionality of a database, a document repository, a semantic hypermedia browser, and a rule-based inference system with specialized modeling and visualization functionality to support accident/mishap investigation teams. This accessible, online structure is designed to support investigators by allowing them to make explicit, shared, and meaningful links among evidence, causal models, findings, and recommendations.

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

The Planetary Virtual Observatory and Laboratory (PVOL) and its integration into the Virtual European Solar and Planetary Access (VESPA)

NASA Astrophysics Data System (ADS)

Hueso, R.; Juaristi, J.; Legarreta, J.; Sánchez-Lavega, A.; Rojas, J. F.; Erard, S.; Cecconi, B.; Le Sidaner, Pierre

2018-01-01

Since 2003 the Planetary Virtual Observatory and Laboratory (PVOL) has been storing and serving publicly through its web site a large database of amateur observations of the Giant Planets (Hueso et al., 2010a). These images are used for scientific research of the atmospheric dynamics and cloud structure on these planets and constitute a powerful resource to address time variable phenomena in their atmospheres. Advances over the last decade in observation techniques, and a wider recognition by professional astronomers of the quality of amateur observations, have resulted in the need to upgrade this database. We here present major advances in the PVOL database, which has evolved into a full virtual planetary observatory encompassing also observations of Mercury, Venus, Mars, the Moon and the Galilean satellites. Besides the new objects, the images can be tagged and the database allows simple and complex searches over the data. The new web service: PVOL2 is available online in http://pvol2.ehu.eus/.

SeqDepot: streamlined database of biological sequences and precomputed features.

PubMed

Ulrich, Luke E; Zhulin, Igor B

2014-01-15

Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot-a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to >28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines. Freely available on the web at http://seqdepot.net/. RESTaccess via http://seqdepot.net/api/v1. Database files and scripts maybe downloaded from http://seqdepot.net/download.

Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

2013-12-01

The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

Accessibility and quality of online information for pediatric orthopaedic surgery fellowships.

PubMed

Davidson, Austin R; Murphy, Robert F; Spence, David D; Kelly, Derek M; Warner, William C; Sawyer, Jeffrey R

2014-12-01

Pediatric orthopaedic fellowship applicants commonly use online-based resources for information on potential programs. Two primary sources are the San Francisco Match (SF Match) database and the Pediatric Orthopaedic Society of North America (POSNA) database. We sought to determine the accessibility and quality of information that could be obtained by using these 2 sources. The online databases of the SF Match and POSNA were reviewed to determine the availability of embedded program links or external links for the included programs. If not available in the SF Match or POSNA data, Web sites for listed programs were located with a Google search. All identified Web sites were analyzed for accessibility, content volume, and content quality. At the time of online review, 50 programs, offering 68 positions, were listed in the SF Match database. Although 46 programs had links included with their information, 36 (72%) of them simply listed http://www.sfmatch.org as their unique Web site. Ten programs (20%) had external links listed, but only 2 (4%) linked directly to the fellowship web page. The POSNA database does not list any links to the 47 programs it lists, which offer 70 positions. On the basis of a Google search of the 50 programs listed in the SF Match database, web pages were found for 35. Of programs with independent web pages, all had a description of the program and 26 (74%) described their application process. Twenty-nine (83%) listed research requirements, 22 (63%) described the rotation schedule, and 12 (34%) discussed the on-call expectations. A contact telephone number and/or email address was provided by 97% of programs. Twenty (57%) listed both the coordinator and fellowship director, 9 (26%) listed the coordinator only, 5 (14%) listed the fellowship director only, and 1 (3%) had no contact information given. The SF Match and POSNA databases provide few direct links to fellowship Web sites, and individual program Web sites either do not exist or do not effectively convey information about the programs. Improved accessibility and accurate information online would allow potential applicants to obtain information about pediatric fellowships in a more efficient manner.

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.

PubMed

Gonzalez, Sergio; Clavijo, Bernardo; Rivarola, Máximo; Moreno, Patricio; Fernandez, Paula; Dopazo, Joaquín; Paniego, Norma

2017-02-22

In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .

BioPepDB: an integrated data platform for food-derived bioactive peptides.

PubMed

Li, Qilin; Zhang, Chao; Chen, Hongjun; Xue, Jitong; Guo, Xiaolei; Liang, Ming; Chen, Ming

2018-03-12

Food-derived bioactive peptides play critical roles in regulating most biological processes and have considerable biological, medical and industrial importance. However, a large number of active peptides data, including sequence, function, source, commercial product information, references and other information are poorly integrated. BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries. Moreover, BioPepDB provides modules of prediction and hydrolysis-simulation for discovering novel peptides. It can serve as a reference database to investigate the function of different bioactive peptides. BioPepDB is available at http://bis.zju.edu.cn/biopepdbr/ . The web page utilises Apache, PHP5 and MySQL to provide the user interface for accessing the database and predict novel peptides. The database itself is operated on a specialised server.

Getting To Know the "Invisible Web."

ERIC Educational Resources Information Center

Smith, C. Brian

2001-01-01

Discusses the portions of the World Wide Web that cannot be accessed via directories or search engines, explains why they can't be accessed, and offers suggestions for reference librarians to find these sites. Lists helpful resources and gives examples of invisible Web sites which are often databases. (LRW)

Artificial intelligence, neural network, and Internet tool integration in a pathology workstation to improve information access

NASA Astrophysics Data System (ADS)

Sargis, J. C.; Gray, W. A.

1999-03-01

The APWS allows user friendly access to several legacy systems which would normally each demand domain expertise for proper utilization. The generalized model, including objects, classes, strategies and patterns is presented. The core components of the APWS are the Microsoft Windows 95 Operating System, Oracle, Oracle Power Objects, Artificial Intelligence tools, a medical hyperlibrary and a web site. The paper includes a discussion of how could be automated by taking advantage of the expert system, object oriented programming and intelligent relational database tools within the APWS.

A Framework for Transparently Accessing Deep Web Sources

ERIC Educational Resources Information Center

Dragut, Eduard Constantin

2010-01-01

An increasing number of Web sites expose their content via query interfaces, many of them offering the same type of products/services (e.g., flight tickets, car rental/purchasing). They constitute the so-called "Deep Web". Accessing the content on the Deep Web has been a long-standing challenge for the database community. For a user interested in…

Simple re-instantiation of small databases using cloud computing.

PubMed

Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M

2013-01-01

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. PMID:24564380

A web-based electronic patient record (ePR) system for data integration in movement analysis research on wheel-chair users to minimize shoulder pain

NASA Astrophysics Data System (ADS)

Deshpande, Ruchi R.; Requejo, Philip; Sutisna, Erry; Wang, Ximing; Liu, Margaret; McNitt-Gray, Sarah; Ruparel, Puja; Liu, Brent J.

2012-02-01

Patients confined to manual wheel-chairs are at an added risk of shoulder injury. There is a need for developing optimal bio-mechanical techniques for wheel-chair propulsion through movement analysis. Data collected is diverse and in need of normalization and integration. Current databases are ad-hoc and do not provide flexibility, extensibility and ease of access. The need for an efficient means to retrieve specific trial data, display it and compare data from multiple trials is unmet through lack of data association and synchronicity. We propose the development of a robust web-based ePR system that will enhance workflow and facilitate efficient data management.

DRUMS: a human disease related unique gene mutation search engine.

PubMed

Li, Zuofeng; Liu, Xingnan; Wen, Jingran; Xu, Ye; Zhao, Xin; Li, Xuan; Liu, Lei; Zhang, Xiaoyan

2011-10-01

With the completion of the human genome project and the development of new methods for gene variant detection, the integration of mutation data and its phenotypic consequences has become more important than ever. Among all available resources, locus-specific databases (LSDBs) curate one or more specific genes' mutation data along with high-quality phenotypes. Although some genotype-phenotype data from LSDB have been integrated into central databases little effort has been made to integrate all these data by a search engine approach. In this work, we have developed disease related unique gene mutation search engine (DRUMS), a search engine for human disease related unique gene mutation as a convenient tool for biologists or physicians to retrieve gene variant and related phenotype information. Gene variant and phenotype information were stored in a gene-centred relational database. Moreover, the relationships between mutations and diseases were indexed by the uniform resource identifier from LSDB, or another central database. By querying DRUMS, users can access the most popular mutation databases under one interface. DRUMS could be treated as a domain specific search engine. By using web crawling, indexing, and searching technologies, it provides a competitively efficient interface for searching and retrieving mutation data and their relationships to diseases. The present system is freely accessible at http://www.scbit.org/glif/new/drums/index.html. © 2011 Wiley-Liss, Inc.

A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake).

PubMed

Yamamoto, Naoki; Suzuki, Tomohiro; Kobayashi, Masaaki; Dohra, Hideo; Sasaki, Yohei; Hirai, Hirofumi; Yokoyama, Koji; Kawagishi, Hirokazu; Yano, Kentaro

2014-12-03

The angel's wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclose the genes underlying the accident and provide mechanistic insight, we seek to develop an information infrastructure containing omics data. In our previous work, we sequenced the genome and transcriptome using next-generation sequencing techniques. The next step in achieving our goal is to develop a web database to facilitate the efficient mining of large-scale omics data and identification of genes specifically expressed in the mushroom. This paper introduces a web database A-WINGS (http://bioinf.mind.meiji.ac.jp/a-wings/) that provides integrated genomic and transcriptomic information for the angel's wing oyster mushroom. The database contains structure and functional annotations of transcripts and gene expressions. Functional annotations contain information on homologous sequences from NCBI nr and UniProt, Gene Ontology, and KEGG Orthology. Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia. The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches. The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

A design for the geoinformatics system

NASA Astrophysics Data System (ADS)

Allison, M. L.

2002-12-01

Informatics integrates and applies information technologies with scientific and technical disciplines. A geoinformatics system targets the spatially based sciences. The system is not a master database, but will collect pertinent information from disparate databases distributed around the world. Seamless interoperability of databases promises quantum leaps in productivity not only for scientific researchers but also for many areas of society including business and government. The system will incorporate: acquisition of analog and digital legacy data; efficient information and data retrieval mechanisms (via data mining and web services); accessibility to and application of visualization, analysis, and modeling capabilities; online workspace, software, and tutorials; GIS; integration with online scientific journal aggregates and digital libraries; access to real time data collection and dissemination; user-defined automatic notification and quality control filtering for selection of new resources; and application to field techniques such as mapping. In practical terms, such a system will provide the ability to gather data over the Web from a variety of distributed sources, regardless of computer operating systems, database formats, and servers. Search engines will gather data about any geographic location, above, on, or below ground, covering any geologic time, and at any scale or detail. A distributed network of digital geolibraries can archive permanent copies of databases at risk of being discontinued and those that continue to be maintained by the data authors. The geoinformatics system will generate results from widely distributed sources to function as a dynamic data network. Instead of posting a variety of pre-made tables, charts, or maps based on static databases, the interactive dynamic system creates these products on the fly, each time an inquiry is made, using the latest information in the appropriate databases. Thus, in the dynamic system, a map generated today may differ from one created yesterday and one to be created tomorrow, because the databases used to make it are constantly (and sometimes automatically) being updated.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

PubMed Central

Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F.; Christie, Cole H.; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S.; Westbrook, John D.; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M.; Bourne, Philip E.; Burley, Stephen K.

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. PMID:25428375

BioServices: a common Python package to access biological Web Services programmatically.

PubMed

Cokelaer, Thomas; Pultz, Dennis; Harder, Lea M; Serra-Musach, Jordi; Saez-Rodriguez, Julio

2013-12-15

Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework. BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming. BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2011-01-01

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

WikiPEATia - a web based platform for assembling peatland data through ‘crowd sourcing’

NASA Astrophysics Data System (ADS)

Wisser, D.; Glidden, S.; Fieseher, C.; Treat, C. C.; Routhier, M.; Frolking, S. E.

2009-12-01

The Earth System Science community is realizing that peatlands are an important and unique terrestrial ecosystem that has not yet been well-integrated into large-scale earth system analyses. A major hurdle is the lack of accessible, geospatial data of peatland distribution, coupled with data on peatland properties (e.g., vegetation composition, peat depth, basal dates, soil chemistry, peatland class) at the global scale. This data, however, is available at the local scale. Although a comprehensive global database on peatlands probably lags similar data on more economically important ecosystems such as forests, grasslands, croplands, a large amount of field data have been collected over the past several decades. A few efforts have been made to map peatlands at large scales but existing data have not been assembled into a single geospatial database that is publicly accessible or do not depict data with a level of detail that is needed in the Earth System Science Community. A global peatland database would contribute to advances in a number of research fields such as hydrology, vegetation and ecosystem modeling, permafrost modeling, and earth system modeling. We present a Web 2.0 approach that uses state-of-the-art webserver and innovative online mapping technologies and is designed to create such a global database through ‘crowd-sourcing’. Primary functions of the online system include form-driven textual user input of peatland research metadata, spatial data input of peatland areas via a mapping interface, database editing and querying editing capabilities, as well as advanced visualization and data analysis tools. WikiPEATia provides an integrated information technology platform for assembling, integrating, and posting peatland-related geospatial datasets facilitates and encourages research community involvement. A successful effort will make existing peatland data much more useful to the research community, and will help to identify significant data gaps.

U.S. Geological Survey Community for Data Integration-NWIS Web Services Snapshot Tool for ArcGIS

USGS Publications Warehouse

Holl, Sally

2011-01-01

U.S. Geological Survey (USGS) data resources are so vast that many scientists are unaware of data holdings that may be directly relevant to their research. Data are also difficult to access and large corporate databases, such as the National Water Information System (NWIS) that houses hydrologic data for the Nation, are challenging to use without considerable expertise and investment of time. The USGS Community for Data Integration (CDI) was established in 2009 to address data and information management issues affecting the proficiency of earth science research. A CDI workshop convened in 2009 identified common data integration needs of USGS scientists and targeted high value opportunities that might address these needs by leveraging existing projects in USGS science centers, in-kind contributions, and supplemental funding. To implement this strategy, CDI sponsored a software development project in 2010 to facilitate access and use of NWIS data with ArcGIS, a widely used Geographic Information System. The resulting software product, the NWIS Web Services Snapshot Tool for ArcGIS, is presented here.

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

PubMed Central

2013-01-01

Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

2013-03-01

Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

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

Reddy, Tatiparthi B. K.; Thomas, Alex D.; Stamatis, Dimitri

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencingmore » projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.« less

WaveNet: A Web-Based Metocean Data Access, Processing and Analysis Tool. Part 4 - GLOS/GLCFS Database

DTIC Science & Technology

2014-06-01

and Coastal Data Information Program ( CDIP ). This User’s Guide includes step-by-step instructions for accessing the GLOS/GLCFS database via WaveNet...access, processing and analysis tool; part 3 – CDIP database. ERDC/CHL CHETN-xx-14. Vicksburg, MS: U.S. Army Engineer Research and Development Center

Biological Web Service Repositories Review

PubMed Central

Urdidiales‐Nieto, David; Navas‐Delgado, Ismael

2016-01-01

Abstract Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re‐execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re‐check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well‐known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. PMID:27783459

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

Bikakis, Nikos; Gioldasis, Nektarios; Tsinaraki, Chrisa; Christodoulakis, Stavros

SPARQL is today the standard access language for Semantic Web data. In the recent years XML databases have also acquired industrial importance due to the widespread applicability of XML in the Web. In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases. Our approach assumes that fairly generic mappings between ontology constructs and XML Schema constructs have been automatically derived or manually specified. The mappings are used to automatically translate SPARQL queries to semantically equivalent XQuery queries which are used to access the XML databases. We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

NASA Astrophysics Data System (ADS)

Soppera, N.; Bossant, M.; Dupont, E.

2014-06-01

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

JANIS 4: An Improved Version of the NEA Java-based Nuclear Data Information System

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

Soppera, N., E-mail: nicolas.soppera@oecd.org; Bossant, M.; Dupont, E.

JANIS is software developed to facilitate the visualization and manipulation of nuclear data, giving access to evaluated data libraries, and to the EXFOR and CINDA databases. It is stand-alone Java software, downloadable from the web and distributed on DVD. Used offline, the system also makes use of an internet connection to access the NEA Data Bank database. It is now also offered as a full web application, only requiring a browser. The features added in the latest version of the software and this new web interface are described.

From Chaos to Content: An Integrated Approach to Government Web Sites

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

Demuth, Nora H.; Knudson, Christa K.

2005-01-03

The web development team of the Environmental Technology Directorate (ETD) at the U.S. Department of Energy’s Pacific Northwest National Laboratory (PNNL) redesigned the ETD website as a database-driven system, powered by the newly designed ETD Common Information System (ETD-CIS). The ETD website was redesigned in response to an analysis that showed the previous ETD websites were inefficient, costly, and lacking in a consistent focus. Redesigned and newly created websites based on a new ETD template provide a consistent image, meet or exceed accessibility standards, and are linked through a common database. The protocols used in developing the ETD website supportmore » integration of further organizational sites and facilitate internal use by staff and training on ETD website development and maintenance. Other PNNL organizations have approached the ETD web development team with an interest in applying the methods established by the ETD system. The ETD system protocol could potentially be used by other DOE laboratories to improve their website efficiency and content focus. “The tools by which we share science information must be as extraordinary as the information itself.[ ]” – DOE Science Director Raymond Orbach« less

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

New tools and methods for direct programmatic access to the dbSNP relational database.

PubMed

Saccone, Scott F; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A; Rice, John P

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery.

PubMed

Nowotka, Michał M; Gaulton, Anna; Mendez, David; Bento, A Patricia; Hersey, Anne; Leach, Andrew

2017-08-01

ChEMBL is a manually curated database of bioactivity data on small drug-like molecules, used by drug discovery scientists. Among many access methods, a REST API provides programmatic access, allowing the remote retrieval of ChEMBL data and its integration into other applications. This approach allows scientists to move from a world where they go to the ChEMBL web site to search for relevant data, to one where ChEMBL data can be simply integrated into their everyday tools and work environment. Areas covered: This review highlights some of the audiences who may benefit from using the ChEMBL API, and the goals they can address, through the description of several use cases. The examples cover a team communication tool (Slack), a data analytics platform (KNIME), batch job management software (Luigi) and Rich Internet Applications. Expert opinion: The advent of web technologies, cloud computing and micro services oriented architectures have made REST APIs an essential ingredient of modern software development models. The widespread availability of tools consuming RESTful resources have made them useful for many groups of users. The ChEMBL API is a valuable resource of drug discovery bioactivity data for professional chemists, chemistry students, data scientists, scientific and web developers.

X-ray Photoelectron Spectroscopy Database (Version 4.1)

National Institute of Standards and Technology Data Gateway

SRD 20 X-ray Photoelectron Spectroscopy Database (Version 4.1) (Web, free access)   The NIST XPS Database gives access to energies of many photoelectron and Auger-electron spectral lines. The database contains over 22,000 line positions, chemical shifts, doublet splittings, and energy separations of photoelectron and Auger-electron lines.

Development and implementation of a custom integrated database with dashboards to assist with hematopathology specimen triage and traffic

PubMed Central

Azzato, Elizabeth M.; Morrissette, Jennifer J. D.; Halbiger, Regina D.; Bagg, Adam; Daber, Robert D.

2014-01-01

Background: At some institutions, including ours, bone marrow aspirate specimen triage is complex, with hematopathology triage decisions that need to be communicated to downstream ancillary testing laboratories and many specimen aliquot transfers that are handled outside of the laboratory information system (LIS). We developed a custom integrated database with dashboards to facilitate and streamline this workflow. Methods: We developed user-specific dashboards that allow entry of specimen information by technologists in the hematology laboratory, have custom scripting to present relevant information for the hematopathology service and ancillary laboratories and allow communication of triage decisions from the hematopathology service to other laboratories. These dashboards are web-accessible on the local intranet and accessible from behind the hospital firewall on a computer or tablet. Secure user access and group rights ensure that relevant users can edit or access appropriate records. Results: After database and dashboard design, two-stage beta-testing and user education was performed, with the first focusing on technologist specimen entry and the second on downstream users. Commonly encountered issues and user functionality requests were resolved with database and dashboard redesign. Final implementation occurred within 6 months of initial design; users report improved triage efficiency and reduced need for interlaboratory communications. Conclusions: We successfully developed and implemented a custom database with dashboards that facilitates and streamlines our hematopathology bone marrow aspirate triage. This provides an example of a possible solution to specimen communications and traffic that are outside the purview of a standard LIS. PMID:25250187

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.

PubMed

Krallinger, Martin; Rodriguez-Penagos, Carlos; Tendulkar, Ashish; Valencia, Alfonso

2009-07-01

There is an increasing interest in using literature mining techniques to complement information extracted from annotation databases or generated by bioinformatics applications. Here we present PLAN2L, a web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. Our system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. PLAN2L does not require registration and is freely accessible at http://zope.bioinfo.cnio.es/plan2l.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

XCOM: Photon Cross Sections Database

National Institute of Standards and Technology Data Gateway

SRD 8 XCOM: Photon Cross Sections Database (Web, free access)   A web database is provided which can be used to calculate photon cross sections for scattering, photoelectric absorption and pair production, as well as total attenuation coefficients, for any element, compound or mixture (Z <= 100) at energies from 1 keV to 100 GeV.

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

PubMed

Rattei, Thomas; Tischler, Patrick; Götz, Stefan; Jehl, Marc-André; Hoser, Jonathan; Arnold, Roland; Conesa, Ana; Mewes, Hans-Werner

2010-01-01

The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).

A COSTAR interface using WWW technology.

PubMed Central

Rabbani, U.; Morgan, M.; Barnett, O.

1998-01-01

The concentration of industry on modern relational databases has left many nonrelational and proprietary databases without support for integration with new technologies. Emerging interface tools and data-access methodologies can be applied with difficulty to medical record systems which have proprietary data representation. Users of such medical record systems usually must access the clinical content of such record systems with keyboard-intensive and time-consuming interfaces. COSTAR is a legacy ambulatory medical record system developed over 25 years ago that is still popular and extensively used at the Massachusetts General Hospital. We define a model for using middle layer services to extract and cache data from non-relational databases, and present an intuitive World-Wide Web interface to COSTAR. This model has been implemented and successfully piloted in the Internal Medicine Associates at Massachusetts General Hospital. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:9929310

The ESID Online Database network.

PubMed

Guzman, D; Veit, D; Knerr, V; Kindle, G; Gathmann, B; Eades-Perner, A M; Grimbacher, B

2007-03-01

Primary immunodeficiencies (PIDs) belong to the group of rare diseases. The European Society for Immunodeficiencies (ESID), is establishing an innovative European patient and research database network for continuous long-term documentation of patients, in order to improve the diagnosis, classification, prognosis and therapy of PIDs. The ESID Online Database is a web-based system aimed at data storage, data entry, reporting and the import of pre-existing data sources in an enterprise business-to-business integration (B2B). The online database is based on Java 2 Enterprise System (J2EE) with high-standard security features, which comply with data protection laws and the demands of a modern research platform. The ESID Online Database is accessible via the official website (http://www.esid.org/). Supplementary data are available at Bioinformatics online.

Atomic Spectra Database (ASD)

National Institute of Standards and Technology Data Gateway

SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

Correspondence: World Wide Web access to the British Universities Human Embryo Database

PubMed Central

AITON, JAMES F.; MCDONOUGH, ARIANA; MCLACHLAN, JOHN C.; SMART, STEVEN D.; WHITEN, SUSAN C.

1997-01-01

The British Universities Human Embryo Database has been created by merging information from the Walmsley Collection of Human Embryos at the School of Biological and Medical Sciences, University of St Andrews and from the Boyd Collection of Human Embryos at the Department of Anatomy, University of Cambridge. The database has been made available electronically on the Internet and World Wide Web browsers can be used to implement interactive access to the information stored in the British Universities Human Embryo Database. The database can, therefore, be accessed and searched from remote sites and specific embryos can be identified in terms of their location, age, developmental stage, plane of section, staining technique, and other parameters. It is intended to add information from other similar collections in the UK as it becomes available. PMID:9034891

Transition to a Unified System: Using Perl To Drive Library Databases and Enhance Web Site Functionality.

ERIC Educational Resources Information Center

Fagan, Judy Condit

2001-01-01

Discusses the need for libraries to routinely redesign their Web sites, and presents a case study that describes how a Perl-driven database at Southern Illinois University's library improved Web site organization and patron access, simplified revisions, and allowed staff unfamiliar with HTML to update content. (Contains 56 references.) (Author/LRW)

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

Conceptual Model Formalization in a Semantic Interoperability Service Framework: Transforming Relational Database Schemas to OWL.

PubMed

Bravo, Carlos; Suarez, Carlos; González, Carolina; López, Diego; Blobel, Bernd

2014-01-01

Healthcare information is distributed through multiple heterogeneous and autonomous systems. Access to, and sharing of, distributed information sources are a challenging task. To contribute to meeting this challenge, this paper presents a formal, complete and semi-automatic transformation service from Relational Databases to Web Ontology Language. The proposed service makes use of an algorithm that allows to transform several data models of different domains by deploying mainly inheritance rules. The paper emphasizes the relevance of integrating the proposed approach into an ontology-based interoperability service to achieve semantic interoperability.

TISSUES 2.0: an integrative web resource on mammalian tissue expression

PubMed Central

Palasca, Oana; Santos, Alberto; Stolte, Christian; Gorodkin, Jan; Jensen, Lars Juhl

2018-01-01

Abstract Physiological and molecular similarities between organisms make it possible to translate findings from simpler experimental systems—model organisms—into more complex ones, such as human. This translation facilitates the understanding of biological processes under normal or disease conditions. Researchers aiming to identify the similarities and differences between organisms at the molecular level need resources collecting multi-organism tissue expression data. We have developed a database of gene–tissue associations in human, mouse, rat and pig by integrating multiple sources of evidence: transcriptomics covering all four species and proteomics (human only), manually curated and mined from the scientific literature. Through a scoring scheme, these associations are made comparable across all sources of evidence and across organisms. Furthermore, the scoring produces a confidence score assigned to each of the associations. The TISSUES database (version 2.0) is publicly accessible through a user-friendly web interface and as part of the STRING app for Cytoscape. In addition, we analyzed the agreement between datasets, across and within organisms, and identified that the agreement is mainly affected by the quality of the datasets rather than by the technologies used or organisms compared. Database URL: http://tissues.jensenlab.org/ PMID:29617745

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.

STINGRAY: system for integrated genomic resources and analysis.

PubMed

Wagner, Glauber; Jardim, Rodrigo; Tschoeke, Diogo A; Loureiro, Daniel R; Ocaña, Kary A C S; Ribeiro, Antonio C B; Emmel, Vanessa E; Probst, Christian M; Pitaluga, André N; Grisard, Edmundo C; Cavalcanti, Maria C; Campos, Maria L M; Mattoso, Marta; Dávila, Alberto M R

2014-03-07

The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

STINGRAY: system for integrated genomic resources and analysis

PubMed Central

2014-01-01

Background The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/. PMID:24606808

MAPI: a software framework for distributed biomedical applications

PubMed Central

2013-01-01

Background The amount of web-based resources (databases, tools etc.) in biomedicine has increased, but the integrated usage of those resources is complex due to differences in access protocols and data formats. However, distributed data processing is becoming inevitable in several domains, in particular in biomedicine, where researchers face rapidly increasing data sizes. This big data is difficult to process locally because of the large processing, memory and storage capacity required. Results This manuscript describes a framework, called MAPI, which provides a uniform representation of resources available over the Internet, in particular for Web Services. The framework enhances their interoperability and collaborative use by enabling a uniform and remote access. The framework functionality is organized in modules that can be combined and configured in different ways to fulfil concrete development requirements. Conclusions The framework has been tested in the biomedical application domain where it has been a base for developing several clients that are able to integrate different web resources. The MAPI binaries and documentation are freely available at http://www.bitlab-es.com/mapi under the Creative Commons Attribution-No Derivative Works 2.5 Spain License. The MAPI source code is available by request (GPL v3 license). PMID:23311574

Collaboration systems for classroom instruction

NASA Astrophysics Data System (ADS)

Chen, C. Y. Roger; Meliksetian, Dikran S.; Chang, Martin C.

1996-01-01

In this paper we discuss how classroom instruction can benefit from state-of-the-art technologies in networks, worldwide web access through Internet, multimedia, databases, and computing. Functional requirements for establishing such a high-tech classroom are identified, followed by descriptions of our current experimental implementations. The focus of the paper is on the capabilities of distributed collaboration, which supports both synchronous multimedia information sharing as well as a shared work environment for distributed teamwork and group decision making. Our ultimate goal is to achieve the concept of 'living world in a classroom' such that live and dynamic up-to-date information and material from all over the world can be integrated into classroom instruction on a real-time basis. We describe how we incorporate application developments in a geography study tool, worldwide web information retrievals, databases, and programming environments into the collaborative system.

Java Web Simulation (JWS); a web based database of kinetic models.

PubMed

Snoep, J L; Olivier, B G

2002-01-01

Software to make a database of kinetic models accessible via the internet has been developed and a core database has been set up at http://jjj.biochem.sun.ac.za/. This repository of models, available to everyone with internet access, opens a whole new way in which we can make our models public. Via the database, a user can change enzyme parameters and run time simulations or steady state analyses. The interface is user friendly and no additional software is necessary. The database currently contains 10 models, but since the generation of the program code to include new models has largely been automated the addition of new models is straightforward and people are invited to submit their models to be included in the database.

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

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

Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

2002-01-01

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easymore » access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.« less

Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

PubMed

Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

2014-01-01

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

PomBase: a comprehensive online resource for fission yeast

PubMed Central

Wood, Valerie; Harris, Midori A.; McDowall, Mark D.; Rutherford, Kim; Vaughan, Brendan W.; Staines, Daniel M.; Aslett, Martin; Lock, Antonia; Bähler, Jürg; Kersey, Paul J.; Oliver, Stephen G.

2012-01-01

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance. PMID:22039153

Binary Coded Web Access Pattern Tree in Education Domain

ERIC Educational Resources Information Center

Gomathi, C.; Moorthi, M.; Duraiswamy, K.

2008-01-01

Web Access Pattern (WAP), which is the sequence of accesses pursued by users frequently, is a kind of interesting and useful knowledge in practice. Sequential Pattern mining is the process of applying data mining techniques to a sequential database for the purposes of discovering the correlation relationships that exist among an ordered list of…

Follicle Online: an integrated database of follicle assembly, development and ovulation.

PubMed

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Cooke, Howard J; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43,000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php © The Author(s) 2015. Published by Oxford University Press.

Follicle Online: an integrated database of follicle assembly, development and ovulation

PubMed Central

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database ‘Follicle Online’ that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43 000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php PMID:25931457

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.

PubMed

Nicolazzi, Ezequiel L; Caprera, Andrea; Nazzicari, Nelson; Cozzi, Paolo; Strozzi, Francesco; Lawley, Cindy; Pirani, Ali; Soans, Chandrasen; Brew, Fiona; Jorjani, Hossein; Evans, Gary; Simpson, Barry; Tosser-Klopp, Gwenola; Brauning, Rudiger; Williams, John L; Stella, Alessandra

2015-04-10

In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information. Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion. This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.

FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

PubMed

Tiemann, Johanna K S; Rose, Alexander S; Ismer, Jochen; Darvish, Mitra D; Hilal, Tarek; Spahn, Christian M T; Hildebrand, Peter W

2018-05-21

Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

Students views of integrating web-based learning technology into the nursing curriculum - A descriptive survey.

PubMed

Adams, Audrey; Timmins, Fiona

2006-01-01

This paper describes students' experiences of a Web-based innovation at one university. This paper reports on the first phase of this development where two Web-based modules were developed. Using a survey approach (n=44) students' access to and use of computer technology were explored. Findings revealed that students' prior use of computers and Internet technologies was higher than previously reported, although use of databases was low. Skills in this area increased during the programme, with a significant rise in database, email, search engine and word processing use. Many specific computer skills were learned during the programme, with high numbers reporting ability to deal adequately with files and folders. Overall, the experience was a positive one for students. While a sense of student isolation was not reported, as many students kept in touch by phone and class attendance continued, some individual students did appear to isolate themselves. This teaching methodology has much to offer in the provision of convenient easy to access programmes that can be easily adapted to the individual lifestyle. However, student support mechanisms need careful consideration for students who are at risk of becoming isolated. Staff also need to supported in the provision of this methodology and face-to-face contact with teachers for some part of the programme is preferable.

The Neotoma Paleoecology Database

NASA Astrophysics Data System (ADS)

Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

2015-12-01

The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community. Research is supported by NSF EAR-0622349.

ARIANE: integration of information databases within a hospital intranet.

PubMed

Joubert, M; Aymard, S; Fieschi, D; Volot, F; Staccini, P; Robert, J J; Fieschi, M

1998-05-01

Large information systems handle massive volume of data stored in heterogeneous sources. Each server has its own model of representation of concepts with regard to its aims. One of the main problems end-users encounter when accessing different servers is to match their own viewpoint on biomedical concepts with the various representations that are made in the databases servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet and to propose a method to realize it. This method is based on the knowledge sources provided by the Unified Medical Language System (UMLS) project of the US National Library of Medicine. Experiments concern queries to three different information servers: PubMed, a Medline server of the NLM; Thériaque, a French database on drugs implemented in the Hospital Intranet; and a Web site dedicated to Internet resources in gastroenterology and nutrition, located at the Faculty of Medicine of Nice (France). Accessing to each of these servers is different according to the kind of information delivered and according to the technology used to query it. Dealing with health care professional workstation, the authors introduced in the ARIANE project quality criteria in order to attempt a homogeneous and efficient way to build a query system able to be integrated in existing information systems and to integrate existing and new information sources.

Automated grading of homework assignments and tests in introductory and intermediate statistics courses using active server pages.

PubMed

Stockburger, D W

1999-05-01

Active server pages permit a software developer to customize the Web experience for users by inserting server-side script and database access into Web pages. This paper describes applications of these techniques and provides a primer on the use of these methods. Applications include a system that generates and grades individualized homework assignments and tests for statistics students. The student accesses the system as a Web page, prints out the assignment, does the assignment, and enters the answers on the Web page. The server, running on NT Server 4.0, grades the assignment, updates the grade book (on a database), and returns the answer key to the student.

A scalable architecture for extracting, aligning, linking, and visualizing multi-Int data

NASA Astrophysics Data System (ADS)

Knoblock, Craig A.; Szekely, Pedro

2015-05-01

An analyst today has a tremendous amount of data available, but each of the various data sources typically exists in their own silos, so an analyst has limited ability to see an integrated view of the data and has little or no access to contextual information that could help in understanding the data. We have developed the Domain-Insight Graph (DIG) system, an innovative architecture for extracting, aligning, linking, and visualizing massive amounts of domain-specific content from unstructured sources. Under the DARPA Memex program we have already successfully applied this architecture to multiple application domains, including the enormous international problem of human trafficking, where we extracted, aligned and linked data from 50 million online Web pages. DIG builds on our Karma data integration toolkit, which makes it easy to rapidly integrate structured data from a variety of sources, including databases, spreadsheets, XML, JSON, and Web services. The ability to integrate Web services allows Karma to pull in live data from the various social media sites, such as Twitter, Instagram, and OpenStreetMaps. DIG then indexes the integrated data and provides an easy to use interface for query, visualization, and analysis.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

PubMed Central

Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-01

Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. PMID:29040670

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases. To appear in an article of Journal of Database Management.

Enhanced DIII-D Data Management Through a Relational Database

NASA Astrophysics Data System (ADS)

Burruss, J. R.; Peng, Q.; Schachter, J.; Schissel, D. P.; Terpstra, T. B.

2000-10-01

A relational database is being used to serve data about DIII-D experiments. The database is optimized for queries across multiple shots, allowing for rapid data mining by SQL-literate researchers. The relational database relates different experiments and datasets, thus providing a big picture of DIII-D operations. Users are encouraged to add their own tables to the database. Summary physics quantities about DIII-D discharges are collected and stored in the database automatically. Meta-data about code runs, MDSplus usage, and visualization tool usage are collected, stored in the database, and later analyzed to improve computing. Documentation on the database may be accessed through programming languages such as C, Java, and IDL, or through ODBC compliant applications such as Excel and Access. A database-driven web page also provides a convenient means for viewing database quantities through the World Wide Web. Demonstrations will be given at the poster.

ITS-90 Thermocouple Database

National Institute of Standards and Technology Data Gateway

SRD 60 NIST ITS-90 Thermocouple Database (Web, free access)   Web version of Standard Reference Database 60 and NIST Monograph 175. The database gives temperature -- electromotive force (emf) reference functions and tables for the letter-designated thermocouple types B, E, J, K, N, R, S and T. These reference functions have been adopted as standards by the American Society for Testing and Materials (ASTM) and the International Electrotechnical Commission (IEC).

The integrated web service and genome database for agricultural plants with biotechnology information.

PubMed

Kim, Changkug; Park, Dongsuk; Seol, Youngjoo; Hahn, Jangho

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage.

An integrated multimedia medical information network system.

PubMed

Yamamoto, K; Makino, J; Sasagawa, N; Nagira, M

1998-01-01

An integrated multimedia medical information network system at Shimane Medical university has been developed to organize medical information generated from each section and provide information services useful for education, research and clinical practice. The report describes the outline of our system. It is designed to serve as a distributed database for electronic medical records and images. We are developing the MML engine that is to be linked to the world wide web (WWW) network system. To the users, this system will present an integrated multimedia representation of the patient records, providing access to both the image and text-based data required for an effective clinical decision making and medical education.

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model

PubMed Central

Xia, Kai; Dong, Dong; Han, Jing-Dong J

2006-01-01

Background Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking. Results By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs. Conclusion IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at . Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer. PMID:17112386

Tao of Gateway: Providing Internet Access to Licensed Databases.

ERIC Educational Resources Information Center

McClellan, Gregory A.; Garrison, William V.

1997-01-01

Illustrates an approach for providing networked access to licensed databases over the Internet by positioning the library between patron and vendor. Describes how the gateway systems and database connection servers work and discusses how treatment of security has evolved with the introduction of the World Wide Web. Outlines plans to reimplement…

Globe Teachers Guide and Photographic Data on the Web

NASA Technical Reports Server (NTRS)

Kowal, Dan

2004-01-01

The task of managing the GLOBE Online Teacher s Guide during this time period focused on transforming the technology behind the delivery system of this document. The web application transformed from a flat file retrieval system to a dynamic database access approach. The new methodology utilizes Java Server Pages (JSP) on the front-end and an Oracle relational database on the backend. This new approach allows users of the web site, mainly teachers, to access content efficiently by grade level and/or by investigation or educational concept area. Moreover, teachers can gain easier access to data sheets and lab and field guides. The new online guide also included updated content for all GLOBE protocols. The GLOBE web management team was given documentation for maintaining the new application. Instructions for modifying the JSP templates and managing database content were included in this document. It was delivered to the team by the end of October, 2003. The National Geophysical Data Center (NGDC) continued to manage the school study site photos on the GLOBE website. 333 study site photo images were added to the GLOBE database and posted on the web during this same time period for 64 schools. Documentation for processing study site photos was also delivered to the new GLOBE web management team. Lastly, assistance was provided in transferring reference applications such as the Cloud and LandSat quizzes and Earth Systems Online Poster from NGDC servers to GLOBE servers along with documentation for maintaining these applications.

Global Access to Library of Congress' Digital Resources: National Digital Library and Internet Resources.

ERIC Educational Resources Information Center

Chen, Ching-chih

1996-01-01

Summarizes how the Library of Congress' digital library collections can be accessed globally via the Internet and World Wide Web. Outlines the resources found in each of the various access points: gopher, online catalog, library and legislative Web sites, legal and copyright databases, and FTP (file transfer protocol) sites. (LAM)

Ontology-based geospatial data query and integration

USGS Publications Warehouse

Zhao, T.; Zhang, C.; Wei, M.; Peng, Z.-R.

2008-01-01

Geospatial data sharing is an increasingly important subject as large amount of data is produced by a variety of sources, stored in incompatible formats, and accessible through different GIS applications. Past efforts to enable sharing have produced standardized data format such as GML and data access protocols such as Web Feature Service (WFS). While these standards help enabling client applications to gain access to heterogeneous data stored in different formats from diverse sources, the usability of the access is limited due to the lack of data semantics encoded in the WFS feature types. Past research has used ontology languages to describe the semantics of geospatial data but ontology-based queries cannot be applied directly to legacy data stored in databases or shapefiles, or to feature data in WFS services. This paper presents a method to enable ontology query on spatial data available from WFS services and on data stored in databases. We do not create ontology instances explicitly and thus avoid the problems of data replication. Instead, user queries are rewritten to WFS getFeature requests and SQL queries to database. The method also has the benefits of being able to utilize existing tools of databases, WFS, and GML while enabling query based on ontology semantics. ?? 2008 Springer-Verlag Berlin Heidelberg.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Biofuel Database

National Institute of Standards and Technology Data Gateway

Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

The integrated web service and genome database for agricultural plants with biotechnology information

PubMed Central

Kim, ChangKug; Park, DongSuk; Seol, YoungJoo; Hahn, JangHo

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage. PMID:21887015

New tools and methods for direct programmatic access to the dbSNP relational database

PubMed Central

Saccone, Scott F.; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A.; Rice, John P.

2011-01-01

Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale. PMID:21037260

Lessons Learned Implementing DOORS in a Citrix Environment

NASA Technical Reports Server (NTRS)

Bussman, Marie

2005-01-01

NASA's James Web Space Telescope (JWST) Project is a large multi-national project with geographically dispersed contractors that all need access to the Projects requirement database. Initially, the project utilized multiple DOORS databases with the built-in partitions feature to exchange modules amongst the various contractor sites. As the requirements databases matured the use of partitions became extremely difficult. There have been many issues such as incompatible versions of DOORS, inefficient mechanism for sharing modules, security concerns, performance issues, and inconsistent document import and export formats. Deployment of the client software with limited IT resources available was also an issue. The solution chosen by JWST was to integrate the use of a Citrix environment with the DOORS database to address most of the project concerns. The use of the Citrix solution allowed a single Requirements database in a secure environment via a web interface. The Citrix environment allows JWST to upgrade to the most current version of DOORS without having to coordinate multiple sites and user upgrades. The single requirements database eliminates a multitude of Configuration Management concerns and facilitated the standardization of documentation formats. This paper discusses the obstacles and the lessons learned throughout the installation, implementation, usage and deployment process of a centralized DOORS database solution.

Information System through ANIS at CeSAM

NASA Astrophysics Data System (ADS)

Moreau, C.; Agneray, F.; Gimenez, S.

2015-09-01

ANIS (AstroNomical Information System) is a web generic tool developed at CeSAM to facilitate and standardize the implementation of astronomical data of various kinds through private and/or public dedicated Information Systems. The architecture of ANIS is composed of a database server which contains the project data, a web user interface template which provides high level services (search, extract and display imaging and spectroscopic data using a combination of criteria, an object list, a sql query module or a cone search interfaces), a framework composed of several packages, and a metadata database managed by a web administration entity. The process to implement a new ANIS instance at CeSAM is easy and fast : the scientific project has to submit data or a data secure access, the CeSAM team installs the new instance (web interface template and the metadata database), and the project administrator can configure the instance with the web ANIS-administration entity. Currently, the CeSAM offers through ANIS a web access to VO compliant Information Systems for different projects (HeDaM, HST-COSMOS, CFHTLS-ZPhots, ExoDAT,...).

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks.

PubMed

Wang, Likun; Yang, Luhe; Peng, Zuohan; Lu, Dan; Jin, Yan; McNutt, Michael; Yin, Yuxin

2015-01-01

With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services.

cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks

PubMed Central

2015-01-01

Background With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This paper presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks. Results With this R package, users can easily integrate downloaded protein-protein interaction information from different online databases with private data to construct new and personalized interaction networks. Additional functions allow users to generate specific networks based on private databases. Since the results produced with the use of this package are in the form of web pages, cloud users can easily view and edit the network graphs via the browser, using a mouse or touch screen, without the need to download them to a local computer. This package can also be installed and run on a local desktop computer. Depending on user preference, results can be publicized or shared by uploading to a web server or cloud driver, allowing other users to directly access results via a web browser. Conclusions This package can be installed and run on a variety of platforms. Since all network views are shown in web pages, such package is particularly useful for cloud users. The easy installation and operation is an attractive quality for R beginners and users with no previous experience with cloud services. PMID:25708840

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases.

Integrated remote sensing and visualization (IRSV) system for transportation infrastructure operations and management, phase two, volume 4 : web-based bridge information database--visualization analytics and distributed sensing.

DOT National Transportation Integrated Search

2012-03-01

This report introduces the design and implementation of a Web-based bridge information visual analytics system. This : project integrates Internet, multiple databases, remote sensing, and other visualization technologies. The result : combines a GIS ...

Detection and Prevention of Insider Threats in Database Driven Web Services

NASA Astrophysics Data System (ADS)

Chumash, Tzvi; Yao, Danfeng

In this paper, we take the first step to address the gap between the security needs in outsourced hosting services and the protection provided in the current practice. We consider both insider and outsider attacks in the third-party web hosting scenarios. We present SafeWS, a modular solution that is inserted between server side scripts and databases in order to prevent and detect website hijacking and unauthorized access to stored data. To achieve the required security, SafeWS utilizes a combination of lightweight cryptographic integrity and encryption tools, software engineering techniques, and security data management principles. We also describe our implementation of SafeWS and its evaluation. The performance analysis of our prototype shows the overhead introduced by security verification is small. SafeWS will allow business owners to significantly reduce the security risks and vulnerabilities of outsourcing their sensitive customer data to third-party providers.

NEIBank: Genomics and bioinformatics resources for vision research

PubMed Central

Peterson, Katherine; Gao, James; Buchoff, Patee; Jaworski, Cynthia; Bowes-Rickman, Catherine; Ebright, Jessica N.; Hauser, Michael A.; Hoover, David

2008-01-01

NEIBank is an integrated resource for genomics and bioinformatics in vision research. It includes expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. PMID:18648525

HydroClim: a Continental-Scale Database of Contemporary and Future Streamflow and Stream Temperature Estimates for Aquatic Ecosystem Studies

NASA Astrophysics Data System (ADS)

Knouft, J.; Ficklin, D. L.; Bart, H. L.; Rios, N. E.

2017-12-01

Streamflow and water temperature are primary factors influencing the traits, distribution, and diversity of freshwater species. Ongoing changes in climate are causing directional alteration of these environmental conditions, which can impact local ecological processes. Accurate estimation of these variables is critical for predicting the responses of species to ongoing changes in freshwater habitat, yet ecologically relevant high-resolution data describing variation in streamflow and water temperature across North America are not available. Considering the vast amount of web-accessible freshwater biodiversity data, development and application of appropriate hydrologic data are critical to the advancement of our understanding of freshwater systems. To address this issue, we are developing the "HydroClim" database, which will provide web-accessible (www.hydroclim.org) historical and projected monthly streamflow and water temperature data for stream sections in all major watersheds across the United States and Canada from 1950-2099. These data will also be integrated with FishNet 2 (www.fishnet2.net), an online biodiversity database that provides open access to over 2 million localities of freshwater fish species in the United States and Canada, thus allowing for the characterization of the habitat requirements of freshwater species across this region. HydroClim should provide a vast array of opportunities for a greater understanding of water resources as well as information for the conservation of freshwater biodiversity in the United States and Canada in the coming century.

Deep Web video

ScienceCinema

None Available

2018-02-06

To make the web work better for science, OSTI has developed state-of-the-art technologies and services including a deep web search capability. The deep web includes content in searchable databases available to web users but not accessible by popular search engines, such as Google. This video provides an introduction to the deep web search engine.

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

None Available

To make the web work better for science, OSTI has developed state-of-the-art technologies and services including a deep web search capability. The deep web includes content in searchable databases available to web users but not accessible by popular search engines, such as Google. This video provides an introduction to the deep web search engine.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

PubMed

Rose, Peter W; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S; Westbrook, John D; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E; Burley, Stephen K

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

A Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long-term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional functionalities, for which existing browsers tend to provide only partial solutions. Although functionality for Web accessibility can be found as open source and free software components, their reuse and integration is complex because they were developed in diverse implementation environments, following standards and conventions incompatible with the Web. To address these problems, we have started several activities that aim at exploiting the potential of open-source software for Web accessibility. The first of these activities is the development of Adaptable Multi-Interface COmmunicator (AMICO):WEB, an infrastructure that facilitates efficient reuse and integration of open source software components into the Web environment. The main contribution of AMICO:WEB is in enabling the syntactic and semantic interoperability between Web extension mechanisms and a variety of integration mechanisms used by open source and free software components. Its design is based on our experiences in solving practical problems where we have used open source components to improve accessibility of rich media Web applications. The second of our activities involves improving education, where we have used our platform to teach students how to build advanced accessibility solutions from diverse open-source software. We are also partially involved in the recently started Eclipse projects called Accessibility Tools Framework (ACTF), the aim of which is development of extensible infrastructure, upon which developers can build a variety of utilities that help to evaluate and enhance the accessibility of applications and content for people with disabilities. In this article we briefly report on these activities.

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

PubMed

Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

2015-01-01

Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

Biological Web Service Repositories Review.

PubMed

Urdidiales-Nieto, David; Navas-Delgado, Ismael; Aldana-Montes, José F

2017-05-01

Web services play a key role in bioinformatics enabling the integration of database access and analysis of algorithms. However, Web service repositories do not usually publish information on the changes made to their registered Web services. Dynamism is directly related to the changes in the repositories (services registered or unregistered) and at service level (annotation changes). Thus, users, software clients or workflow based approaches lack enough relevant information to decide when they should review or re-execute a Web service or workflow to get updated or improved results. The dynamism of the repository could be a measure for workflow developers to re-check service availability and annotation changes in the services of interest to them. This paper presents a review on the most well-known Web service repositories in the life sciences including an analysis of their dynamism. Freshness is introduced in this paper, and has been used as the measure for the dynamism of these repositories. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Introduction to TETHYS—an interdisciplinary GIS database for studying continental collisions

NASA Astrophysics Data System (ADS)

Khan, S. D.; Flower, M. F. J.; Sultan, M. I.; Sandvol, E.

2006-05-01

The TETHYS GIS database is being developed as a way to integrate relevant geologic, geophysical, geochemical, geochronologic, and remote sensing data bearing on Tethyan continental plate collisions. The project is predicated on a need for actualistic model 'templates' for interpreting the Earth's geologic record. Because of their time-transgressive character, Tethyan collisions offer 'actualistic' models for features such as continental 'escape', collision-induced upper mantle flow magmatism, and marginal basin opening, associated with modern convergent plate margins. Large integrated geochemical and geophysical databases allow for such models to be tested against the geologic record, leading to a better understanding of continental accretion throughout Earth history. The TETHYS database combines digital topographic and geologic information, remote sensing images, sample-based geochemical, geochronologic, and isotopic data (for pre- and post-collision igneous activity), and data for seismic tomography, shear-wave splitting, space geodesy, and information for plate tectonic reconstructions. Here, we report progress on developing such a database and the tools for manipulating and visualizing integrated 2-, 3-, and 4-d data sets with examples of research applications in progress. Based on an Oracle database system, linked with ArcIMS via ArcSDE, the TETHYS project is an evolving resource for researchers, educators, and others interested in studying the role of plate collisions in the process of continental accretion, and will be accessible as a node of the national Geosciences Cyberinfrastructure Network—GEON via the World-Wide Web and ultra-high speed internet2. Interim partial access to the data and metadata is available at: http://geoinfo.geosc.uh.edu/Tethys/ and http://www.esrs.wmich.edu/tethys.htm. We demonstrate the utility of the TETHYS database in building a framework for lithospheric interactions in continental collision and accretion.

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

cMapper: gene-centric connectivity mapper for EBI-RDF platform.

PubMed

Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

2017-01-15

In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at http://cmapper.ewostech.net Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapperContact:smahn@gachon.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

Digital Earth system based river basin data integration

NASA Astrophysics Data System (ADS)

Zhang, Xin; Li, Wanqing; Lin, Chao

2014-12-01

Digital Earth is an integrated approach to build scientific infrastructure. The Digital Earth systems provide a three-dimensional visualization and integration platform for river basin data which include the management data, in situ observation data, remote sensing observation data and model output data. This paper studies the Digital Earth system based river basin data integration technology. Firstly, the construction of the Digital Earth based three-dimensional river basin data integration environment is discussed. Then the river basin management data integration technology is presented which is realized by general database access interface, web service and ActiveX control. Thirdly, the in situ data stored in database tables as records integration is realized with three-dimensional model of the corresponding observation apparatus display in the Digital Earth system by a same ID code. In the next two parts, the remote sensing data and the model output data integration technologies are discussed in detail. The application in the Digital Zhang River basin System of China shows that the method can effectively improve the using efficiency and visualization effect of the data.

Tile-in-ONE: A web platform which integrates Tile Calorimeter data quality and calibration assessment

NASA Astrophysics Data System (ADS)

Sivolella, A.; Ferreira, F.; Maidantchik, C.; Solans, C.; Solodkov, A.; Burghgrave, B.; Smirnov, Y.

2015-12-01

The ATLAS Tile Calorimeter collaboration assesses the quality of calibration data in order to ensure its proper operation. A number of tasks is then performed by executing several tools and accessing web systems, which were independently developed to meet distinct collaboration's requirements and do not necessarily are connected with each other. Thus, to attend the collaboration needs, several programs are usually implemented without a global perspective of the detector, requiring basic software features. In addition, functionalities may overlap in their objectives and frequently replicate resources retrieval mechanisms. Tile-in-ONE is a designed and implemented platform that assembles various web systems used by the calorimeter community through a single framework and a standard technology. It provides an infrastructure to support the code implementation, avoiding duplication of work while integrating with an overall view of the detector status. Database connectors smooth the process of information access since developers do not need to be aware of where records are placed and how to extract them. Within the environment, a dashboard stands for a particular Tile operation aspect and gets together plug-ins, i.e. software components that add specific features to an existing application. A server contains the platform core, which represents the basic environment to deal with the configuration, manage user settings and load plug-ins at runtime. A web middleware assists users to develop their own plug-ins, perform tests and integrate them into the platform as a whole. Backends are employed to allow that any type of application is interpreted and displayed in a uniform way. This paper describes Tile-in-ONE web platform.

ESTuber db: an online database for Tuber borchii EST sequences.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cosentino, Cristian; Stella, Alessandra; Milanesi, Luciano; Viotti, Angelo

2007-03-08

The ESTuber database (http://www.itb.cnr.it/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface. Sequences included in the ESTuber db were clustered and annotated against three databases: the GenBank nr database, the UniProtKB database and a third in-house prepared database of fungi genomic sequences. An algorithm was implemented to infer statistical classification among Gene Ontology categories from the ontology occurrences deduced from the annotation procedure against the UniProtKB database. Ontologies were also deduced from the annotation of more than 130,000 EST sequences from five filamentous fungi, for intra-species comparison purposes. Further analyses were performed on the ESTuber db dataset, including tandem repeats search and comparison of the putative protein dataset inferred from the EST sequences to the PROSITE database for protein patterns identification. All the analyses were performed both on the complete sequence dataset and on the contig consensus sequences generated by the EST assembly procedure. The resulting web site is a resource of data and links related to truffle expressed genes. The Sequence Report and Contig Report pages are the web interface core structures which, together with the Text search utility and the Blast utility, allow easy access to the data stored in the database.

Accessibility and Use of Web-Based Electronic Resources by Physicians in a Psychiatric Institution in Nigeria

ERIC Educational Resources Information Center

Oduwole, Adebambo Adewale; Oyewumi, Olatundun

2010-01-01

Purpose: This study aims to examine the accessibility and use of web-based electronic databases on the Health InterNetwork Access to Research Initiative (HINARI) portal by physicians in the Neuropsychiatric Hospital, Aro--a psychiatry health institution in Nigeria. Design/methodology/approach: Collection of data was through the use of a three-part…

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

PubMed

Ramirez-Gonzalez, Ricardo; Caccamo, Mario; MacLean, Daniel

2011-10-01

Scientists now use high-throughput sequencing technologies and short-read assembly methods to create draft genome assemblies in just days. Tools and pipelines like the assembler, and the workflow management environments make it easy for a non-specialist to implement complicated pipelines to produce genome assemblies and annotations very quickly. Such accessibility results in a proliferation of assemblies and associated files, often for many organisms. These assemblies get used as a working reference by lots of different workers, from a bioinformatician doing gene prediction or a bench scientist designing primers for PCR. Here we describe Gee Fu, a database tool for genomic assembly and feature data, including next-generation sequence alignments. Gee Fu is an instance of a Ruby-On-Rails web application on a feature database that provides web and console interfaces for input, visualization of feature data via AnnoJ, access to data through a web-service interface, an API for direct data access by Ruby scripts and access to feature data stored in BAM files. Gee Fu provides a platform for storing and sharing different versions of an assembly and associated features that can be accessed and updated by bench biologists and bioinformaticians in ways that are easy and useful for each. http://tinyurl.com/geefu dan.maclean@tsl.ac.uk.

IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data.

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.Graphical abstractFDA approved drug data integration for predictive modeling.

The NIF DISCO Framework: Facilitating Automated Integration of Neuroscience Content on the Web

PubMed Central

Marenco, Luis; Wang, Rixin; Shepherd, Gordon M.; Miller, Perry L.

2013-01-01

This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are “harvested” on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource’s content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) “LinkOut” to a resource’s data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource’s lexicon and ontology, 5) sharing a resource’s database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research. PMID:20387131

The NIF DISCO Framework: facilitating automated integration of neuroscience content on the web.

PubMed

Marenco, Luis; Wang, Rixin; Shepherd, Gordon M; Miller, Perry L

2010-06-01

This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are "harvested" on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource's content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) "LinkOut" to a resource's data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource's lexicon and ontology, 5) sharing a resource's database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research.

Climatic Data Integration and Analysis - Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA)

NASA Astrophysics Data System (ADS)

Seamon, E.; Gessler, P. E.; Flathers, E.; Sheneman, L.; Gollberg, G.

2013-12-01

The Regional Approaches to Climate Change for Pacific Northwest Agriculture (REACCH PNA) is a five-year USDA/NIFA-funded coordinated agriculture project to examine the sustainability of cereal crop production systems in the Pacific Northwest, in relationship to ongoing climate change. As part of this effort, an extensive data management system has been developed to enable researchers, students, and the public, to upload, manage, and analyze various data. The REACCH PNA data management team has developed three core systems to encompass cyberinfrastructure and data management needs: 1) the reacchpna.org portal (https://www.reacchpna.org) is the entry point for all public and secure information, with secure access by REACCH PNA members for data analysis, uploading, and informational review; 2) the REACCH PNA Data Repository is a replicated, redundant database server environment that allows for file and database storage and access to all core data; and 3) the REACCH PNA Libraries which are functional groupings of data for REACCH PNA members and the public, based on their access level. These libraries are accessible thru our https://www.reacchpna.org portal. The developed system is structured in a virtual server environment (data, applications, web) that includes a geospatial database/geospatial web server for web mapping services (ArcGIS Server), use of ESRI's Geoportal Server for data discovery and metadata management (under the ISO 19115-2 standard), Thematic Realtime Environmental Distributed Data Services (THREDDS) for data cataloging, and Interactive Python notebook server (IPython) technology for data analysis. REACCH systems are housed and maintained by the Northwest Knowledge Network project (www.northwestknowledge.net), which provides data management services to support research. Initial project data harvesting and meta-tagging efforts have resulted in the interrogation and loading of over 10 terabytes of climate model output, regional entomological data, agricultural and atmospheric information, as well as imagery, publications, videos, and other soft content. In addition, the outlined data management approach has focused on the integration and interconnection of hard data (raw data output) with associated publications, presentations, or other narrative documentation - through metadata lineage associations. This harvest-and-consume data management methodology could additionally be applied to other research team environments that involve large and divergent data.

Semantic Annotations and Querying of Web Data Sources

NASA Astrophysics Data System (ADS)

Hornung, Thomas; May, Wolfgang

A large part of the Web, actually holding a significant portion of the useful information throughout the Web, consists of views on hidden databases, provided by numerous heterogeneous interfaces that are partly human-oriented via Web forms ("Deep Web"), and partly based on Web Services (only machine accessible). In this paper we present an approach for annotating these sources in a way that makes them citizens of the Semantic Web. We illustrate how queries can be stated in terms of the ontology, and how the annotations are used to selected and access appropriate sources and to answer the queries.

Web Accessibility Policies at Land-Grant Universities

ERIC Educational Resources Information Center

Bradbard, David A.; Peters, Cara; Caneva, Yoana

2010-01-01

The Web has become an integral part of postsecondary education within the United States. There are specific laws that legally mandate postsecondary institutions to have Web sites that are accessible for students with disabilities (e.g., the Americans with Disabilities Act (ADA)). Web accessibility policies are a way for universities to provide a…

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

PubMed

Lefkowitz, Elliot J; Dempsey, Donald M; Hendrickson, Robert Curtis; Orton, Richard J; Siddell, Stuart G; Smith, Donald B

2018-01-04

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Web-based healthcare hand drawing management system.

PubMed

Hsieh, Sheau-Ling; Weng, Yung-Ching; Chen, Chi-Huang; Hsu, Kai-Ping; Lin, Jeng-Wei; Lai, Feipei

2010-01-01

The paper addresses Medical Hand Drawing Management System architecture and implementation. In the system, we developed four modules: hand drawing management module; patient medical records query module; hand drawing editing and upload module; hand drawing query module. The system adapts windows-based applications and encompasses web pages by ASP.NET hosting mechanism under web services platforms. The hand drawings implemented as files are stored in a FTP server. The file names with associated data, e.g. patient identification, drawing physician, access rights, etc. are reposited in a database. The modules can be conveniently embedded, integrated into any system. Therefore, the system possesses the hand drawing features to support daily medical operations, effectively improve healthcare qualities as well. Moreover, the system includes the printing capability to achieve a complete, computerized medical document process. In summary, the system allows web-based applications to facilitate the graphic processes for healthcare operations.

BioData: a national aquatic bioassessment database

USGS Publications Warehouse

MacCoy, Dorene

2011-01-01

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services. BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 816 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 477 samples from 39 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis. BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN's). A simple web-data input interface and self-guided, public data-retrieval web site provides access to bioassessment data. BioData currently accepts data collected using two national protocols: (1) NAWQA and (2) U.S. Environmental Protection Agency (USEPA) National Rivers and Streams Assessment (NRSA). Additional collection protocols are planned for future versions.

Querying Semi-Structured Data

NASA Technical Reports Server (NTRS)

Abiteboul, Serge

1997-01-01

The amount of data of all kinds available electronically has increased dramatically in recent years. The data resides in different forms, ranging from unstructured data in the systems to highly structured in relational database systems. Data is accessible through a variety of interfaces including Web browsers, database query languages, application-specic interfaces, or data exchange formats. Some of this data is raw data, e.g., images or sound. Some of it has structure even if the structure is often implicit, and not as rigid or regular as that found in standard database systems. Sometimes the structure exists but has to be extracted from the data. Sometimes also it exists but we prefer to ignore it for certain purposes such as browsing. We call here semi-structured data this data that is (from a particular viewpoint) neither raw data nor strictly typed, i.e., not table-oriented as in a relational model or sorted-graph as in object databases. As will seen later when the notion of semi-structured data is more precisely de ned, the need for semi-structured data arises naturally in the context of data integration, even when the data sources are themselves well-structured. Although data integration is an old topic, the need to integrate a wider variety of data- formats (e.g., SGML or ASN.1 data) and data found on the Web has brought the topic of semi-structured data to the forefront of research. The main purpose of the paper is to isolate the essential aspects of semi- structured data. We also survey some proposals of models and query languages for semi-structured data. In particular, we consider recent works at Stanford U. and U. Penn on semi-structured data. In both cases, the motivation is found in the integration of heterogeneous data.

Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience

PubMed Central

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

2011-01-01

Summary Objective Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases. Methods Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources. Conclusion We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/ PMID:20006477

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience.

PubMed

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

2010-01-01

Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases. Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources. We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/. 2009 Elsevier B.V. All rights reserved.

Integrative interactive visualization of crystal structure, band structure, and Brillouin zone

NASA Astrophysics Data System (ADS)

Hanson, Robert; Hinke, Ben; van Koevering, Matthew; Oses, Corey; Toher, Cormac; Hicks, David; Gossett, Eric; Plata Ramos, Jose; Curtarolo, Stefano; Aflow Collaboration

The AFLOW library is an open-access database for high throughput ab-initio calculations that serves as a resource for the dissemination of computational results in the area of materials science. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, band structure, and Brillouin zone. Interactivity is obtained using two synchronized JSmol implementations, one for the crystal structure and one for the Brillouin zone, along with a D3-based band-structure diagram produced on the fly from data obtained from the AFLOW database. The current website portal (http://aflowlib.mems.duke.edu/users/jmolers/matt/website) allows interactive access and visualization of crystal structure, Brillouin zone and band structure for more than 55,000 inorganic crystal structures. This work was supported by the US Navy Office of Naval Research through a Broad Area Announcement administered by Duke University.

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

PubMed Central

Turner, Brian; Razick, Sabry; Turinsky, Andrei L.; Vlasblom, James; Crowdy, Edgard K.; Cho, Emerson; Morrison, Kyle; Wodak, Shoshana J.

2010-01-01

We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein–protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

Distributed data discovery, access and visualization services to Improve Data Interoperability across different data holdings

NASA Astrophysics Data System (ADS)

Palanisamy, G.; Krassovski, M.; Devarakonda, R.; Santhana Vannan, S.

2012-12-01

The current climate debate is highlighting the importance of free, open, and authoritative sources of high quality climate data that are available for peer review and for collaborative purposes. It is increasingly important to allow various organizations around the world to share climate data in an open manner, and to enable them to perform dynamic processing of climate data. This advanced access to data can be enabled via Web-based services, using common "community agreed" standards without having to change their internal structure used to describe the data. The modern scientific community has become diverse and increasingly complex in nature. To meet the demands of such diverse user community, the modern data supplier has to provide data and other related information through searchable, data and process oriented tool. This can be accomplished by setting up on-line, Web-based system with a relational database as a back end. The following common features of the web data access/search systems will be outlined in the proposed presentation: - A flexible data discovery - Data in commonly used format (e.g., CSV, NetCDF) - Preparing metadata in standard formats (FGDC, ISO19115, EML, DIF etc.) - Data subseting capabilities and ability to narrow down to individual data elements - Standards based data access protocols and mechanisms (SOAP, REST, OpenDAP, OGC etc.) - Integration of services across different data systems (discovery to access, visualizations and subseting) This presentation will also include specific examples of integration of various data systems that are developed by Oak Ridge National Laboratory's - Climate Change Science Institute, their ability to communicate between each other to enable better data interoperability and data integration. 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, R., Shrestha, B., Palanisamy, G., Hook, L. A., Killeffer, T. S., Boden, T. A., ... & Lazer, K. (2014). THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA. Oak Ridge National Laboratory (ORNL).

Database of Novel and Emerging Adsorbent Materials

National Institute of Standards and Technology Data Gateway

SRD 205 NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials (Web, free access)   The NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials is a free, web-based catalog of adsorbent materials and measured adsorption properties of numerous materials obtained from article entries from the scientific literature. Search fields for the database include adsorbent material, adsorbate gas, experimental conditions (pressure, temperature), and bibliographic information (author, title, journal), and results from queries are provided as a list of articles matching the search parameters. The database also contains adsorption isotherms digitized from the cataloged articles, which can be compared visually online in the web application or exported for offline analysis.

Androgen-responsive gene database: integrated knowledge on androgen-responsive genes.

PubMed

Jiang, Mei; Ma, Yunsheng; Chen, Congcong; Fu, Xuping; Yang, Shu; Li, Xia; Yu, Guohua; Mao, Yumin; Xie, Yi; Li, Yao

2009-11-01

Androgen signaling plays an important role in many biological processes. Androgen Responsive Gene Database (ARGDB) is devoted to providing integrated knowledge on androgen-controlled genes. Gene records were collected on the basis of PubMed literature collections. More than 6000 abstracts and 950 original publications were manually screened, leading to 1785 human genes, 993 mouse genes, and 583 rat genes finally included in the database. All the collected genes were experimentally proved to be regulated by androgen at the expression level or to contain androgen-responsive regions. For each gene important details of the androgen regulation experiments were collected from references, such as expression change, androgen-responsive sequence, response time, tissue/cell type, experimental method, ligand identity, and androgen amount, which will facilitate further evaluation by researchers. Furthermore, the database was integrated with multiple annotation resources, including National Center for Biotechnology Information, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway, to reveal the biological characteristics and significance of androgen-regulated genes. The ARGDB web site is mainly composed of the Browse, Search, Element Scan, and Submission modules. It is user friendly and freely accessible at http://argdb.fudan.edu.cn. Preliminary analysis of the collected data was performed. Many disease pathways, such as prostate carcinogenesis, were found to be enriched in androgen-regulated genes. The discovered androgen-response motifs were similar to those in previous reports. The analysis results are displayed in the web site. In conclusion, ARGDB provides a unified gateway to storage, retrieval, and update of information on androgen-regulated genes.

BGD: a database of bat genomes.

PubMed

Fang, Jianfei; Wang, Xuan; Mu, Shuo; Zhang, Shuyi; Dong, Dong

2015-01-01

Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

Using GenBank.

PubMed

Wheeler, David

2007-01-01

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

The USA-NPN Information Management System: A tool in support of phenological assessments

NASA Astrophysics Data System (ADS)

Rosemartin, A.; Vazquez, R.; Wilson, B. E.; Denny, E. G.

2009-12-01

The USA National Phenology Network (USA-NPN) serves science and society by promoting a broad understanding of plant and animal phenology and the relationships among phenological patterns and all aspects of environmental change. Data management and information sharing are central to the USA-NPN mission. The USA-NPN develops, implements, and maintains a comprehensive Information Management System (IMS) to serve the needs of the network, including the collection, storage and dissemination of phenology data, access to phenology-related information, tools for data interpretation, and communication among partners of the USA-NPN. The IMS includes components for data storage, such as the National Phenology Database (NPD), and several online user interfaces to accommodate data entry, data download, data visualization and catalog searches for phenology-related information. The IMS is governed by a set of standards to ensure security, privacy, data access, and data quality. The National Phenology Database is designed to efficiently accommodate large quantities of phenology data, to be flexible to the changing needs of the network, and to provide for quality control. The database stores phenology data from multiple sources (e.g., partner organizations, researchers and citizen observers), and provides for integration with legacy datasets. Several services will be created to provide access to the data, including reports, visualization interfaces, and web services. These services will provide integrated access to phenology and related information for scientists, decision-makers and general audiences. Phenological assessments at any scale will rely on secure and flexible information management systems for the organization and analysis of phenology data. The USA-NPN’s IMS can serve phenology assessments directly, through data management and indirectly as a model for large-scale integrated data management.

Automating Information Discovery Within the Invisible Web

NASA Astrophysics Data System (ADS)

Sweeney, Edwina; Curran, Kevin; Xie, Ermai

A Web crawler or spider crawls through the Web looking for pages to index, and when it locates a new page it passes the page on to an indexer. The indexer identifies links, keywords, and other content and stores these within its database. This database is searched by entering keywords through an interface and suitable Web pages are returned in a results page in the form of hyperlinks accompanied by short descriptions. The Web, however, is increasingly moving away from being a collection of documents to a multidimensional repository for sounds, images, audio, and other formats. This is leading to a situation where certain parts of the Web are invisible or hidden. The term known as the "Deep Web" has emerged to refer to the mass of information that can be accessed via the Web but cannot be indexed by conventional search engines. The concept of the Deep Web makes searches quite complex for search engines. Google states that the claim that conventional search engines cannot find such documents as PDFs, Word, PowerPoint, Excel, or any non-HTML page is not fully accurate and steps have been taken to address this problem by implementing procedures to search items such as academic publications, news, blogs, videos, books, and real-time information. However, Google still only provides access to a fraction of the Deep Web. This chapter explores the Deep Web and the current tools available in accessing it.

Katherine Fleming | NREL

Science.gov Websites

Fleming Photo of Katherine Fleming Katherine Fleming Database and Web Applications Engineer and web application development in the Commercial Buildings Research group. Her projects include the , Katherine was pursuing a Ph.D. with a focus on robotics and working as a Web developer and Web accessibility

eButterfly: Leveraging Massive Online Citizen Science for Butterfly Conservation

PubMed Central

Prudic, Kathleen L.; McFarland, Kent P.; Oliver, Jeffrey C.; Hutchinson, Rebecca A.; Long, Elizabeth C.; Kerr, Jeremy T.; Larrivée, Maxim

2017-01-01

Data collection, storage, analysis, visualization, and dissemination are changing rapidly due to advances in new technologies driven by computer science and universal access to the internet. These technologies and web connections place human observers front and center in citizen science-driven research and are critical in generating new discoveries and innovation in such fields as astronomy, biodiversity, and meteorology. Research projects utilizing a citizen science approach address scientific problems at regional, continental, and even global scales otherwise impossible for a single lab or even a small collection of academic researchers. Here we describe eButterfly an integrative checklist-based butterfly monitoring and database web-platform that leverages the skills and knowledge of recreational butterfly enthusiasts to create a globally accessible unified database of butterfly observations across North America. Citizen scientists, conservationists, policy makers, and scientists are using eButterfly data to better understand the biological patterns of butterfly species diversity and how environmental conditions shape these patterns in space and time. eButterfly in collaboration with thousands of butterfly enthusiasts has created a near real-time butterfly data resource producing tens of thousands of observations per year open to all to share and explore. PMID:28524117

eButterfly: Leveraging Massive Online Citizen Science for Butterfly Consevation.

PubMed

Prudic, Kathleen L; McFarland, Kent P; Oliver, Jeffrey C; Hutchinson, Rebecca A; Long, Elizabeth C; Kerr, Jeremy T; Larrivée, Maxim

2017-05-18

Data collection, storage, analysis, visualization, and dissemination are changing rapidly due to advances in new technologies driven by computer science and universal access to the internet. These technologies and web connections place human observers front and center in citizen science-driven research and are critical in generating new discoveries and innovation in such fields as astronomy, biodiversity, and meteorology. Research projects utilizing a citizen science approach address scientific problems at regional, continental, and even global scales otherwise impossible for a single lab or even a small collection of academic researchers. Here we describe eButterfly an integrative checklist-based butterfly monitoring and database web-platform that leverages the skills and knowledge of recreational butterfly enthusiasts to create a globally accessible unified database of butterfly observations across North America. Citizen scientists, conservationists, policy makers, and scientists are using eButterfly data to better understand the biological patterns of butterfly species diversity and how environmental conditions shape these patterns in space and time. eButterfly in collaboration with thousands of butterfly enthusiasts has created a near real-time butterfly data resource producing tens of thousands of observations per year open to all to share and explore.

The Cardiac Atlas Project--an imaging database for computational modeling and statistical atlases of the heart.

PubMed

Fonseca, Carissa G; Backhaus, Michael; Bluemke, David A; Britten, Randall D; Chung, Jae Do; Cowan, Brett R; Dinov, Ivo D; Finn, J Paul; Hunter, Peter J; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Medrano-Gracia, Pau; Shivkumar, Kalyanam; Suinesiaputra, Avan; Tao, Wenchao; Young, Alistair A

2011-08-15

Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups. Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt). http://www.cardiacatlas.org a.young@auckland.ac.nz Supplementary data are available at Bioinformatics online.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

PubMed

May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

The Case for Creating a Scholars Portal to the Web: A White Paper.

ERIC Educational Resources Information Center

Campbell, Jerry D.

2001-01-01

Considers the need for reliable, scholarly access to the Web and suggests that the Association for Research Libraries, in partnership with OCLC and the Library of Congress, develop a so-called scholar's portal. Topics include quality content; enhanced library services; and gateway functions, including access to commercial databases and focused…

An overview of biomedical literature search on the World Wide Web in the third millennium.

PubMed

Kumar, Prince; Goel, Roshni; Jain, Chandni; Kumar, Ashish; Parashar, Abhishek; Gond, Ajay Ratan

2012-06-01

Complete access to the existing pool of biomedical literature and the ability to "hit" upon the exact information of the relevant specialty are becoming essential elements of academic and clinical expertise. With the rapid expansion of the literature database, it is almost impossible to keep up to date with every innovation. Using the Internet, however, most people can freely access this literature at any time, from almost anywhere. This paper highlights the use of the Internet in obtaining valuable biomedical research information, which is mostly available from journals, databases, textbooks and e-journals in the form of web pages, text materials, images, and so on. The authors present an overview of web-based resources for biomedical researchers, providing information about Internet search engines (e.g., Google), web-based bibliographic databases (e.g., PubMed, IndMed) and how to use them, and other online biomedical resources that can assist clinicians in reaching well-informed clinical decisions.

Integration of NASA/GSFC and USGS Rock Magnetic Databases.

NASA Astrophysics Data System (ADS)

Nazarova, K. A.; Glen, J. M.

2004-05-01

A global Magnetic Petrology Database (MPDB) was developed and continues to be updated at NASA/Goddard Space Flight Center. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via the Internet for a more realistic interpretation of satellite (as well as aeromagnetic and ground) lithospheric magnetic anomalies. The MPDB contains data on rocks from localities around the world (about 19,000 samples) including the Ukranian and Baltic Shields, Kamchatka, Iceland, Urals Mountains, etc. The MPDB is designed, managed and presented on the web as a research oriented database. Several database applications have been specifically developed for data manipulation and analysis of the MPDB. The geophysics unit at the USGS in Menlo Park has over 17,000 rock-property data, largely from sites within the western U.S. This database contains rock-density and rock-magnetic parameters collected for use in gravity and magnetic field modeling, and paleomagnetic studies. Most of these data were taken from surface outcrops and together they span a broad range of rock types. Measurements were made either in-situ at the outcrop, or in the laboratory on hand samples and paleomagnetic cores acquired in the field. The USGS and NASA/GSFC data will be integrated as part of an effort to provide public access to a single, uniformly maintained database. Due to the large number of data and the very large area sampled, the database can yield rock-property statistics on a broad range of rock types; it is thus applicable to study areas beyond the geographic scope of the database. The intent of this effort is to provide incentive for others to further contribute to the database, and a tool with which the geophysical community can entertain studies formerly precluded.

iDrug: a web-accessible and interactive drug discovery and design platform

PubMed Central

2014-01-01

Background The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. As programs are developed by various research groups, a consistent user-friendly online graphical working environment, combining computational techniques such as pharmacophore mapping, similarity calculation, scoring, and target identification is needed. Results We presented a versatile, user-friendly, and efficient online tool for computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing. All the customized configurations of the functional modules can be accessed through featured session files provided, which can be saved to the local disk and uploaded to resume or update the history work. Conclusions iDrug is easy to use, and provides a novel, fast and reliable tool for conducting drug design experiments. By using iDrug, various molecular design processing tasks can be submitted and visualized simply in one browser without installing locally any standalone modeling softwares. iDrug is accessible free of charge at http://lilab.ecust.edu.cn/idrug. PMID:24955134

Regulators of Androgen Action Resource: a one-stop shop for the comprehensive study of androgen receptor action.

PubMed

DePriest, Adam D; Fiandalo, Michael V; Schlanger, Simon; Heemers, Frederike; Mohler, James L; Liu, Song; Heemers, Hannelore V

2016-01-01

Androgen receptor (AR) is a ligand-activated transcription factor that is the main target for treatment of non-organ-confined prostate cancer (CaP). Failure of life-prolonging AR-targeting androgen deprivation therapy is due to flexibility in steroidogenic pathways that control intracrine androgen levels and variability in the AR transcriptional output. Androgen biosynthesis enzymes, androgen transporters and AR-associated coregulators are attractive novel CaP treatment targets. These proteins, however, are characterized by multiple transcript variants and isoforms, are subject to genomic alterations, and are differentially expressed among CaPs. Determining their therapeutic potential requires evaluation of extensive, diverse datasets that are dispersed over multiple databases, websites and literature reports. Mining and integrating these datasets are cumbersome, time-consuming tasks and provide only snapshots of relevant information. To overcome this impediment to effective, efficient study of AR and potential drug targets, we developed the Regulators of Androgen Action Resource (RAAR), a non-redundant, curated and user-friendly searchable web interface. RAAR centralizes information on gene function, clinical relevance, and resources for 55 genes that encode proteins involved in biosynthesis, metabolism and transport of androgens and for 274 AR-associated coregulator genes. Data in RAAR are organized in two levels: (i) Information pertaining to production of androgens is contained in a 'pre-receptor level' database, and coregulator gene information is provided in a 'post-receptor level' database, and (ii) an 'other resources' database contains links to additional databases that are complementary to and useful to pursue further the information provided in RAAR. For each of its 329 entries, RAAR provides access to more than 20 well-curated publicly available databases, and thus, access to thousands of data points. Hyperlinks provide direct access to gene-specific entries in the respective database(s). RAAR is a novel, freely available resource that provides fast, reliable and easy access to integrated information that is needed to develop alternative CaP therapies. Database URL: http://www.lerner.ccf.org/cancerbio/heemers/RAAR/search/. © The Author(s) 2016. Published by Oxford University Press.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

Integration of Evidence Base into a Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

Saile, Lyn; Lopez, Vilma; Bickham, Grandin; Kerstman, Eric; FreiredeCarvalho, Mary; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

INTRODUCTION: A probabilistic decision support model such as the Integrated Medical Model (IMM) utilizes an immense amount of input data that necessitates a systematic, integrated approach for data collection, and management. As a result of this approach, IMM is able to forecasts medical events, resource utilization and crew health during space flight. METHODS: Inflight data is the most desirable input for the Integrated Medical Model. Non-attributable inflight data is collected from the Lifetime Surveillance for Astronaut Health study as well as the engineers, flight surgeons, and astronauts themselves. When inflight data is unavailable cohort studies, other models and Bayesian analyses are used, in addition to subject matters experts input on occasion. To determine the quality of evidence of a medical condition, the data source is categorized and assigned a level of evidence from 1-5; the highest level is one. The collected data reside and are managed in a relational SQL database with a web-based interface for data entry and review. The database is also capable of interfacing with outside applications which expands capabilities within the database itself. Via the public interface, customers can access a formatted Clinical Findings Form (CLiFF) that outlines the model input and evidence base for each medical condition. Changes to the database are tracked using a documented Configuration Management process. DISSCUSSION: This strategic approach provides a comprehensive data management plan for IMM. The IMM Database s structure and architecture has proven to support additional usages. As seen by the resources utilization across medical conditions analysis. In addition, the IMM Database s web-based interface provides a user-friendly format for customers to browse and download the clinical information for medical conditions. It is this type of functionality that will provide Exploratory Medicine Capabilities the evidence base for their medical condition list. CONCLUSION: The IMM Database in junction with the IMM is helping NASA aerospace program improve the health care and reduce risk for the astronauts crew. Both the database and model will continue to expand to meet customer needs through its multi-disciplinary evidence based approach to managing data. Future expansion could serve as a platform for a Space Medicine Wiki of medical conditions.

The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

A Model Based Mars Climate Database for the Mission Design

NASA Technical Reports Server (NTRS)

2005-01-01

A viewgraph presentation on a model based climate database is shown. The topics include: 1) Why a model based climate database?; 2) Mars Climate Database v3.1 Who uses it ? (approx. 60 users!); 3) The new Mars Climate database MCD v4.0; 4) MCD v4.0: what's new ? 5) Simulation of Water ice clouds; 6) Simulation of Water ice cycle; 7) A new tool for surface pressure prediction; 8) Acces to the database MCD 4.0; 9) How to access the database; and 10) New web access

Access to Space Interactive Design Web Site

NASA Technical Reports Server (NTRS)

Leon, John; Cutlip, William; Hametz, Mark

2000-01-01

The Access To Space (ATS) Group at NASA's Goddard Space Flight Center (GSFC) supports the science and technology community at GSFC by facilitating frequent and affordable opportunities for access to space. Through partnerships established with access mode suppliers, the ATS Group has developed an interactive Mission Design web site. The ATS web site provides both the information and the tools necessary to assist mission planners in selecting and planning their ride to space. This includes the evaluation of single payloads vs. ride-sharing opportunities to reduce the cost of access to space. Features of this site include the following: (1) Mission Database. Our mission database contains a listing of missions ranging from proposed missions to manifested. Missions can be entered by our user community through data input tools. Data is then accessed by users through various search engines: orbit parameters, ride-share opportunities, spacecraft parameters, other mission notes, launch vehicle, and contact information. (2) Launch Vehicle Toolboxes. The launch vehicle toolboxes provide the user a full range of information on vehicle classes and individual configurations. Topics include: general information, environments, performance, payload interface, available volume, and launch sites.

Using CORBA to integrate manufacturing cells to a virtual enterprise

NASA Astrophysics Data System (ADS)

Pancerella, Carmen M.; Whiteside, Robert A.

1997-01-01

It is critical in today's enterprises that manufacturing facilities are not isolated from design, planning, and other business activities and that information flows easily and bidirectionally between these activities. It is also important and cost-effective that COTS software, databases, and corporate legacy codes are well integrated in the information architecture. Further, much of the information generated during manufacturing must be dynamically accessible to engineering and business operations both in a restricted corporate intranet and on the internet. The software integration strategy in the Sandia Agile Manufacturing Testbed supports these enterprise requirements. We are developing a CORBA-based distributed object software system for manufacturing. Each physical machining device is a CORBA object and exports a common IDL interface to allow for rapid and dynamic insertion, deletion, and upgrading within the manufacturing cell. Cell management CORBA components access manufacturing devices without knowledge of any device-specific implementation. To support information flow from design to planning data is accessible to machinists on the shop floor. CORBA allows manufacturing components to be easily accessible to the enterprise. Dynamic clients can be created using web browsers and portable Java GUI's. A CORBA-OLE adapter allows integration to PC desktop applications. Other commercial software can access CORBA network objects in the information architecture through vendor API's.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission.

PubMed

Hankeln, Wolfgang; Buttigieg, Pier Luigi; Fink, Dennis; Kottmann, Renzo; Yilmaz, Pelin; Glöckner, Frank Oliver

2010-06-30

Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

PubMed Central

2010-01-01

Background Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft® Excel® spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data. PMID:20591175

Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1.

PubMed

Park, Jeongbin; Bae, Sangsu

2018-03-15

Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time. Free access at http://www.rgenome.net/cpf1-database/. sangsubae@hanyang.ac.kr.

Image query and indexing for digital x rays

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1998-12-01

The web-based medical information retrieval system (WebMIRS) allows interned access to databases containing 17,000 digitized x-ray spine images and associated text data from National Health and Nutrition Examination Surveys (NHANES). WebMIRS allows SQL query of the text, and viewing of the returned text records and images using a standard browser. We are now working (1) to determine utility of data directly derived from the images in our databases, and (2) to investigate the feasibility of computer-assisted or automated indexing of the images to support image retrieval of images of interest to biomedical researchers in the field of osteoarthritis. To build an initial database based on image data, we are manually segmenting a subset of the vertebrae, using techniques from vertebral morphometry. From this, we will derive and add to the database vertebral features. This image-derived data will enhance the user's data access capability by enabling the creation of combined SQL/image-content queries.

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

PubMed

Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

2012-01-01

Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and relationship errors in KEGG). We turn complicated and incompatible xml data formats and inconsistent gene and gene relationship representations from different source databases into normalized and unified pathway-gene and pathway-gene pair relationships neatly recorded in simple tab-delimited text format and MySQL tables, which facilitates convenient automatic computation and large-scale referencing in many related studies. IntPath data can be downloaded in text format or MySQL dump. IntPath data can also be retrieved and analyzed conveniently through web service by local programs or through web interface by mouse clicks. Several useful analysis tools are also provided in IntPath. We have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath.

DHLAS: A web-based information system for statistical genetic analysis of HLA population data.

PubMed

Thriskos, P; Zintzaras, E; Germenis, A

2007-03-01

DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.

Design of Knowledge Bases for Plant Gene Regulatory Networks.

PubMed

Mukundi, Eric; Gomez-Cano, Fabio; Ouma, Wilberforce Zachary; Grotewold, Erich

2017-01-01

Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary information and resources, and outline the methods for obtaining data. The second stage consists of designing the schema, which involves defining the entire arrangement of the database in a systematic plan. The third stage is the implementation, defined by actualization of the database by using software according to a predefined schema. The final stage is development, where the database is made available to users in a web-accessible system. The result is a knowledgebase that integrates all the information pertaining to gene regulation, and which is easily expandable and transferable.

Web based information on clinical toxicology for the United Kingdom: uptake and utilization of TOXBASE in 2000

PubMed Central

Nicholas Bateman, D; Good, Alison M; Kelly, Catherine A; Laing, William J

2002-01-01

Aims To examine the use and uptake of TOXBASE, an Internet database for point of care provision of poisons information in the United Kingdom during its first calendar year of web-based access. Methods Interrogation of the database software to examine: use by different types of user and geographical origin; profile of ingredient and product access; time of access to the system; profile of access to other parts of the database. Results Registered users of the system increased in the first full year of operation (1224 new users) and usage of the system increased to 111 410 sessions with 190 223 product monograph accesses in 2000. Major users were hospitals, in particular accident and emergency departments. NHS Direct, a public access information service staffed by nurses, also made increasing use of the system. Usage per head of population was highest in Northern Ireland and Scotland, and least in southern England. Ingredients accessed most frequently were similar in all four countries of the UK. Times of use of the system reflect clinical activity, with hospitals making many accesses during night-time hours. The most popular parts of the database other than poisons information were those dealing with childhood poisoning, information on decontamination procedures, teratology information and slang terms for drugs of abuse. Conclusions This Internet system has been widely used in its first full year of operation. The provision of clinically relevant, up to date, information at the point of delivery of patient care is now possible using this approach. It has wide implications for the provision of other types of therapeutic information in clinical areas. Web-based technology represents an opportunity for clinical pharmacologists to provide therapeutic information for clinical colleagues at the bedside. PMID:12100219

Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

PubMed

Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio

2015-03-01

In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2008-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2009-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Plant Genome Resources at the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Smith-White, Brian; Chetvernin, Vyacheslav; Resenchuk, Sergei; Dombrowski, Susan M.; Pechous, Steven W.; Tatusova, Tatiana; Ostell, James

2005-01-01

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI. PMID:16010002

Development of a GIService based on spatial data mining for location choice of convenience stores in Taipei City

NASA Astrophysics Data System (ADS)

Jung, Chinte; Sun, Chih-Hong

2006-10-01

Motivated by the increasing accessibility of technology, more and more spatial data are being made digitally available. How to extract the valuable knowledge from these large (spatial) databases is becoming increasingly important to businesses, as well. It is essential to be able to analyze and utilize these large datasets, convert them into useful knowledge, and transmit them through GIS-enabled instruments and the Internet, conveying the key information to business decision-makers effectively and benefiting business entities. In this research, we combine the techniques of GIS, spatial decision support system (SDSS), spatial data mining (SDM), and ArcGIS Server to achieve the following goals: (1) integrate databases from spatial and non-spatial datasets about the locations of businesses in Taipei, Taiwan; (2) use the association rules, one of the SDM methods, to extract the knowledge from the integrated databases; and (3) develop a Web-based SDSS GIService as a location-selection tool for business by the product of ArcGIS Server.

Global Ocean Currents Database

NASA Astrophysics Data System (ADS)

Boyer, T.; Sun, L.

2016-02-01

The NOAA's National Centers for Environmental Information has released an ocean currents database portal that aims 1) to integrate global ocean currents observations from a variety of instruments with different resolution, accuracy and response to spatial and temporal variability into a uniform network common data form (NetCDF) format and 2) to provide a dedicated online data discovery, access to NCEI-hosted and distributed data sources for ocean currents data. The portal provides a tailored web application that allows users to search for ocean currents data by platform types and spatial/temporal ranges of their interest. The dedicated web application is available at http://www.nodc.noaa.gov/gocd/index.html. The NetCDF format supports widely-used data access protocols and catalog services such as OPeNDAP (Open-source Project for a Network Data Access Protocol) and THREDDS (Thematic Real-time Environmental Distributed Data Services), which the GOCD users can use data files with their favorite analysis and visualization client software without downloading to their local machine. The potential users of the ocean currents database include, but are not limited to, 1) ocean modelers for their model skills assessments, 2) scientists and researchers for studying the impact of ocean circulations on the climate variability, 3) ocean shipping industry for safety navigation and finding optimal routes for ship fuel efficiency, 4) ocean resources managers while planning for the optimal sites for wastes and sewages dumping and for renewable hydro-kinematic energy, and 5) state and federal governments to provide historical (analyzed) ocean circulations as an aid for search and rescue

The National Extreme Events Data and Research Center (NEED)

NASA Astrophysics Data System (ADS)

Gulledge, J.; Kaiser, D. P.; Wilbanks, T. J.; Boden, T.; Devarakonda, R.

2014-12-01

The Climate Change Science Institute at Oak Ridge National Laboratory (ORNL) is establishing the National Extreme Events Data and Research Center (NEED), with the goal of transforming how the United States studies and prepares for extreme weather events in the context of a changing climate. NEED will encourage the myriad, distributed extreme events research communities to move toward the adoption of common practices and will develop a new database compiling global historical data on weather- and climate-related extreme events (e.g., heat waves, droughts, hurricanes, etc.) and related information about impacts, costs, recovery, and available research. Currently, extreme event information is not easy to access and is largely incompatible and inconsistent across web sites. NEED's database development will take into account differences in time frames, spatial scales, treatments of uncertainty, and other parameters and variables, and leverage informatics tools developed at ORNL (i.e., the Metadata Editor [1] and Mercury [2]) to generate standardized, robust documentation for each database along with a web-searchable catalog. In addition, NEED will facilitate convergence on commonly accepted definitions and standards for extreme events data and will enable integrated analyses of coupled threats, such as hurricanes/sea-level rise/flooding and droughts/wildfires. Our goal and vision is that NEED will become the premiere integrated resource for the general study of extreme events. References: [1] Devarakonda, Ranjeet, et al. "OME: Tool for generating and managing metadata to handle BigData." Big Data (Big Data), 2014 IEEE International Conference on. IEEE, 2014. [2] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94.

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Social Validation of Institutional Indicators to Promote System-Wide Web Accessibility in Postsecondary Institutions

ERIC Educational Resources Information Center

Mariger, Heather Ann

2011-01-01

The Internet is an integral part of higher education today. Students, faculty, and staff must have access to the institutional web for essential activities. For persons with disabilities, the web is a double-edged sword. While an accessibly designed website can mitigate or remove barriers, an inaccessible one can make access impossible. If…

Public outreach and communications of the Alaska Volcano Observatory during the 2005-2006 eruption of Augustine Volcano: Chapter 27 in The 2006 eruption of Augustine Volcano, Alaska

USGS Publications Warehouse

Adleman, Jennifer N.; Cameron, Cheryl E.; Snedigar, Seth F.; Neal, Christina A.; Wallace, Kristi L.; Power, John A.; Coombs, Michelle L.; Freymueller, Jeffrey T.

2010-01-01

The AVO Web site, with its accompanying database, is the backbone of AVO's external and internal communications. This was the first Cook Inlet volcanic eruption with a public expectation of real-time access to data, updates, and hazards information over the Internet. In March 2005, AVO improved the Web site from individual static pages to a dynamic, database-driven site. This new system provided quick and straightforward access to the latest information for (1) staff within the observatory, (2) emergency managers from State and local governments and organizations, (3) the media, and (4) the public. From mid-December 2005 through April 2006, the AVO Web site served more than 45 million Web pages and about 5.5 terabytes of data.

WaveNet: A Web-Based Metocean Data Access, Processing, and Analysis Tool. Part 3 - CDIP Database

DTIC Science & Technology

2014-06-01

and Analysis Tool; Part 3 – CDIP Database by Zeki Demirbilek, Lihwa Lin, and Derek Wilson PURPOSE: This Coastal and Hydraulics Engineering...Technical Note (CHETN) describes coupling of the Coastal Data Information Program ( CDIP ) database to WaveNet, the first module of MetOcnDat (Meteorological...provides a step-by-step procedure to access, process, and analyze wave and wind data from the CDIP database. BACKGROUND: WaveNet addresses a basic

Fungal genome resources at NCBI.

PubMed

Robbertse, B; Tatusova, T

2011-09-01

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

Earth science big data at users' fingertips: the EarthServer Science Gateway Mobile

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Fargetta, Marco; Pappalardo, Marco; Rundo, Francesco

2014-05-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. In this contribution we will report on the EarthServer Science Gateway Mobile, an app for both iOS and Android-based devices that allows users to seamlessly access some of the EarthServer applications using SAML-based federated authentication and fine-grained authorisation mechanisms.

The Index to Marine and Lacustrine Geological Samples (IMLGS): Linking Digital Data to Physical Samples for the Marine Community

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Jencks, J. H.; Eakins, B.

2016-12-01

The Index to Marine and Lacustrine Geological Samples (IMLGS) is a community designed and maintained resource enabling researchers to locate and request seafloor and lakebed geologic samples curated by partner institutions. The Index was conceived in the dawn of the digital age by representatives from U.S. academic and government marine core repositories and the NOAA National Geophysical Data Center, now the National Centers for Environmental Information (NCEI), at a 1977 meeting convened by the National Science Foundation (NSF). The Index is based on core concepts of community oversight, common vocabularies, consistent metadata and a shared interface. The Curators Consortium, international in scope, meets biennially to share ideas and discuss best practices. NCEI serves the group by providing database access and maintenance, a list server, digitizing support and long-term archival of sample metadata, data and imagery. Over three decades, participating curators have performed the laborious task of creating and contributing metadata for over 205,000 sea floor and lake-bed cores, grabs, and dredges archived in their collections. Some partners use the Index for primary web access to their collections while others use it to increase exposure of more in-depth institutional systems. The IMLGS has a persistent URL/Digital Object Identifier (DOI), as well as DOIs assigned to partner collections for citation and to provide a persistent link to curator collections. The Index is currently a geospatially-enabled relational database, publicly accessible via Web Feature and Web Map Services, and text- and ArcGIS map-based web interfaces. To provide as much knowledge as possible about each sample, the Index includes curatorial contact information and links to related data, information and images : 1) at participating institutions, 2) in the NCEI archive, and 3) through a Linked Data interface maintained by the Rolling Deck to Repository R2R. Over 43,000 International GeoSample Numbers (IGSNs) linking to the System for Earth Sample Registration (SESAR) are included in anticipation of opportunities for interconnectivity with Integrated Earth Data Applications (IEDA) systems. The paper will discuss the database with a goal to increase the connections and links to related data at partner institutions.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

ChEMBL web services: streamlining access to drug discovery data and utilities

PubMed Central

Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P.

2015-01-01

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. PMID:25883136

Enabling Scientists: Serving Sci-Tech Library Users with Disabilities.

ERIC Educational Resources Information Center

Coonin, Bryna

2001-01-01

Discusses how librarians in scientific and technical libraries can contribute to an accessible electronic library environment for users with disabilities to ensure independent access to information. Topics include relevant assistive technologies; creating accessible Web pages; monitoring accessibility of electronic databases; preparing accessible…

The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases

PubMed Central

Whetzel, Patricia L.; Grethe, Jeffrey S.; Banks, Davis E.; Martone, Maryann E.

2015-01-01

The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). By research resources, we mean the multitude of data, software tools, materials, services, projects and organizations available to researchers in the public domain. Most of these are accessed via web-accessible databases or web portals, each developed, designed and maintained by numerous different projects, organizations and individuals. While many of the large government funded databases, maintained by agencies such as European Bioinformatics Institute and the National Center for Biotechnology Information, are well known to researchers, many more that have been developed by and for the biomedical research community are unknown or underutilized. At least part of the problem is the nature of dynamic databases, which are considered part of the “hidden” web, that is, content that is not easily accessed by search engines. dkNET was created specifically to address the challenge of connecting researchers to research resources via these types of community databases and web portals. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. A primary focus of dkNET are centers and projects specifically created to provide high quality data and resources to NIDDK researchers. Through the novel data ingest process used in dkNET, additional data sources can easily be incorporated, allowing it to scale with the growth of digital data and the needs of the dkNET community. Here, we provide an overview of the dkNET portal and its functions. We show how dkNET can be used to address a variety of use cases that involve searching for research resources. PMID:26393351

Integrating Mathematics, Science, and Language Arts Instruction Using the World Wide Web.

ERIC Educational Resources Information Center

Clark, Kenneth; Hosticka, Alice; Kent, Judi; Browne, Ron

1998-01-01

Addresses issues of access to World Wide Web sites, mathematics and science content-resources available on the Web, and methods for integrating mathematics, science, and language arts instruction. (Author/ASK)

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

PubMed Central

Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

2009-01-01

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

MEIMAN: Database exploring Medicinal and Edible insects of Manipur

PubMed Central

Shantibala, Tourangbam; Lokeshwari, Rajkumari; Thingnam, Gourshyam; Somkuwar, Bharat Gopalrao

2012-01-01

We have developed MEIMAN, a unique database on medicinal and edible insects of Manipur which comprises 51 insects species collected through extensive survey and questionnaire for two years. MEIMAN provides integrated access to insect species thorough sophisticated web interface which has following capabilities a) Graphical interface of seasonality, b) Method of preparation, c) Form of use - edible and medicinal, d) habitat, e) medicinal uses, f) commercial importance and g) economic status. This database will be useful for scientific validations and updating of traditional wisdom in bioprospecting aspects. It will be useful in analyzing the insect biodiversity for the development of virgin resources and their industrialization. Further, the features will be suited for detailed investigation on potential medicinal and edible insects that make MEIMAN a powerful tool for sustainable management. Availability The database is available for free at www.ibsd.gov.in/meiman PMID:22715305

A community effort to construct a gravity database for the United States and an associated Web portal

USGS Publications Warehouse

Keller, Gordon R.; Hildenbrand, T.G.; Kucks, R.; Webring, M.; Briesacher, A.; Rujawitz, K.; Hittleman, A.M.; Roman, D.R.; Winester, D.; Aldouri, R.; Seeley, J.; Rasillo, J.; Torres, R.; Hinze, W. J.; Gates, A.; Kreinovich, V.; Salayandia, L.

2006-01-01

Potential field data (gravity and magnetic measurements) are both useful and costeffective tools for many geologic investigations. Significant amounts of these data are traditionally in the public domain. A new magnetic database for North America was released in 2002, and as a result, a cooperative effort between government agencies, industry, and universities to compile an upgraded digital gravity anomaly database, grid, and map for the conterminous United States was initiated and is the subject of this paper. This database is being crafted into a data system that is accessible through a Web portal. This data system features the database, software tools, and convenient access. The Web portal will enhance the quality and quantity of data contributed to the gravity database that will be a shared community resource. The system's totally digital nature ensures that it will be flexible so that it can grow and evolve as new data, processing procedures, and modeling and visualization tools become available. Another goal of this Web-based data system is facilitation of the efforts of researchers and students who wish to collect data from regions currently not represented adequately in the database. The primary goal of upgrading the United States gravity database and this data system is to provide more reliable data that support societal and scientific investigations of national importance. An additional motivation is the international intent to compile an enhanced North American gravity database, which is critical to understanding regional geologic features, the tectonic evolution of the continent, and other issues that cross national boundaries. ?? 2006 Geological Society of America. All rights reserved.

S/MARt DB: a database on scaffold/matrix attached regions.

PubMed

Liebich, Ines; Bode, Jürgen; Frisch, Matthias; Wingender, Edgar

2002-01-01

S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt DB is closely linked to the TRANSFAC database on transcription factors and their binding sites. It is freely accessible through the World Wide Web (http://transfac.gbf.de/SMARtDB/) for non-profit research.

Delivering integrated HAZUS-MH flood loss analyses and flood inundation maps over the Web.

PubMed

Hearn, Paul P; Longenecker, Herbert E; Aguinaldo, John J; Rahav, Ami N

2013-01-01

Catastrophic flooding is responsible for more loss of life and damages to property than any other natural hazard. Recently developed flood inundation mapping technologies make it possible to view the extent and depth of flooding on the land surface over the Internet; however, by themselves these technologies are unable to provide estimates of losses to property and infrastructure. The Federal Emergency Management Agency's (FEMA's) HAZUS-MH software is extensively used to conduct flood loss analyses in the United States, providing a nationwide database of population and infrastructure at risk. Unfortunately, HAZUS-MH requires a dedicated Geographic Information System (GIS) workstation and a trained operator, and analyses are not adapted for convenient delivery over the Web. This article describes a cooperative effort by the US Geological Survey (USGS) and FEMA to make HAZUS-MH output GIS and Web compatible and to integrate these data with digital flood inundation maps in USGS's newly developed Inundation Mapping Web Portal. By running the computationally intensive HAZUS-MH flood analyses offline and converting the output to a Web-GIS compatible format, detailed estimates of flood losses can now be delivered to anyone with Internet access, thus dramatically increasing the availability of these forecasts to local emergency planners and first responders.

Delivering integrated HAZUS-MH flood loss analyses and flood inundation maps over the Web

USGS Publications Warehouse

Hearn,, Paul P.; Longenecker, Herbert E.; Aguinaldo, John J.; Rahav, Ami N.

2013-01-01

Catastrophic flooding is responsible for more loss of life and damages to property than any other natural hazard. Recently developed flood inundation mapping technologies make it possible to view the extent and depth of flooding on the land surface over the Internet; however, by themselves these technologies are unable to provide estimates of losses to property and infrastructure. The Federal Emergency Management Agency’s (FEMA's) HAZUS-MH software is extensively used to conduct flood loss analyses in the United States, providing a nationwide database of population and infrastructure at risk. Unfortunately, HAZUS-MH requires a dedicated Geographic Information System (GIS) workstation and a trained operator, and analyses are not adapted for convenient delivery over the Web. This article describes a cooperative effort by the US Geological Survey (USGS) and FEMA to make HAZUS-MH output GIS and Web compatible and to integrate these data with digital flood inundation maps in USGS’s newly developed Inundation Mapping Web Portal. By running the computationally intensive HAZUS-MH flood analyses offline and converting the output to a Web-GIS compatible format, detailed estimates of flood losses can now be delivered to anyone with Internet access, thus dramatically increasing the availability of these forecasts to local emergency planners and first responders.

Handprinted Forms and Characters

National Institute of Standards and Technology Data Gateway

NIST Handprinted Forms and Characters (Web, free access)   NIST Special Database 19 contains NIST's entire corpus of training materials for handprinted document and character recognition. It supersedes NIST Special Databases 3 and 7.

InverPep: A database of invertebrate antimicrobial peptides.

PubMed

Gómez, Esteban A; Giraldo, Paula; Orduz, Sergio

2017-03-01

The aim of this work was to construct InverPep, a database specialised in experimentally validated antimicrobial peptides (AMPs) from invertebrates. AMP data contained in InverPep were manually curated from other databases and the scientific literature. MySQL was integrated with the development platform Laravel; this framework allows to integrate programming in PHP with HTML and was used to design the InverPep web page's interface. InverPep contains 18 separated fields, including InverPep code, phylum and species source, peptide name, sequence, peptide length, secondary structure, molar mass, charge, isoelectric point, hydrophobicity, Boman index, aliphatic index and percentage of hydrophobic amino acids. CALCAMPI, an algorithm to calculate the physicochemical properties of multiple peptides simultaneously, was programmed in PERL language. To date, InverPep contains 702 experimentally validated AMPs from invertebrate species. All of the peptides contain information associated with their source, physicochemical properties, secondary structure, biological activity and links to external literature. Most AMPs in InverPep have a length between 10 and 50 amino acids, a positive charge, a Boman index between 0 and 2 kcal/mol, and 30-50% hydrophobic amino acids. InverPep includes 33 AMPs not reported in other databases. Besides, CALCAMPI and statistical analysis of InverPep data is presented. The InverPep database is available in English and Spanish. InverPep is a useful database to study invertebrate AMPs and its information could be used for the design of new peptides. The user-friendly interface of InverPep and its information can be freely accessed via a web-based browser at http://ciencias.medellin.unal.edu.co/gruposdeinvestigacion/prospeccionydisenobiomoleculas/InverPep/public/home_en. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Recent improvements in the NASA technical report server

NASA Technical Reports Server (NTRS)

Maa, Ming-Hokng; Nelson, Michael L.

1995-01-01

The NASA Technical Report Server (NTRS), a World Wide Web (WWW) report distribution service, has been modified to allow parallel database queries, significantly decreasing user access time by an average factor of 2.3, access from clients behind firewalls and/or proxies which truncate excessively long Uniform Resource Locators (URL's), access to non-Wide Area Information Server (WAIS) databases, and compatibility with the Z39-50.3 protocol.

In-Memory Graph Databases for Web-Scale Data

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

Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++more » compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.« less

Tags Extarction from Spatial Documents in Search Engines

NASA Astrophysics Data System (ADS)

Borhaninejad, S.; Hakimpour, F.; Hamzei, E.

2015-12-01

Nowadays the selective access to information on the Web is provided by search engines, but in the cases which the data includes spatial information the search task becomes more complex and search engines require special capabilities. The purpose of this study is to extract the information which lies in spatial documents. To that end, we implement and evaluate information extraction from GML documents and a retrieval method in an integrated approach. Our proposed system consists of three components: crawler, database and user interface. In crawler component, GML documents are discovered and their text is parsed for information extraction; storage. The database component is responsible for indexing of information which is collected by crawlers. Finally the user interface component provides the interaction between system and user. We have implemented this system as a pilot system on an Application Server as a simulation of Web. Our system as a spatial search engine provided searching capability throughout the GML documents and thus an important step to improve the efficiency of search engines has been taken.

The CMS dataset bookkeeping service

NASA Astrophysics Data System (ADS)

Afaq, A.; Dolgert, A.; Guo, Y.; Jones, C.; Kosyakov, S.; Kuznetsov, V.; Lueking, L.; Riley, D.; Sekhri, V.

2008-07-01

The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires processing and analysis activities at various service levels and the DBS system provides support for localized processing or private analysis, as well as global access for CMS users at large. Catalog entries can be moved among the various service levels with a simple set of migration tools, thus forming a loose federation of databases. DBS is available to CMS users via a Python API, Command Line, and a Discovery web page interfaces. The system is built as a multi-tier web application with Java servlets running under Tomcat, with connections via JDBC to Oracle or MySQL database backends. Clients connect to the service through HTTP or HTTPS with authentication provided by GRID certificates and authorization through VOMS. DBS is an integral part of the overall CMS Data Management and Workflow Management systems.

ClearedLeavesDB: an online database of cleared plant leaf images

PubMed Central

2014-01-01

Background Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers. Description The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database. Conclusions We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at http://clearedleavesdb.org. PMID:24678985

ClearedLeavesDB: an online database of cleared plant leaf images.

PubMed

Das, Abhiram; Bucksch, Alexander; Price, Charles A; Weitz, Joshua S

2014-03-28

Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers. The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database. We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at http://clearedleavesdb.org.

The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis.

PubMed

Van Doorslaer, Koenraad; Tan, Qina; Xirasagar, Sandhya; Bandaru, Sandya; Gopalan, Vivek; Mohamoud, Yasmin; Huyen, Yentram; McBride, Alison A

2013-01-01

The goal of the Papillomavirus Episteme (PaVE) is to provide an integrated resource for the analysis of papillomavirus (PV) genome sequences and related information. The PaVE is a freely accessible, web-based tool (http://pave.niaid.nih.gov) created around a relational database, which enables storage, analysis and exchange of sequence information. From a design perspective, the PaVE adopts an Open Source software approach and stresses the integration and reuse of existing tools. Reference PV genome sequences have been extracted from publicly available databases and reannotated using a custom-created tool. To date, the PaVE contains 241 annotated PV genomes, 2245 genes and regions, 2004 protein sequences and 47 protein structures, which users can explore, analyze or download. The PaVE provides scientists with the data and tools needed to accelerate scientific progress for the study and treatment of diseases caused by PVs.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher; Carracedo, Angel

2008-10-10

In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.

Science Initiatives of the US Virtual Astronomical Observatory

NASA Astrophysics Data System (ADS)

Hanisch, R. J.

2012-09-01

The United States Virtual Astronomical Observatory program is the operational facility successor to the National Virtual Observatory development project. The primary goal of the US VAO is to build on the standards, protocols, and associated infrastructure developed by NVO and the International Virtual Observatory Alliance partners and to bring to fruition a suite of applications and web-based tools that greatly enhance the research productivity of professional astronomers. To this end, and guided by the advice of our Science Council (Fabbiano et al. 2011), we have focused on five science initiatives in the first two years of VAO operations: 1) scalable cross-comparisons between astronomical source catalogs, 2) dynamic spectral energy distribution construction, visualization, and model fitting, 3) integration and periodogram analysis of time series data from the Harvard Time Series Center and NASA Star and Exoplanet Database, 4) integration of VO data discovery and access tools into the IRAF data analysis environment, and 5) a web-based portal to VO data discovery, access, and display tools. We are also developing tools for data linking and semantic discovery, and have a plan for providing data mining and advanced statistical analysis resources for VAO users. Initial versions of these applications and web-based services are being released over the course of the summer and fall of 2011, with further updates and enhancements planned for throughout 2012 and beyond.

A System for Web-based Access to the HSOS Database

NASA Astrophysics Data System (ADS)

Lin, G.

Huairou Solar Observing Station's (HSOS) magnetogram and dopplergram are world-class instruments. Access to their data has opened to the world. Web-based access to the data will provide a powerful, convenient tool for data searching and solar physics. It is necessary that our data be provided to users via the Web when it is opened to the world. In this presentation, the author describes general design and programming construction of the system. The system will be generated by PHP and MySQL. The author also introduces basic feature of PHP and MySQL.

Methodology for Localized and Accessible Image Formation and Elucidation

ERIC Educational Resources Information Center

Patil, Sandeep R.; Katiyar, Manish

2009-01-01

Accessibility is one of the key checkpoints in all software products, applications, and Web sites. Accessibility with digital images has always been a major challenge for the industry. Images form an integral part of certain type of documents and most Web 2.0-compliant Web sites. Individuals challenged with blindness and many dyslexics only make…

The Qatar National Historic Environment Record: a Platform for the Development of a Fully-Integrated Cultural Heritage Management Application

NASA Astrophysics Data System (ADS)

Cuttler, R. T. H.; Tonner, T. W. W.; Al-Naimi, F. A.; Dingwall, L. M.; Al-Hemaidi, N.

2013-07-01

The development of the Qatar National Historic Environment Record (QNHER) by the Qatar Museums Authority and the University of Birmingham in 2008 was based on a customised, bilingual Access database and ArcGIS. While both platforms are stable and well supported, neither was designed for the documentation and retrieval of cultural heritage data. As a result it was decided to develop a custom application using Open Source code. The core module of this application is now completed and is orientated towards the storage and retrieval of geospatial heritage data for the curation of heritage assets. Based on MIDAS Heritage data standards and regionally relevant thesauri, it is a truly bilingual system. Significant attention has been paid to the user interface, which is userfriendly and intuitive. Based on a suite of web services and accessed through a web browser, the system makes full use of internet resources such as Google Maps and Bing Maps. The application avoids long term vendor ''tie-ins'' and as a fully integrated data management system, is now an important tool for both cultural resource managers and heritage researchers in Qatar.

100 Colleges Sign Up with Google to Speed Access to Library Resources

ERIC Educational Resources Information Center

Young, Jeffrey R.

2005-01-01

More than 100 colleges and universities have arranged to give people using the Google Scholar search engine on their campuses more-direct access to library materials. Google Scholar is a free tool that searches scholarly materials on the Web and in academic databases. The new arrangements essentially let Google know which online databases the…

Building an integrated neurodegenerative disease database at an academic health center.

PubMed

Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

2011-07-01

It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens.

PubMed

Amadoz, Alicia; González-Candelas, Fernando

2007-04-20

Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their needs. The database schema, tool scripts and web-based interface are free software but data stored in our database server are not publicly available. epiPATH is distributed under the terms of GNU General Public License. More details about epiPATH can be found at http://genevo.uv.es/epipath.

Moving toward a universally accessible web: Web accessibility and education.

PubMed

Kurt, Serhat

2017-12-08

The World Wide Web is an extremely powerful source of information, inspiration, ideas, and opportunities. As such, it has become an integral part of daily life for a great majority of people. Yet, for a significant number of others, the internet offers only limited value due to the existence of barriers which make accessing the Web difficult, if not impossible. This article illustrates some of the reasons that achieving equality of access to the online world of education is so critical, explores the current status of Web accessibility, discusses evaluative tools and methods that can help identify accessibility issues in educational websites, and provides practical recommendations and guidelines for resolving some of the obstacles that currently hinder the achievability of the goal of universal Web access.

Discovering, Indexing and Interlinking Information Resources

PubMed Central

Celli, Fabrizio; Keizer, Johannes; Jaques, Yves; Konstantopoulos, Stasinos; Vudragović, Dušan

2015-01-01

The social media revolution is having a dramatic effect on the world of scientific publication. Scientists now publish their research interests, theories and outcomes across numerous channels, including personal blogs and other thematic web spaces where ideas, activities and partial results are discussed. Accordingly, information systems that facilitate access to scientific literature must learn to cope with this valuable and varied data, evolving to make this research easily discoverable and available to end users. In this paper we describe the incremental process of discovering web resources in the domain of agricultural science and technology. Making use of Linked Open Data methodologies, we interlink a wide array of custom-crawled resources with the AGRIS bibliographic database in order to enrich the user experience of the AGRIS website. We also discuss the SemaGrow Stack, a query federation and data integration infrastructure used to estimate the semantic distance between crawled web resources and AGRIS. PMID:26834982

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

PubMed

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

2015-12-01

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Computational framework to support integration of biomolecular and clinical data within a translational approach.

PubMed

Miyoshi, Newton Shydeo Brandão; Pinheiro, Daniel Guariz; Silva, Wilson Araújo; Felipe, Joaquim Cezar

2013-06-06

The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.

Tripal: a construction toolkit for online genome databases.

PubMed

Ficklin, Stephen P; Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net.

Tripal: a construction toolkit for online genome databases

PubMed Central

Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E.; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E.; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net PMID:21959868

Dealing with an information overload of health science data: structured utilisation of libraries, distributed knowledge in databases and Web content.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Rieger, Joerg; Meyer, Michael

2006-01-01

The organizational structures of web contents and electronic information resources must adapt to the demands of a growing volume of information and user requirements. Otherwise the information society will be threatened by disinformation. The biomedical sciences are especially vulnerable in this regard, since they are strongly oriented toward text-based knowledge sources. Here sustainable improvement can only be achieved by using a comprehensive, integrated approach that not only includes data management but also specifically incorporates the editorial processes, including structuring information sources and publication. The technical resources needed to effectively master these tasks are already available in the form of the data standards and tools of the Semantic Web. They include Rich Site Summaries (RSS), which have become an established means of distributing and syndicating conventional news messages and blogs. They can also provide access to the contents of the previously mentioned information sources, which are conventionally classified as 'deep web' content.

Colorado Late Cenozoic Fault and Fold Database and Internet Map Server: User-friendly technology for complex information

USGS Publications Warehouse

Morgan, K.S.; Pattyn, G.J.; Morgan, M.L.

2005-01-01

Internet mapping applications for geologic data allow simultaneous data delivery and collection, enabling quick data modification while efficiently supplying the end user with information. Utilizing Web-based technologies, the Colorado Geological Survey's Colorado Late Cenozoic Fault and Fold Database was transformed from a monothematic, nonspatial Microsoft Access database into a complex information set incorporating multiple data sources. The resulting user-friendly format supports easy analysis and browsing. The core of the application is the Microsoft Access database, which contains information compiled from available literature about faults and folds that are known or suspected to have moved during the late Cenozoic. The database contains nonspatial fields such as structure type, age, and rate of movement. Geographic locations of the fault and fold traces were compiled from previous studies at 1:250,000 scale to form a spatial database containing information such as length and strike. Integration of the two databases allowed both spatial and nonspatial information to be presented on the Internet as a single dataset (http://geosurvey.state.co.us/pubs/ceno/). The user-friendly interface enables users to view and query the data in an integrated manner, thus providing multiple ways to locate desired information. Retaining the digital data format also allows continuous data updating and quick delivery of newly acquired information. This dataset is a valuable resource to anyone interested in earthquake hazards and the activity of faults and folds in Colorado. Additional geologic hazard layers and imagery may aid in decision support and hazard evaluation. The up-to-date and customizable maps are invaluable tools for researchers or the public.

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

Reactome Pengine: A web-logic API to the homo sapiens reactome.

PubMed

Neaves, Samuel R; Tsoka, Sophia; Millard, Louise A C

2018-03-30

Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API), or they have to download the whole database. Reactome Pengine is a web service providing a logic programming based API to the human reactome. This gives researchers greater flexibility in data access than existing APIs, as users can send their own small programs (alongside queries) to Reactome Pengine. The server and an example notebook can be found at https://apps.nms.kcl.ac.uk/reactome-pengine. Source code is available at https://github.com/samwalrus/reactome-pengine and a Docker image is available at https://hub.docker.com/r/samneaves/rp4/ . samuel.neaves@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

Thomson Scientific's expanding Web of Knowledge: beyond citation databases and current awareness services.

PubMed

London, Sue; Brahmi, Frances A

2005-01-01

As end-user demand for easy access to electronic full text continues to climb, an increasing number of information providers are combining that access with their other products and services, making navigating their Web sites by librarians seeking information on a given product or service more daunting than ever. One such provider of a complex array of products and services is Thomson Scientific. This paper looks at some of the many products and tools available from two of Thomson Scientific's businesses, Thomson ISI and Thomson ResearchSoft. Among the items of most interest to health sciences and veterinary librarians and their users are the variety of databases available via the ISI Web of Knowledge platform and the information management products available from ResearchSoft.

Design of a web portal for interdisciplinary image retrieval from multiple online image resources.

PubMed

Kammerer, F J; Frankewitsch, T; Prokosch, H-U

2009-01-01

Images play an important role in medicine. Finding the desired images within the multitude of online image databases is a time-consuming and frustrating process. Existing websites do not meet all the requirements for an ideal learning environment for medical students. This work intends to establish a new web portal providing a centralized access point to a selected number of online image databases. A back-end system locates images on given websites and extracts relevant metadata. The images are indexed using UMLS and the MetaMap system provided by the US National Library of Medicine. Specially developed functions allow to create individual navigation structures. The front-end system suits the specific needs of medical students. A navigation structure consisting of several medical fields, university curricula and the ICD-10 was created. The images may be accessed via the given navigation structure or using different search functions. Cross-references are provided by the semantic relations of the UMLS. Over 25,000 images were identified and indexed. A pilot evaluation among medical students showed good first results concerning the acceptance of the developed navigation structures and search features. The integration of the images from different sources into the UMLS semantic network offers a quick and an easy-to-use learning environment.

Study on resources and environmental data integration towards data warehouse construction covering trans-boundary area of China, Russia and Mongolia

NASA Astrophysics Data System (ADS)

Wang, J.; Song, J.; Gao, M.; Zhu, L.

2014-02-01

The trans-boundary area between Northern China, Mongolia and eastern Siberia of Russia is a continuous geographical area located in north eastern Asia. Many common issues in this region need to be addressed based on a uniform resources and environmental data warehouse. Based on the practice of joint scientific expedition, the paper presented a data integration solution including 3 steps, i.e., data collection standards and specifications making, data reorganization and process, data warehouse design and development. A series of data collection standards and specifications were drawn up firstly covering more than 10 domains. According to the uniform standard, 20 resources and environmental survey databases in regional scale, and 11 in-situ observation databases were reorganized and integrated. North East Asia Resources and Environmental Data Warehouse was designed, which included 4 layers, i.e., resources layer, core business logic layer, internet interoperation layer, and web portal layer. The data warehouse prototype was developed and deployed initially. All the integrated data in this area can be accessed online.

Criteria for Comparing Children's Web Search Tools.

ERIC Educational Resources Information Center

Kuntz, Jerry

1999-01-01

Presents criteria for evaluating and comparing Web search tools designed for children. Highlights include database size; accountability; categorization; search access methods; help files; spell check; URL searching; links to alternative search services; advertising; privacy policy; and layout and design. (LRW)

The CoFactor database: organic cofactors in enzyme catalysis.

PubMed

Fischer, Julia D; Holliday, Gemma L; Thornton, Janet M

2010-10-01

Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes. The database is publicly available and can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/CoFactor.

Oceanography Information System of Spanish Institute of Oceanography (IEO)

NASA Astrophysics Data System (ADS)

Tello, Olvido; Gómez, María; González, Sonsoles

2016-04-01

Since 1914, the Spanish Institute of Oceanography (IEO) performs multidisciplinary studies of the marine environment. In same case are systematic studies and in others are specific studies for special requirements (El Hierro submarine volcanic episode, spill Prestige, others.). Different methodologies and data acquisition techniques are used depending on studies aims. The acquired data are stored and presented in different formats. The information is organized into different databases according to the subject and the variables represented (geology, fisheries, aquaculture, pollution, habitats, etc.). Related to physical and chemical oceanography data, in 1964 was created the DATA CENTER of IEO (CEDO), in order to organize the data about physical and chemical variables, to standardize this information and to serve the international data network SeaDataNet. www.seadatanet.org. This database integrates data about temperature, salinity, nutrients, and tidal data. CEDO allows consult and download the data. http://indamar.ieo.es On the other hand, related to data about marine species in 1999 was developed SIRENO DATABASE. All data about species collected in oceanographic surveys carried out by researches of IEO, and data from observers on fishing vessels are incorporated in SIRENO database. In this database is stored catch data, biomass, abundance, etc. This system is based on architecture ORACLE. Due to the large amount of information collected over the 100 years of IEO history, there is a clear need to organize, standardize, integrate and relate the different databases and information, and to provide interoperability and access to the information. Consequently, in 2000 it emerged the first initiative to organize the IEO spatial information in an Oceanography Information System, based on a Geographical Information System (GIS). The GIS was consolidated as IEO institutional GIS and was created the Spatial Data Infrastructure of IEO (IDEO) following trend of INSPIRE. All data included in the GIS have their corresponding metadata about ISO19115 and INSPIRE. IDEO is based on Web services, Quality of Services, Open standards, ISO (OGC) and INSPIRE standards, and both provide access to the geographical marine information of IEO. The GIS allows the information to be organized, visualized, consulted and analyzed. The data from different IEO databases are integrated into a GIS corporate Geodatabase (Esri format). This tool is essential in the decision making of aspects like: - Protection of marine environment - Sustainable management of resources - Natural Hazards. - Marine spatial planning. Examples of the use of GIS as a spatial analysis tool are: - Mud volcanoes explored in LIFE-INDEMARES project. - Cartographic series about Spanish continental shelf, developed from data integrated in IEO marine GIS, acquired from oceanographic surveys in ESPACE project. - Cartography developed from the information gathered in Initial Assessment of Marine Strategy Framework Directive. - Studies of natural hazards related to submarine canyons in southeast region marine Spanish. Currently the IEO is participating in many European initiatives, especially in several lots of EMODNET. The IEO besides is working in consonance with INSPIRE, Growth Blue, Horizon 2020, etc., to contribute to, the knowledge of marine environment, its protection and its spatial planning are extremely relevant issues. In order to facilitate the access to the Spatial Data Infrastructure of IEO, the IEO Geoportal was developed in 2012. It mainly involves a metadata catalog, access to the data viewers and Web Services of IDEO. http://www.geo-ideo.ieo.es/geoportalideo/catalog/main/home.page

Six Online Periodical Databases: A Librarian's View.

ERIC Educational Resources Information Center

Willems, Harry

1999-01-01

Compares the following World Wide Web-based periodical databases, focusing on their usefulness in K-12 school libraries: EBSCO, Electric Library, Facts on File, SIRS, Wilson, and UMI. Search interfaces, display options, help screens, printing, home access, copyright restrictions, database administration, and making a decision are discussed. A…

Web Design Matters

ERIC Educational Resources Information Center

Mathews, Brian

2009-01-01

The web site is a library's most important feature. Patrons use the web site for numerous functions, such as renewing materials, placing holds, requesting information, and accessing databases. The homepage is the place they turn to look up the hours, branch locations, policies, and events. Whether users are at work, at home, in a building, or on…

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens

PubMed Central

2012-01-01

Background Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. Results In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and relationship errors in KEGG). We turn complicated and incompatible xml data formats and inconsistent gene and gene relationship representations from different source databases into normalized and unified pathway-gene and pathway-gene pair relationships neatly recorded in simple tab-delimited text format and MySQL tables, which facilitates convenient automatic computation and large-scale referencing in many related studies. IntPath data can be downloaded in text format or MySQL dump. IntPath data can also be retrieved and analyzed conveniently through web service by local programs or through web interface by mouse clicks. Several useful analysis tools are also provided in IntPath. Conclusions We have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath. PMID:23282057

Featured Article: Genotation: Actionable knowledge for the scientific reader

PubMed Central

Willis, Ethan; Sakauye, Mark; Jose, Rony; Chen, Hao; Davis, Robert L

2016-01-01

We present an article viewer application that allows a scientific reader to easily discover and share knowledge by linking genomics-related concepts to knowledge of disparate biomedical databases. High-throughput data streams generated by technical advancements have contributed to scientific knowledge discovery at an unprecedented rate. Biomedical Informaticists have created a diverse set of databases to store and retrieve the discovered knowledge. The diversity and abundance of such resources present biomedical researchers a challenge with knowledge discovery. These challenges highlight a need for a better informatics solution. We use a text mining algorithm, Genomine, to identify gene symbols from the text of a journal article. The identified symbols are supplemented with information from the GenoDB knowledgebase. Self-updating GenoDB contains information from NCBI Gene, Clinvar, Medgen, dbSNP, KEGG, PharmGKB, Uniprot, and Hugo Gene databases. The journal viewer is a web application accessible via a web browser. The features described herein are accessible on www.genotation.org. The Genomine algorithm identifies gene symbols with an accuracy shown by .65 F-Score. GenoDB currently contains information regarding 59,905 gene symbols, 5633 drug–gene relationships, 5981 gene–disease relationships, and 713 pathways. This application provides scientific readers with actionable knowledge related to concepts of a manuscript. The reader will be able to save and share supplements to be visualized in a graphical manner. This provides convenient access to details of complex biological phenomena, enabling biomedical researchers to generate novel hypothesis to further our knowledge in human health. This manuscript presents a novel application that integrates genomic, proteomic, and pharmacogenomic information to supplement content of a biomedical manuscript and enable readers to automatically discover actionable knowledge. PMID:26900164

Featured Article: Genotation: Actionable knowledge for the scientific reader.

PubMed

Nagahawatte, Panduka; Willis, Ethan; Sakauye, Mark; Jose, Rony; Chen, Hao; Davis, Robert L

2016-06-01

We present an article viewer application that allows a scientific reader to easily discover and share knowledge by linking genomics-related concepts to knowledge of disparate biomedical databases. High-throughput data streams generated by technical advancements have contributed to scientific knowledge discovery at an unprecedented rate. Biomedical Informaticists have created a diverse set of databases to store and retrieve the discovered knowledge. The diversity and abundance of such resources present biomedical researchers a challenge with knowledge discovery. These challenges highlight a need for a better informatics solution. We use a text mining algorithm, Genomine, to identify gene symbols from the text of a journal article. The identified symbols are supplemented with information from the GenoDB knowledgebase. Self-updating GenoDB contains information from NCBI Gene, Clinvar, Medgen, dbSNP, KEGG, PharmGKB, Uniprot, and Hugo Gene databases. The journal viewer is a web application accessible via a web browser. The features described herein are accessible on www.genotation.org The Genomine algorithm identifies gene symbols with an accuracy shown by .65 F-Score. GenoDB currently contains information regarding 59,905 gene symbols, 5633 drug-gene relationships, 5981 gene-disease relationships, and 713 pathways. This application provides scientific readers with actionable knowledge related to concepts of a manuscript. The reader will be able to save and share supplements to be visualized in a graphical manner. This provides convenient access to details of complex biological phenomena, enabling biomedical researchers to generate novel hypothesis to further our knowledge in human health. This manuscript presents a novel application that integrates genomic, proteomic, and pharmacogenomic information to supplement content of a biomedical manuscript and enable readers to automatically discover actionable knowledge. © 2016 by the Society for Experimental Biology and Medicine.

An Integrated Information System for Supporting Quality Management Tasks

NASA Astrophysics Data System (ADS)

Beyer, N.; Helmreich, W.

2004-08-01

In a competitive environment, well defined processes become the strategic advantage of a company. Hence, targeted Quality Management ensures efficiency, trans- parency and, ultimately, customer satisfaction. In the particular context of a Space Test Centre, a num- ber of specific Quality Management standards have to be applied. According to the revision of ISO 9001 dur- ing 2000, and due to the adaptation of ECSS-Q20-07, process orientation and data analysis are key tasks for ensuring and evaluating the efficiency of a company's processes. In line with these requirements, an integrated management system for accessing the necessary infor- mation to support Quality Management and other proc- esses has been established. Some of its test-related fea- tures are presented here. Easy access to the integrated management system from any work place at IABG's Space Test Centre is ensured by means of an intranet portal. It comprises a full set of quality-related process descriptions, information on test facilities, emergency procedures, and other relevant in- formation. The portal's web interface provides direct access to a couple of external applications. Moreover, easy updating of all information and low cost mainte- nance are features of this integrated information system. The timely and transparent management of non- conformances is covered by a dedicated NCR database which incorporates full documentation capability, elec- tronic signature and e-mail notification of concerned staff. A search interface allows for queries across all documented non-conformances. Furthermore, print ver- sions can be generated at any stage in the process, e.g. for distribution to customers. Feedback on customer satisfaction is sought through a web-based questionnaire. The process is initiated by the responsible test manager through submission of an e- mail that contains a hyperlink to a secure website, ask- ing the customer to complete the brief online form, which is directly fed to a database for subsequent evaluation by the Quality Manager. All such information can be processed and presented in an appropriate manner for internal or external audits, as well as for regular management reviews.

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

PedAM: a database for Pediatric Disease Annotation and Medicine.

PubMed

Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Li, Xin; Liang, Yunxiang; Guo, Dongming; Tai, Jun; Chen, Geng; Jin, Yaqiong; Liu, Zhimei; Ni, Xin; Shi, Tieliu

2018-01-04

There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration. It also uses disease-manifestation (D-M) integrated from existing biomedical ontologies as prior knowledge to automatically recognize text-mined, D-M-specific syntactic patterns from 774 514 full-text articles and 8 848 796 abstracts in MEDLINE. Additionally, disease connections based on phenotypes or genes can be visualized on the web page of PedAM. Currently, the PedAM contains standardized 8528 pediatric disease terms (4542 unique disease concepts and 3986 synonyms) with eight annotation fields for each disease, including definition synonyms, gene, symptom, cross-reference (Xref), human phenotypes and its corresponding phenotypes in the mouse. The database PedAM is freely accessible at http://www.unimd.org/pedam/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electronic Biomedical Literature Search for Budding Researcher

PubMed Central

Thakre, Subhash B.; Thakre S, Sushama S.; Thakre, Amol D.

2013-01-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research. PMID:24179937

Electronic biomedical literature search for budding researcher.

PubMed

Thakre, Subhash B; Thakre S, Sushama S; Thakre, Amol D

2013-09-01

Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.

Innovative technology for web-based data management during an outbreak

PubMed Central

Mukhi, Shamir N; Chester, Tammy L Stuart; Klaver-Kibria, Justine DA; Nowicki, Deborah L; Whitlock, Mandy L; Mahmud, Salah M; Louie, Marie; Lee, Bonita E

2011-01-01

Lack of automated and integrated data collection and management, and poor linkage of clinical, epidemiological and laboratory data during an outbreak can inhibit effective and timely outbreak investigation and response. This paper describes an innovative web-based technology, referred to as Web Data, developed for the rapid set-up and provision of interactive and adaptive data management during outbreak situations. We also describe the benefits and limitations of the Web Data technology identified through a questionnaire that was developed to evaluate the use of Web Data implementation and application during the 2009 H1N1 pandemic by Winnipeg Regional Health Authority and Provincial Laboratory for Public Health of Alberta. Some of the main benefits include: improved and secure data access, increased efficiency and reduced error, enhanced electronic collection and transfer of data, rapid creation and modification of the database, conversion of specimen-level to case-level data, and user-defined data extraction and query capabilities. Areas requiring improvement include: better understanding of privacy policies, increased capability for data sharing and linkages between jurisdictions to alleviate data entry duplication. PMID:23569597

DoSSiER: Database of scientific simulation and experimental results

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

Wenzel, Hans; Yarba, Julia; Genser, Krzystof

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

DoSSiER: Database of scientific simulation and experimental results

DOE PAGES

Wenzel, Hans; Yarba, Julia; Genser, Krzystof; ...

2016-08-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

CADB: Conformation Angles DataBase of proteins

PubMed Central

Sheik, S. S.; Ananthalakshmi, P.; Bhargavi, G. Ramya; Sekar, K.

2003-01-01

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/. PMID:12520049

CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803.

PubMed

Hernandez-Prieto, Miguel A; Futschik, Matthias E

2012-01-01

Synechocystis sp. PCC6803 is one of the best studied cyanobacteria and an important model organism for our understanding of photosynthesis. The early availability of its complete genome sequence initiated numerous transcriptome studies, which have generated a wealth of expression data. Analysis of the accumulated data can be a powerful tool to study transcription in a comprehensive manner and to reveal underlying regulatory mechanisms, as well as to annotate genes whose functions are yet unknown. However, use of divergent microarray platforms, as well as distributed data storage make meta-analyses of Synechocystis expression data highly challenging, especially for researchers with limited bioinformatic expertise and resources. To facilitate utilisation of the accumulated expression data for a wider research community, we have developed CyanoEXpress, a web database for interactive exploration and visualisation of transcriptional response patterns in Synechocystis. CyanoEXpress currently comprises expression data for 3073 genes and 178 environmental and genetic perturbations obtained in 31 independent studies. At present, CyanoEXpress constitutes the most comprehensive collection of expression data available for Synechocystis and can be freely accessed. The database is available for free at http://cyanoexpress.sysbiolab.eu.

A network of web multimedia medical information servers for a medical school and university hospital.

PubMed

Denier, P; Le Beux, P; Delamarre, D; Fresnel, A; Cleret, M; Courtin, C; Seka, L P; Pouliquen, B; Cleran, L; Riou, C; Burgun, A; Jarno, P; Leduff, F; Lesaux, H; Duvauferrier, R

1997-08-01

Modern medicine requires a rapid access to information including clinical data from medical records, bibliographic databases, knowledge bases and nomenclature databases. This is especially true for University Hospitals and Medical Schools for training as well as for fundamental and clinical research for diagnosis and therapeutic purposes. This implies the development of local, national and international cooperation which can be enhanced via the use and access to computer networks such as Internet. The development of professional cooperative networks goes with the development of the telecommunication and computer networks and our project is to make these new tools and technologies accessible to the medical students both during the teaching time in Medical School and during the training periods at the University Hospital. We have developed a local area network which communicates between the School of Medicine and the Hospital which takes advantage of the new Web client-server technology both internally (Intranet) and externally by access to the National Research Network (RENATER in France) connected to the Internet network. The address of our public web server is http:(/)/www.med.univ-rennesl.fr.

Introducing the PRIDE Archive RESTful web services.

PubMed

Reisinger, Florian; del-Toro, Noemi; Ternent, Tobias; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-07-01

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

EMAGE mouse embryo spatial gene expression database: 2010 update

PubMed Central

Richardson, Lorna; Venkataraman, Shanmugasundaram; Stevenson, Peter; Yang, Yiya; Burton, Nicholas; Rao, Jianguo; Fisher, Malcolm; Baldock, Richard A.; Davidson, Duncan R.; Christiansen, Jeffrey H.

2010-01-01

EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Here, we describe recent enhancements to EMAGE including: the release of a completely re-designed website, which offers integration of many different search functions in HTML web pages, improved user feedback and the ability to find similar expression patterns at the click of a button; back-end refactoring from an object oriented to relational architecture, allowing associated SQL access; and the provision of further access by standard formatted URLs and a Java API. We have also increased data coverage by sourcing from a greater selection of journals and developed automated methods for spatial data annotation that are being applied to spatially incorporate the genome-wide (∼19 000 gene) ‘EURExpress’ dataset into EMAGE. PMID:19767607

Smart Cities Intelligence System (SMACiSYS) Integrating Sensor Web with Spatial Data Infrastructures (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; Painho, M.

2017-09-01

The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC) keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

Implementation of a Big Data Accessing and Processing Platform for Medical Records in Cloud.

PubMed

Yang, Chao-Tung; Liu, Jung-Chun; Chen, Shuo-Tsung; Lu, Hsin-Wen

2017-08-18

Big Data analysis has become a key factor of being innovative and competitive. Along with population growth worldwide and the trend aging of population in developed countries, the rate of the national medical care usage has been increasing. Due to the fact that individual medical data are usually scattered in different institutions and their data formats are varied, to integrate those data that continue increasing is challenging. In order to have scalable load capacity for these data platforms, we must build them in good platform architecture. Some issues must be considered in order to use the cloud computing to quickly integrate big medical data into database for easy analyzing, searching, and filtering big data to obtain valuable information.This work builds a cloud storage system with HBase of Hadoop for storing and analyzing big data of medical records and improves the performance of importing data into database. The data of medical records are stored in HBase database platform for big data analysis. This system performs distributed computing on medical records data processing through Hadoop MapReduce programming, and to provide functions, including keyword search, data filtering, and basic statistics for HBase database. This system uses the Put with the single-threaded method and the CompleteBulkload mechanism to import medical data. From the experimental results, we find that when the file size is less than 300MB, the Put with single-threaded method is used and when the file size is larger than 300MB, the CompleteBulkload mechanism is used to improve the performance of data import into database. This system provides a web interface that allows users to search data, filter out meaningful information through the web, and analyze and convert data in suitable forms that will be helpful for medical staff and institutions.

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

PubMed Central

Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

2015-01-01

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

Global Location-Based Access to Web Applications Using Atom-Based Automatic Update

NASA Astrophysics Data System (ADS)

Singh, Kulwinder; Park, Dong-Won

We propose an architecture which enables people to enquire about information available in directory services by voice using regular phones. We implement a Virtual User Agent (VUA) which mediates between the human user and a business directory service. The system enables the user to search for the nearest clinic, gas station by price, motel by price, food / coffee, banks/ATM etc. and fix an appointment, or automatically establish a call between the user and the business party if the user prefers. The user also has an option to receive appointment confirmation by phone, SMS, or e-mail. The VUA is accessible by a toll free DID (Direct Inward Dialing) number using a phone by anyone, anywhere, anytime. We use the Euclidean formula for distance measurement. Since, shorter geodesic distances (on the Earth’s surface) correspond to shorter Euclidean distances (measured by a straight line through the Earth). Our proposed architecture uses Atom XML syndication format protocol for data integration, VoiceXML for creating the voice user interface (VUI) and CCXML for controlling the call components. We also provide an efficient algorithm for parsing Atom feeds which provide data to the system. Moreover, we describe a cost-effective way for providing global access to the VUA based on Asterisk (an open source IP-PBX). We also provide some information on how our system can be integrated with GPS for locating the user coordinates and therefore efficiently and spontaneously enhancing the system response. Additionally, the system has a mechanism for validating the phone numbers in its database, and it updates the number and other information such as daily price of gas, motel etc. automatically using an Atom-based feed. Currently, the commercial directory services (Example 411) do not have facilities to update the listing in the database automatically, so that why callers most of the times get out-of-date phone numbers or other information. Our system can be integrated very easily with an existing web infrastructure, thereby making the wealth of Web information easily available to the user by phone. This kind of system can be deployed as an extension to 911 and 411 services to share the workload with human operators. This paper presents all the underlying principles, architecture, features, and an example of the real world deployment of our proposed system. The source code and documentations are available for commercial productions.

WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

PubMed Central

Wangkumhang, Pongsakorn; Chaichoompu, Kridsadakorn; Ngamphiw, Chumpol; Ruangrit, Uttapong; Chanprasert, Juntima; Assawamakin, Anunchai; Tongsima, Sissades

2007-01-01

Background Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. Results This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. Conclusion WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at . PMID:17697334

A Data Management Framework for Real-Time Water Quality Monitoring

NASA Astrophysics Data System (ADS)

Mulyono, E.; Yang, D.; Craig, M.

2007-12-01

CSU East Bay operates two in-situ, near-real-time water quality monitoring stations in San Francisco Bay as a member of the Center for Integrative Coastal Ocean Observation, Research, and Education (CICORE) and the Central and Northern California Ocean Observing System (CeNCOOS). We have been operating stations at Dumbarton Pier and San Leandro Marina for the past two years. At each station, a sonde measures seven water quality parameters every six minutes. During the first year of operation, we retrieved data from the sondes every few weeks by visiting the sites and uploading data to a handheld logger. Last year we implemented a telemetry system utilizing a cellular CDMA modem to transfer data from the field to our data center on an hourly basis. Data from each station are initially stored in monthly files in native format. We import data from these files into a SQL database every hour. SQL is handled by Django, an open source web framework. Django provides a user- friendly web user interface (UI) to administer the data. We utilized parts of the Django UI for our database web- front, which allows users to access our database via the World Wide Web and perform basic queries. We also serve our data to other aggregating sites, including the central CICORE website and NOAA's National Data Buoy Center (NDBC). Since Django is written in Python, it allows us to integrate other Python modules into our software, such as the Matplot library for scientific graphics. We store our code in a Subversion repository, which keeps track of software revisions. Code is tested using Python's unittest and doctest modules within Django's testing facility, which warns us when our code modifications cause other parts of the software to break. During the past two years of data acquisition, we have incrementally updated our data model to accommodate changes in physical hardware, including equipment moves, instrument replacements, and sensor upgrades that affected data format.

An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow.

PubMed

Paterson, Trevor; Law, Andy

2009-08-14

Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an ad hoc manner. We have developed a simple generic XML schema (GenomicMappingData.xsd - GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows. The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.

An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow

PubMed Central

Paterson, Trevor; Law, Andy

2009-01-01

Background Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an ad hoc manner. Results We have developed a simple generic XML schema (GenomicMappingData.xsd – GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows. Conclusion The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data. PMID:19682365

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

CottonDB: A resource for cotton genome research

USDA-ARS?s Scientific Manuscript database

CottonDB (http://cottondb.org/) is a database and web resource for cotton genomic and genetic research. Created in 1995, CottonDB was among the first plant genome databases established by the USDA-ARS. Accessed through a website interface, the database aims to be a convenient, inclusive medium of ...

HIV Structural Database

National Institute of Standards and Technology Data Gateway

SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

RayPlus: a Web-Based Platform for Medical Image Processing.

PubMed

Yuan, Rong; Luo, Ming; Sun, Zhi; Shi, Shuyue; Xiao, Peng; Xie, Qingguo

2017-04-01

Medical image can provide valuable information for preclinical research, clinical diagnosis, and treatment. As the widespread use of digital medical imaging, many researchers are currently developing medical image processing algorithms and systems in order to accommodate a better result to clinical community, including accurate clinical parameters or processed images from the original images. In this paper, we propose a web-based platform to present and process medical images. By using Internet and novel database technologies, authorized users can easily access to medical images and facilitate their workflows of processing with server-side powerful computing performance without any installation. We implement a series of algorithms of image processing and visualization in the initial version of Rayplus. Integration of our system allows much flexibility and convenience for both research and clinical communities.

Improving healthcare services using web based platform for management of medical case studies.

PubMed

Ogescu, Cristina; Plaisanu, Claudiu; Udrescu, Florian; Dumitru, Silviu

2008-01-01

The paper presents a web based platform for management of medical cases, support for healthcare specialists in taking the best clinical decision. Research has been oriented mostly on multimedia data management, classification algorithms for querying, retrieving and processing different medical data types (text and images). The medical case studies can be accessed by healthcare specialists and by students as anonymous case studies providing trust and confidentiality in Internet virtual environment. The MIDAS platform develops an intelligent framework to manage sets of medical data (text, static or dynamic images), in order to optimize the diagnosis and the decision process, which will reduce the medical errors and will increase the quality of medical act. MIDAS is an integrated project working on medical information retrieval from heterogeneous, distributed medical multimedia database.

BIOZON: a system for unification, management and analysis of heterogeneous biological data.

PubMed

Birkland, Aaron; Yona, Golan

2006-02-15

Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. Here we present a system (Biozon) that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways). It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at http://biozon.org.

Evaluation of the Content and Accessibility of Web Sites for Accredited Orthopaedic Trauma Surgery Fellowships.

PubMed

Shaath, M Kareem; Yeranosian, Michael G; Ippolito, Joseph A; Adams, Mark R; Sirkin, Michael S; Reilly, Mark C

2018-05-02

Orthopaedic trauma fellowship applicants use online-based resources when researching information on potential U.S. fellowship programs. The 2 primary sources for identifying programs are the Orthopaedic Trauma Association (OTA) database and the San Francisco Match (SF Match) database. Previous studies in other orthopaedic subspecialty areas have demonstrated considerable discrepancies among fellowship programs. The purpose of this study was to analyze content and availability of information on orthopaedic trauma surgery fellowship web sites. The online databases of the OTA and SF Match were reviewed to determine the availability of embedded program links or external links for the included programs. Thereafter, a Google search was performed for each program individually by typing the program's name, followed by the term "orthopaedic trauma fellowship." All identified fellowship web sites were analyzed for accessibility and content. Web sites were evaluated for comprehensiveness in mentioning key components of the orthopaedic trauma surgery curriculum. By consensus, we refined the final list of variables utilizing the methodology of previous studies on the topic. We identified 54 OTA-accredited fellowship programs, offering 87 positions. The majority (94%) of programs had web sites accessible through a Google search. Of the 51 web sites found, all (100%) described their program. Most commonly, hospital affiliation (88%), operative experiences (76%), and rotation overview (65%) were listed, and, least commonly, interview dates (6%), selection criteria (16%), on-call requirements (20%), and fellow evaluation criteria (20%) were listed. Programs with ≥2 fellows provided more information with regard to education content (p = 0.0001) and recruitment content (p = 0.013). Programs with Accreditation Council for Graduate Medical Education (ACGME) accreditation status also provided greater information with regard to education content (odds ratio, 4.0; p = 0.0001). Otherwise, no differences were seen by region, residency affiliation, medical school affiliation, or hospital affiliation. The SF Match and OTA databases provide few direct links to fellowship web sites. Individual program web sites do not effectively and completely convey information about the programs. The Internet is an underused resource for fellow recruitment. The lack of information on these sites allows for future opportunity to optimize this resource.

ChEMBL web services: streamlining access to drug discovery data and utilities.

PubMed

Davies, Mark; Nowotka, Michał; Papadatos, George; Dedman, Nathan; Gaulton, Anna; Atkinson, Francis; Bellis, Louisa; Overington, John P

2015-07-01

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

NASA Astrophysics Data System (ADS)

Kadow, C.; Illing, S.; Kunst, O.; Cubasch, U.

2014-12-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced by other users-saving CPU time, I/O and disk space. This study presents the different techniques and advantages of such a hybrid evaluation system making use of a Big Data HPC in climate science. website: www-miklip.dkrz.de visitor-login: guest password: miklip

A Hybrid Evaluation System Framework (Shell & Web) with Standardized Access to Climate Model Data and Verification Tools for a Clear Climate Science Infrastructure on Big Data High Performance Computers

NASA Astrophysics Data System (ADS)

Kadow, Christopher; Illing, Sebastian; Kunst, Oliver; Ulbrich, Uwe; Cubasch, Ulrich

2015-04-01

The project 'Integrated Data and Evaluation System for Decadal Scale Prediction' (INTEGRATION) as part of the German decadal prediction project MiKlip develops a central evaluation system. The fully operational hybrid features a HPC shell access and an user friendly web-interface. It employs one common system with a variety of verification tools and validation data from different projects in- and outside of MiKlip. The evaluation system is located at the German Climate Computing Centre (DKRZ) and has direct access to the bulk of its ESGF node including millions of climate model data sets, e.g. from CMIP5 and CORDEX. The database is organized by the international CMOR standard using the meta information of the self-describing model, reanalysis and observational data sets. Apache Solr is used for indexing the different data projects into one common search environment. This implemented meta data system with its advanced but easy to handle search tool supports users, developers and their tools to retrieve the required information. A generic application programming interface (API) allows scientific developers to connect their analysis tools with the evaluation system independently of the programming language used. Users of the evaluation techniques benefit from the common interface of the evaluation system without any need to understand the different scripting languages. Facilitating the provision and usage of tools and climate data increases automatically the number of scientists working with the data sets and identify discrepancies. Additionally, the history and configuration sub-system stores every analysis performed with the evaluation system in a MySQL database. Configurations and results of the tools can be shared among scientists via shell or web-system. Therefore, plugged-in tools gain automatically from transparency and reproducibility. Furthermore, when configurations match while starting a evaluation tool, the system suggests to use results already produced by other users-saving CPU time, I/O and disk space. This study presents the different techniques and advantages of such a hybrid evaluation system making use of a Big Data HPC in climate science. website: www-miklip.dkrz.de visitor-login: click on "Guest"

The ChEMBL database as linked open data

PubMed Central

2013-01-01

Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

The development of a new database of gas emissions: MAGA, a collaborative web environment for collecting data

NASA Astrophysics Data System (ADS)

Cardellini, C.; Chiodini, G.; Frigeri, A.; Bagnato, E.; Aiuppa, A.; McCormick, B.

2013-12-01

The data on volcanic and non-volcanic gas emissions available online are, as today, incomplete and most importantly, fragmentary. Hence, there is need for common frameworks to aggregate available data, in order to characterize and quantify the phenomena at various spatial and temporal scales. Building on the Googas experience we are now extending its capability, particularly on the user side, by developing a new web environment for collecting and publishing data. We have started to create a new and detailed web database (MAGA: MApping GAs emissions) for the deep carbon degassing in the Mediterranean area. This project is part of the Deep Earth Carbon Degassing (DECADE) research initiative, lunched in 2012 by the Deep Carbon Observatory (DCO) to improve the global budget of endogenous carbon from volcanoes. MAGA database is planned to complement and integrate the work in progress within DECADE in developing CARD (Carbon Degassing) database. MAGA database will allow researchers to insert data interactively and dynamically into a spatially referred relational database management system, as well as to extract data. MAGA kicked-off with the database set up and a complete literature survey on publications on volcanic gas fluxes, by including data on active craters degassing, diffuse soil degassing and fumaroles both from dormant closed-conduit volcanoes (e.g., Vulcano, Phlegrean Fields, Santorini, Nysiros, Teide, etc.) and open-vent volcanoes (e.g., Etna, Stromboli, etc.) in the Mediterranean area and Azores. For each geo-located gas emission site, the database holds images and description of the site and of the emission type (e.g., diffuse emission, plume, fumarole, etc.), gas chemical-isotopic composition (when available), gas temperature and gases fluxes magnitude. Gas sampling, analysis and flux measurement methods are also reported together with references and contacts to researchers expert of the site. Data can be accessed on the network from a web interface or as a data-driven web service, where software clients can request data directly from the database. This way Geographical Information Systems (GIS) and Virtual Globes (e.g., Google Earth) can easily access the database, and data can be exchanged with other database. In details the database now includes: i) more than 1000 flux data about volcanic plume degassing from Etna (4 summit craters and bulk degassing) and Stromboli volcanoes, with time averaged CO2 fluxes of ~ 18000 and 766 t/d, respectively; ii) data from ~ 30 sites of diffuse soil degassing from Napoletan volcanoes, Azores, Canary, Etna, Stromboli, and Vulcano Island, with a wide range of CO2 fluxes (from les than 1 to 1500 t/d) and iii) several data on fumarolic emissions (~ 7 sites) with CO2 fluxes up to 1340 t/day (i.e., Stromboli). When available, time series of compositional data have been archived in the database (e.g., for Campi Flegrei fumaroles). We believe MAGA data-base is an important starting point to develop a large scale, expandable data-base aimed to excite, inspire, and encourage participation among researchers. In addition, the possibility to archive location and qualitative information for gas emission/sites not yet investigated, could stimulate the scientific community for future researches and will provide an indication on the current uncertainty on deep carbon fluxes global estimates.

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

Accessing the public MIMIC-II intensive care relational database for clinical research.

PubMed

Scott, Daniel J; Lee, Joon; Silva, Ikaro; Park, Shinhyuk; Moody, George B; Celi, Leo A; Mark, Roger G

2013-01-10

The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge "Predicting mortality of ICU Patients". QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database.

VO Access to BASECOL Database

NASA Astrophysics Data System (ADS)

Moreau, N.; Dubernet, M. L.

2006-07-01

Basecol is a combination of a website (using PHP and HTML) and a MySQL database concerning molecular ro-vibrational transitions induced by collisions with atoms or molecules. This database has been created in view of the scientific preparation of the Heterodyne Instrument for the Far-Infrared on board the Herschel Space Observatory (HSO). Basecol offers an access to numerical and bibliographic data through various output methods such as ASCII, HTML or VOTable (which is a first step towards a VO compliant system). A web service using Apache Axis has been developed in order to provide a direct access to data for external applications.

Molecular Identification and Databases in Fusarium

USDA-ARS?s Scientific Manuscript database

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

PubMed

Zhang, C; Crasta, O; Cammer, S; Will, R; Kenyon, R; Sullivan, D; Yu, Q; Sun, W; Jha, R; Liu, D; Xue, T; Zhang, Y; Moore, M; McGarvey, P; Huang, H; Chen, Y; Zhang, J; Mazumder, R; Wu, C; Sobral, B

2008-01-01

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

Core Technical Capability Laboratory Management System

NASA Technical Reports Server (NTRS)

Shaykhian, Linda; Dugger, Curtis; Griffin, Laurie

2008-01-01

The Core Technical Capability Lab - oratory Management System (CTCLMS) consists of dynamically generated Web pages used to access a database containing detailed CTC lab data with the software hosted on a server that allows users to have remote access.

MyEnviroMapper

EPA Pesticide Factsheets

EnviroMapper for Envirofacts is a single point of access to select U.S. EPA environmental data. This Web site provides access to several EPA databases to provide you with information about environmental activities that may affect air, water, and l

MITOPRED: a web server for the prediction of mitochondrial proteins

PubMed Central

Guda, Chittibabu; Guda, Purnima; Fahy, Eoin; Subramaniam, Shankar

2004-01-01

MITOPRED web server enables prediction of nucleus-encoded mitochondrial proteins in all eukaryotic species. Predictions are made using a new algorithm based primarily on Pfam domain occurrence patterns in mitochondrial and non-mitochondrial locations. Pre-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. Automated updates are scheduled for the pre-calculated prediction database so as to provide access to the most current data. The server, its documentation and the data are available from http://mitopred.sdsc.edu. PMID:15215413

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.

The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati

The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria

PubMed Central

Rangel, Luiz Thibério; Novaes, Jeniffer; Durham, Alan M.; Madeira, Alda Maria B. N.; Gruber, Arthur

2013-01-01

Parasites of the genus Eimeria infect a wide range of vertebrate hosts, including chickens. We have recently reported a comparative analysis of the transcriptomes of Eimeria acervulina, Eimeria maxima and Eimeria tenella, integrating ORESTES data produced by our group and publicly available Expressed Sequence Tags (ESTs). All cDNA reads have been assembled, and the reconstructed transcripts have been submitted to a comprehensive functional annotation pipeline. Additional studies included orthology assignment across apicomplexan parasites and clustering analyses of gene expression profiles among different developmental stages of the parasites. To make all this body of information publicly available, we constructed the Eimeria Transcript Database (EimeriaTDB), a web repository that provides access to sequence data, annotation and comparative analyses. Here, we describe the web interface, available sequence data sets and query tools implemented on the site. The main goal of this work is to offer a public repository of sequence and functional annotation data of reconstructed transcripts of parasites of the genus Eimeria. We believe that EimeriaTDB will represent a valuable and complementary resource for the Eimeria scientific community and for those researchers interested in comparative genomics of apicomplexan parasites. Database URL: http://www.coccidia.icb.usp.br/eimeriatdb/ PMID:23411718

The NOAO Data Lab PHAT Photometry Database

NASA Astrophysics Data System (ADS)

Olsen, Knut; Williams, Ben; Fitzpatrick, Michael; PHAT Team

2018-01-01

We present a database containing both the combined photometric object catalog and the single epoch measurements from the Panchromatic Hubble Andromeda Treasury (PHAT). This database is hosted by the NOAO Data Lab (http://datalab.noao.edu), and as such exposes a number of data services to the PHAT photometry, including access through a Table Access Protocol (TAP) service, direct PostgreSQL queries, web-based and programmatic query interfaces, remote storage space for personal database tables and files, and a JupyterHub-based Notebook analysis environment, as well as image access through a Simple Image Access (SIA) service. We show how the Data Lab database and Jupyter Notebook environment allow for straightforward and efficient analyses of PHAT catalog data, including maps of object density, depth, and color, extraction of light curves of variable objects, and proper motion exploration.

Accounting Data to Web Interface Using PERL

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

Hargeaves, C

2001-08-13

This document will explain the process to create a web interface for the accounting information generated by the High Performance Storage Systems (HPSS) accounting report feature. The accounting report contains useful data but it is not easily accessed in a meaningful way. The accounting report is the only way to see summarized storage usage information. The first step is to take the accounting data, make it meaningful and store the modified data in persistent databases. The second step is to generate the various user interfaces, HTML pages, that will be used to access the data. The third step is tomore » transfer all required files to the web server. The web pages pass parameters to Common Gateway Interface (CGI) scripts that generate dynamic web pages and graphs. The end result is a web page with specific information presented in text with or without graphs. The accounting report has a specific format that allows the use of regular expressions to verify if a line is storage data. Each storage data line is stored in a detailed database file with a name that includes the run date. The detailed database is used to create a summarized database file that also uses run date in its name. The summarized database is used to create the group.html web page that includes a list of all storage users. Scripts that query the database folder to build a list of available databases generate two additional web pages. A master script that is run monthly as part of a cron job, after the accounting report has completed, manages all of these individual scripts. All scripts are written in the PERL programming language. Whenever possible data manipulation scripts are written as filters. All scripts are written to be single source, which means they will function properly on both the open and closed networks at LLNL. The master script handles the command line inputs for all scripts, file transfers to the web server and records run information in a log file. The rest of the scripts manipulate the accounting data or use the files created to generate HTML pages. Each script will be described in detail herein. The following is a brief description of HPSS taken directly from an HPSS web site. ''HPSS is a major development project, which began in 1993 as a Cooperative Research and Development Agreement (CRADA) between government and industry. The primary objective of HPSS is to move very large data objects between high performance computers, workstation clusters, and storage libraries at speeds many times faster than is possible with today's software systems. For example, HPSS can manage parallel data transfers from multiple network-connected disk arrays at rates greater than 1 Gbyte per second, making it possible to access high definition digitized video in real time.'' The HPSS accounting report is a canned report whose format is controlled by the HPSS developers.« less

EntrezAJAX: direct web browser access to the Entrez Programming Utilities.

PubMed

Loman, Nicholas J; Pallen, Mark J

2010-06-21

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

Using Web-based Tutorials To Enhance Library Instruction.

ERIC Educational Resources Information Center

Kocour, Bruce G.

2000-01-01

Describes the development of a Web site for library instruction at Carson-Newman College (TN) and its integration into English composition courses. Describes the use of a virtual tour, a tutorial on database searching, tutorials on specific databases, and library guides to specific disciplines to create an effective mechanism for active learning.…

Accessing Digital Libraries: A Study of ARL Members' Digital Projects

ERIC Educational Resources Information Center

Kahl, Chad M.; Williams, Sarah C.

2006-01-01

To ensure efficient access to and integrated searching capabilities for their institution's new digital library projects, the authors studied Web sites of the Association of Research Libraries' (ARL) 111 academic, English-language libraries. Data were gathered on 1117 digital projects, noting library Web site and project access, metadata, and…

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

Ground Support Software for Spaceborne Instrumentation

NASA Technical Reports Server (NTRS)

Anicich, Vincent; Thorpe, rob; Fletcher, Greg; Waite, Hunter; Xu, Hykua; Walter, Erin; Frick, Kristie; Farris, Greg; Gell, Dave; Furman, Jufy;

Nuclear Science References Database

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

Pritychenko, B., E-mail: pritychenko@bnl.gov; Běták, E.; Singh, B.

2014-06-15

The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energymore » Agency (http://www-nds.iaea.org/nsr)« less

Development of a medical module for disaster information systems.

PubMed

Calik, Elif; Atilla, Rıdvan; Kaya, Hilal; Aribaş, Alirıza; Cengiz, Hakan; Dicle, Oğuz

2014-01-01

This study aims to improve a medical module which provides a real-time medical information flow about pre-hospital processes that gives health care in disasters; transferring, storing and processing the records that are in electronic media and over internet as a part of disaster information systems. In this study which is handled within the frame of providing information flow among professionals in a disaster case, to supply the coordination of healthcare team and transferring complete information to specified people at real time, Microsoft Access database and SQL query language were used to inform database applications. System was prepared on Microsoft .Net platform using C# language. Disaster information system-medical module was designed to be used in disaster area, field hospital, nearby hospitals, temporary inhabiting areas like tent city, vehicles that are used for dispatch, and providing information flow between medical officials and data centres. For fast recording of the disaster victim data, accessing to database which was used by health care professionals was provided (or granted) among analysing process steps and creating minimal datasets. Database fields were created in the manner of giving opportunity to enter new data and search old data which is recorded before disaster. Web application which provides access such as data entry to the database and searching towards the designed interfaces according to the login credentials access level. In this study, homepage and users' interfaces which were built on database in consequence of system analyses were provided with www.afmedinfo.com web site to the user access. With this study, a recommendation was made about how to use disaster-based information systems in the field of health. Awareness has been developed about the fact that disaster information system should not be perceived only as an early warning system. Contents and the differences of the health care practices of disaster information systems were revealed. A web application was developed supplying a link between the user and the database to make date entry and data query practices by the help of the developed interfaces.

Academic medical center libraries on the Web.

PubMed Central

Tannery, N H; Wessel, C B

1998-01-01

Academic medical center libraries are moving towards publishing electronically, utilizing networked technologies, and creating digital libraries. The catalyst for this movement has been the Web. An analysis of academic medical center library Web pages was undertaken to assess the information created and communicated in early 1997. A summary of present uses and suggestions for future applications is provided. A method for evaluating and describing the content of library Web sites was designed. The evaluation included categorizing basic information such as description and access to library services, access to commercial databases, and use of interactive forms. The main goal of the evaluation was to assess original resources produced by these libraries. PMID:9803298

Optimizing the NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maa, Ming-Hokng

1996-01-01

The NASA Technical Report Server (NTRS), a World Wide Web report distribution NASA technical publications service, is modified for performance enhancement, greater protocol support, and human interface optimization. Results include: Parallel database queries, significantly decreasing user access times by an average factor of 2.3; access from clients behind firewalls and/ or proxies which truncate excessively long Uniform Resource Locators (URLs); access to non-Wide Area Information Server (WAIS) databases and compatibility with the 239-50.3 protocol; and a streamlined user interface.

Towards structured sharing of raw and derived neuroimaging data across existing resources

PubMed Central

Keator, D.B.; Helmer, K.; Steffener, J.; Turner, J.A.; Van Erp, T.G.M.; Gadde, S.; Ashish, N.; Burns, G.A.; Nichols, B.N.

2013-01-01

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery. PMID:23727024

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

Web-Enabled Systems for Student Access.

ERIC Educational Resources Information Center

Harris, Chad S.; Herring, Tom

1999-01-01

California State University, Fullerton is developing a suite of server-based, Web-enabled applications that distribute the functionality of its student information system software to external customers without modifying the mainframe applications or databases. The cost-effective, secure, and rapidly deployable business solution involves using the…

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

PubMed

Choubey, Jyotsna; Choudhari, Jyoti Kant; Patel, Ashish; Verma, Mukesh Kumar

2017-01-01

Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

QuakeSim: a Web Service Environment for Productive Investigations with Earth Surface Sensor Data

NASA Astrophysics Data System (ADS)

Parker, J. W.; Donnellan, A.; Granat, R. A.; Lyzenga, G. A.; Glasscoe, M. T.; McLeod, D.; Al-Ghanmi, R.; Pierce, M.; Fox, G.; Grant Ludwig, L.; Rundle, J. B.

2011-12-01

The QuakeSim science gateway environment includes a visually rich portal interface, web service access to data and data processing operations, and the QuakeTables ontology-based database of fault models and sensor data. The integrated tools and services are designed to assist investigators by covering the entire earthquake cycle of strain accumulation and release. The Web interface now includes Drupal-based access to diverse and changing content, with new ability to access data and data processing directly from the public page, as well as the traditional project management areas that require password access. The system is designed to make initial browsing of fault models and deformation data particularly engaging for new users. Popular data and data processing include GPS time series with data mining techniques to find anomalies in time and space, experimental forecasting methods based on catalogue seismicity, faulted deformation models (both half-space and finite element), and model-based inversion of sensor data. The fault models include the CGS and UCERF 2.0 faults of California and are easily augmented with self-consistent fault models from other regions. The QuakeTables deformation data include the comprehensive set of UAVSAR interferograms as well as a growing collection of satellite InSAR data.. Fault interaction simulations are also being incorporated in the web environment based on Virtual California. A sample usage scenario is presented which follows an investigation of UAVSAR data from viewing as an overlay in Google Maps, to selection of an area of interest via a polygon tool, to fast extraction of the relevant correlation and phase information from large data files, to a model inversion of fault slip followed by calculation and display of a synthetic model interferogram.

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

PubMed Central

Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel J; Turner, John P; Vidović, Dušica; Forlin, Michele; Kelley, Tanya T; D’Urso, Alessandro; Allen, Bryce K; Torre, Denis; Jagodnik, Kathleen M; Wang, Lily; Jenkins, Sherry L; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma’ayan, Avi; Pillai, Ajay

2018-01-01

Abstract The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content. PMID:29140462

CCDST: A free Canadian climate data scraping tool

NASA Astrophysics Data System (ADS)

Bonifacio, Charmaine; Barchyn, Thomas E.; Hugenholtz, Chris H.; Kienzle, Stefan W.

2015-02-01

In this paper we present a new software tool that automatically fetches, downloads and consolidates climate data from a Web database where the data are contained on multiple Web pages. The tool is called the Canadian Climate Data Scraping Tool (CCDST) and was developed to enhance access and simplify analysis of climate data from Canada's National Climate Data and Information Archive (NCDIA). The CCDST deconstructs a URL for a particular climate station in the NCDIA and then iteratively modifies the date parameters to download large volumes of data, remove individual file headers, and merge data files into one output file. This automated sequence enhances access to climate data by substantially reducing the time needed to manually download data from multiple Web pages. To this end, we present a case study of the temporal dynamics of blowing snow events that resulted in ~3.1 weeks time savings. Without the CCDST, the time involved in manually downloading climate data limits access and restrains researchers and students from exploring climate trends. The tool is coded as a Microsoft Excel macro and is available to researchers and students for free. The main concept and structure of the tool can be modified for other Web databases hosting geophysical data.

EarthChem: International Collaboration for Solid Earth Geochemistry in Geoinformatics

NASA Astrophysics Data System (ADS)

Walker, J. D.; Lehnert, K. A.; Hofmann, A. W.; Sarbas, B.; Carlson, R. W.

2005-12-01

The current on-line information systems for igneous rock geochemistry - PetDB, GEOROC, and NAVDAT - convincingly demonstrate the value of rigorous scientific data management of geochemical data for research and education. The next generation of hypothesis formulation and testing can be vastly facilitated by enhancing these electronic resources through integration of available datasets, expansion of data coverage in location, time, and tectonic setting, timely updates with new data, and through intuitive and efficient access and data analysis tools for the broader geosciences community. PetDB, GEOROC, and NAVDAT have therefore formed the EarthChem consortium (www.earthchem.org) as a international collaborative effort to address these needs and serve the larger earth science community by facilitating the compilation, communication, serving, and visualization of geochemical data, and their integration with other geological, geochronological, geophysical, and geodetic information to maximize their scientific application. We report on the status of and future plans for EarthChem activities. EarthChem's development plan includes: (1) expanding the functionality of the web portal to become a `one-stop shop for geochemical data' with search capability across databases, standardized and integrated data output, generally applicable tools for data quality assessment, and data analysis/visualization including plotting methods and an information-rich map interface; and (2) expanding data holdings by generating new datasets as identified and prioritized through community outreach, and facilitating data contributions from the community by offering web-based data submission capability and technical assistance for design, implementation, and population of new databases and their integration with all EarthChem data holdings. Such federated databases and datasets will retain their identity within the EarthChem system. We also plan on working with publishers to ease the assimilation of geochemical data into the EarthChem database. As a community resource, EarthChem will address user concerns and respond to broad scientific and educational needs. EarthChem will hold yearly workshops, town hall meetings, and/or exhibits at major meetings. The group has established a two-tier committee structure to help ease the communication and coordination of database and IT issues between existing data management projects, and to receive feedback and support from individuals and groups from the larger geosciences community.

Developing a kidney and urinary pathway knowledge base

PubMed Central

2011-01-01

Background Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration. Results We present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney. Conclusions The KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain’s ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself. Availability The KUPKB may be accessed via http://www.e-lico.eu/kupkb. PMID:21624162

The INFN-CNAF Tier-1 GEMSS Mass Storage System and database facility activity

NASA Astrophysics Data System (ADS)

Ricci, Pier Paolo; Cavalli, Alessandro; Dell'Agnello, Luca; Favaro, Matteo; Gregori, Daniele; Prosperini, Andrea; Pezzi, Michele; Sapunenko, Vladimir; Zizzi, Giovanni; Vagnoni, Vincenzo

2015-05-01

The consolidation of Mass Storage services at the INFN-CNAF Tier1 Storage department that has occurred during the last 5 years, resulted in a reliable, high performance and moderately easy-to-manage facility that provides data access, archive, backup and database services to several different use cases. At present, the GEMSS Mass Storage System, developed and installed at CNAF and based upon an integration between the IBM GPFS parallel filesystem and the Tivoli Storage Manager (TSM) tape management software, is one of the largest hierarchical storage sites in Europe. It provides storage resources for about 12% of LHC data, as well as for data of other non-LHC experiments. Files are accessed using standard SRM Grid services provided by the Storage Resource Manager (StoRM), also developed at CNAF. Data access is also provided by XRootD and HTTP/WebDaV endpoints. Besides these services, an Oracle database facility is in production characterized by an effective level of parallelism, redundancy and availability. This facility is running databases for storing and accessing relational data objects and for providing database services to the currently active use cases. It takes advantage of several Oracle technologies, like Real Application Cluster (RAC), Automatic Storage Manager (ASM) and Enterprise Manager centralized management tools, together with other technologies for performance optimization, ease of management and downtime reduction. The aim of the present paper is to illustrate the state-of-the-art of the INFN-CNAF Tier1 Storage department infrastructures and software services, and to give a brief outlook to forthcoming projects. A description of the administrative, monitoring and problem-tracking tools that play a primary role in managing the whole storage framework is also given.

Simulation in the Internet age: the place of web-based simulation in nursing education. An integrative review.

PubMed

Cant, Robyn P; Cooper, Simon J

2014-12-01

The objective of this article was to review the literature on utilisation and place of Web-based simulation within nursing education. Web-based simulation combines electronic multimedia options with a central video or virtual world to produce interactive learning activities mediated by the learner. An integrative review. A search was conducted of healthcare databases between 2000 and 2014 and of Internet sources for hosted simulation programs in nursing. Eighteen primary programs were identified for inclusion. A strategy for integrative review was adopted in which studies were identified, filtered, classified, analysed and compared. Of 18 programs, two game-based programs were identified which represented a 'virtual world' in which students could simultaneously or individually immerse themselves in a character role-play. However, most programs (n=10) taught an aspect of procedural patient care using multimedia (e.g. video, audio, graphics, quiz, text, memo). Time-limited sequences, feedback and reflective activities were often incorporated. Other studies (n=8) taught interpersonal communication skills or technical skills for equipment use. Descriptive study outcomes indicated ease of program use, strong satisfaction with learning and appreciation of program accessibility. Additionally, four studies reported significant improvements in knowledge post-intervention. Web-based simulation is highly acceptable to students and appears to provide learning benefits that align with other simulation approaches and it augments face-to-face teaching. Web-based simulation is likely to have a major place in nursing curricula in the next decade, yet further research is necessary to objectively evaluate learner outcomes and to justify its use. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Geospatial Database that Supports Derivation of Climatological Features of Severe Weather

NASA Astrophysics Data System (ADS)

Phillips, M.; Ansari, S.; Del Greco, S.

2007-12-01

The Severe Weather Data Inventory (SWDI) at NOAA's National Climatic Data Center (NCDC) provides user access to archives of several datasets critical to the detection and evaluation of severe weather. These datasets include archives of: · NEXRAD Level-III point features describing general storm structure, hail, mesocyclone and tornado signatures · National Weather Service Storm Events Database · National Weather Service Local Storm Reports collected from storm spotters · National Weather Service Warnings · Lightning strikes from Vaisala's National Lightning Detection Network (NLDN) SWDI archives all of these datasets in a spatial database that allows for convenient searching and subsetting. These data are accessible via the NCDC web site, Web Feature Services (WFS) or automated web services. The results of interactive web page queries may be saved in a variety of formats, including plain text, XML, Google Earth's KMZ, standards-based NetCDF and Shapefile. NCDC's Storm Risk Assessment Project (SRAP) uses data from the SWDI database to derive gridded climatology products that show the spatial distributions of the frequency of various events. SRAP also can relate SWDI events to other spatial data such as roads, population, watersheds, and other geographic, sociological, or economic data to derive products that are useful in municipal planning, emergency management, the insurance industry, and other areas where there is a need to quantify and qualify how severe weather patterns affect people and property.

Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

1999-07-01

The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

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

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

The CMS dataset bookkeeping service

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

Afaq, Anzar,; /Fermilab; Dolgert, Andrew

2007-10-01

The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires processing and analysis activities at various service levels and the DBS system provides support for localized processing or private analysis, as well as global access for CMS users at large. Catalog entries can be moved among the various service levels with a simple set of migration tools, thus forming a loose federation of databases. DBS ismore » available to CMS users via a Python API, Command Line, and a Discovery web page interfaces. The system is built as a multi-tier web application with Java servlets running under Tomcat, with connections via JDBC to Oracle or MySQL database backends. Clients connect to the service through HTTP or HTTPS with authentication provided by GRID certificates and authorization through VOMS. DBS is an integral part of the overall CMS Data Management and Workflow Management systems.« less

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

DOE PAGES

Putman, Tim E.; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian; ...

2017-03-06

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomicmore » data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.« less

Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice

PubMed Central

Shrestha, Rosemary; Matteis, Luca; Skofic, Milko; Portugal, Arllet; McLaren, Graham; Hyman, Glenn; Arnaud, Elizabeth

2012-01-01

The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP. PMID:22934074

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

PubMed Central

2010-01-01

Background Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. Results In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. Conclusions CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu. PMID:20946609

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

PubMed

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu.

DEFENSE RTD&E ONLINE SYSTEM (DROLS)

EPA Science Inventory

Web Enabled DROLS (WED) is a free subscription service available to registered users that provides online access to DTIC's Technical Reports and Research Summaries Databases. It replaces the former unclassified dial-up access to DROLS, DTIC's Defense RDT&E Online System. The Defe...

[The database server for the medical bibliography database at Charles University].

PubMed

Vejvalka, J; Rojíková, V; Ulrych, O; Vorísek, M

1998-01-01

In the medical community, bibliographic databases are widely accepted as a most important source of information both for theoretical and clinical disciplines. To improve access to medical bibliographic databases at Charles University, a database server (ERL by Silver Platter) was set up at the 2nd Faculty of Medicine in Prague. The server, accessible by Internet 24 hours/7 days, hosts now 14 years' MEDLINE and 10 years' EMBASE Paediatrics. Two different strategies are available for connecting to the server: a specialized client program that communicates over the Internet (suitable for professional searching) and a web-based access that requires no specialized software (except the WWW browser) on the client side. The server is now offered to academic community to host further databases, possibly subscribed by consortia whose individual members would not subscribe them by themselves.

DynAstVO : a Europlanet database of NEA orbits

NASA Astrophysics Data System (ADS)

Desmars, J.; Thuillot, W.; Hestroffer, D.; David, P.; Le Sidaner, P.

2017-09-01

DynAstVO is a new orbital database developed within the Europlanet 2020 RI and the Virtual European Solar and Planetary Access (VESPA) frameworks. The database is dedicated to Near-Earth asteroids and provide parameters related to orbits: osculating elements, observational information, ephemeris through SPICE kernel, and in particular, orbit uncertainty and associated covariance matrix. DynAstVO is daily updated on a automatic process of orbit determination on the basis of the Minor Planet Electronic Circulars that reports new observations or the discover of a new asteroid. This database conforms to EPN-TAP environment and is accessible through VO protocols and on the VESPA portal web access (http://vespa.obspm.fr/). A comparison with other classical databases such as Astorb, MPCORB, NEODyS and JPL is also presented.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry.

PubMed

Williams, Antony J; Grulke, Christopher M; Edwards, Jeff; McEachran, Andrew D; Mansouri, Kamel; Baker, Nancy C; Patlewicz, Grace; Shah, Imran; Wambaugh, John F; Judson, Richard S; Richard, Ann M

2017-11-28

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency's (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA's DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a flexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists.

Web-based X-ray quality control documentation.

PubMed

David, George; Burnett, Lou Ann; Schenkel, Robert

2003-01-01

The department of radiology at the Medical College of Georgia Hospital and Clinics has developed an equipment quality control web site. Our goal is to provide immediate access to virtually all medical physics survey data. The web site is designed to assist equipment engineers, department management and technologists. By improving communications and access to equipment documentation, we believe productivity is enhanced. The creation of the quality control web site was accomplished in three distinct steps. First, survey data had to be placed in a computer format. The second step was to convert these various computer files to a format supported by commercial web browsers. Third, a comprehensive home page had to be designed to provide convenient access to the multitude of surveys done in the various x-ray rooms. Because we had spent years previously fine-tuning the computerization of the medical physics quality control program, most survey documentation was already in spreadsheet or database format. A major technical decision was the method of conversion of survey spreadsheet and database files into documentation appropriate for the web. After an unsatisfactory experience with a HyperText Markup Language (HTML) converter (packaged with spreadsheet and database software), we tried creating Portable Document Format (PDF) files using Adobe Acrobat software. This process preserves the original formatting of the document and takes no longer than conventional printing; therefore, it has been very successful. Although the PDF file generated by Adobe Acrobat is a proprietary format, it can be displayed through a conventional web browser using the freely distributed Adobe Acrobat Reader program that is available for virtually all platforms. Once a user installs the software, it is automatically invoked by the web browser whenever the user follows a link to a file with a PDF extension. Although no confidential patient information is available on the web site, our legal department recommended that we secure the site in order to keep out those wishing to make mischief. Our interim solution has not been to password protect the page, which we feared would hinder access for occasional legitimate users, but also not to provide links to it from other hospital and department pages. Utility and productivity were improved and time and money were saved by making radiological equipment quality control documentation instantly available on-line.

Sensor Webs and Virtual Globes: Enabling Understanding of Changes in a partially Glaciated Watershed

NASA Astrophysics Data System (ADS)

Heavner, M.; Fatland, D. R.; Habermann, M.; Berner, L.; Hood, E.; Connor, C.; Galbraith, J.; Knuth, E.; O'Brien, W.

2008-12-01

The University of Alaska Southeast is currently implementing a sensor web identified as the SouthEast Alaska MOnitoring Network for Science, Telecommunications, Education, and Research (SEAMONSTER). SEAMONSTER is operating in the partially glaciated Mendenhall and Lemon Creek Watersheds, in the Juneau area, on the margins of the Juneau Icefield. These watersheds are studied for both 1. long term monitoring of changes, and 2. detection and analysis of transient events (such as glacier lake outburst floods). The heterogeneous sensors (meteorologic, dual frequency GPS, water quality, lake level, etc), power and bandwidth constraints, and competing time scales of interest require autonomous reactivity of the sensor web. They also present challenges for operational management of the sensor web. The harsh conditions on the glaciers provide additional operating constraints. The tight integration of the sensor web and virtual global enabling technology enhance the project in multiple ways. We are utilizing virtual globe infrastructures to enhance both sensor web management and data access. SEAMONSTER utilizes virtual globes for education and public outreach, sensor web management, data dissemination, and enabling collaboration. Using a PosgreSQL with GIS extensions database coupled to the Open Geospatial Consortium (OGC) Geoserver, we generate near-real-time auto-updating geobrowser files of the data in multiple OGC standard formats (e.g KML, WCS). Additionally, embedding wiki pages in this database allows the development of a geospatially aware wiki describing the projects for better public outreach and education. In this presentation we will describe how we have implemented these technologies to date, the lessons learned, and our efforts towards greater OGC standard implementation. A major focus will be on demonstrating how geobrowsers and virtual globes have made this project possible.

Upgrades to the TPSX Material Properties Database

NASA Technical Reports Server (NTRS)

Squire, T. H.; Milos, F. S.; Partridge, Harry (Technical Monitor)

2001-01-01

The TPSX Material Properties Database is a web-based tool that serves as a database for properties of advanced thermal protection materials. TPSX provides an easy user interface for retrieving material property information in a variety of forms, both graphical and text. The primary purpose and advantage of TPSX is to maintain a high quality source of often used thermal protection material properties in a convenient, easily accessible form, for distribution to government and aerospace industry communities. Last year a major upgrade to the TPSX web site was completed. This year, through the efforts of researchers at several NASA centers, the Office of the Chief Engineer awarded funds to update and expand the databases in TPSX. The FY01 effort focuses on updating correcting the Ames and Johnson thermal protection materials databases. In this session we will summarize the improvements made to the web site last year, report on the status of the on-going database updates, describe the planned upgrades for FY02 and FY03, and provide a demonstration of TPSX.

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

SNPversity: a web-based tool for visualizing diversity

PubMed Central

Schott, David A; Vinnakota, Abhinav G; Portwood, John L; Andorf, Carson M

2018-01-01

Abstract Many stand-alone desktop software suites exist to visualize single nucleotide polymorphism (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualization tool that can be implemented on a Unix-like machine and served through a web browser that can be accessible worldwide. SNPversity consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. SNPversity displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state. SNPversity is currently available at MaizeGDB, the maize community’s database, and will be soon available at GrainGenes, the clade-oriented database for Triticeae and Avena species, including wheat, barley, rye, and oat. The code and documentation are uploaded onto github, and they are freely available to the public. We expect that the tool will be highly useful for other biological databases with a similar need to display SNP diversity through their web interfaces. Database URL: https://www.maizegdb.org/snpversity PMID:29688387

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean.

PubMed

Pagliosa, Paulo R; Doria, João G; Misturini, Dairana; Otegui, Mariana B P; Oortman, Mariana S; Weis, Wilson A; Faroni-Perez, Larisse; Alves, Alexandre P; Camargo, Maurício G; Amaral, A Cecília Z; Marques, Antonio C; Lana, Paulo C

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/.

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

PubMed Central

Pagliosa, Paulo R.; Doria, João G.; Misturini, Dairana; Otegui, Mariana B. P.; Oortman, Mariana S.; Weis, Wilson A.; Faroni-Perez, Larisse; Alves, Alexandre P.; Camargo, Maurício G.; Amaral, A. Cecília Z.; Marques, Antonio C.; Lana, Paulo C.

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/ PMID:24573879

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

PubMed Central

2011-01-01

Background Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. Results OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. Conclusions OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. Availability http://www.ontocat.org PMID:21619703

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

PubMed

Adamusiak, Tomasz; Burdett, Tony; Kurbatova, Natalja; Joeri van der Velde, K; Abeygunawardena, Niran; Antonakaki, Despoina; Kapushesky, Misha; Parkinson, Helen; Swertz, Morris A

2011-05-29

Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups. OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application. OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases. http://www.ontocat.org.

Using the STOQS Web Application for Access to in situ Oceanographic Data

NASA Astrophysics Data System (ADS)

McCann, M. P.

2012-12-01

Using the STOQS Web Application for Access to in situ Oceanographic Data Mike McCann 7 August 2012 With increasing measurement and sampling capabilities of autonomous oceanographic platforms (e.g. Gliders, Autonomous Underwater Vehicles, Wavegliders), the need to efficiently access and visualize the data they collect is growing. The Monterey Bay Aquarium Research Institute has designed and built the Spatial Temporal Oceanographic Query System (STOQS) specifically to address this issue. The need for STOQS arises from inefficiencies discovered from using CF-NetCDF point observation conventions for these data. The problem is that access efficiency decreases with decreasing dimension of CF-NetCDF data. For example, the Trajectory Common Data Model feature type has only one coordinate dimension, usually Time - positions of the trajectory (Depth, Latitude, Longitude) are stored as non-indexed record variables within the NetCDF file. If client software needs to access data between two depth values or from a bounded geographic area, then the whole data set must be read and the selection made within the client software. This is very inefficient. What is needed is a way to easily select data of interest from an archive given any number of spatial, temporal, or other constraints. Geospatial relational database technology provides this capability. The full STOQS application consists of a Postgres/PostGIS database, Mapserver, and Python-Django running on a server and Web 2.0 technology (jQuery, OpenLayers, Twitter Bootstrap) running in a modern web browser. The web application provides faceted search capabilities allowing a user to quickly drill into the data of interest. Data selection can be constrained by spatial, temporal, and depth selections as well as by parameter value and platform name. The web application layer also provides a REST (Representational State Transfer) Application Programming Interface allowing tools such as the Matlab stoqstoolbox to retrieve data directly from the database. STOQS is an open source software project built upon a framework of free and open source software and is available for anyone to use for making their data more accessible and usable. For more information please see: http://code.google.com/p/stoqs/.; In the above screen grab a user has selected the "mass_concentrtion_of_chlorophyll_in_sea_water" parameter and a time depth range that includes three weeks of AUV missions of just the upper 5 meters.

PRGdb: a bioinformatics platform for plant resistance gene analysis

PubMed Central

Sanseverino, Walter; Roma, Guglielmo; De Simone, Marco; Faino, Luigi; Melito, Sara; Stupka, Elia; Frusciante, Luigi; Ercolano, Maria Raffaella

2010-01-01

PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16 000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and linked with useful biological information. The complete database includes a set of 73 manually curated reference R-genes, 6308 putative R-genes collected from NCBI and 10463 computationally predicted putative R-genes. Thanks to a user-friendly interface, data can be examined using different query tools. A home-made prediction pipeline called Disease Resistance Analysis and Gene Orthology (DRAGO), based on reference R-gene sequence data, was developed to search for plant resistance genes in public datasets such as Unigene and Genbank. New putative R-gene classes containing unknown domain combinations were discovered and characterized. The development of the PRG platform represents an important starting point to conduct various experimental tasks. The inferred cross-link between genomic and phenotypic information allows access to a large body of information to find answers to several biological questions. The database structure also permits easy integration with other data types and opens up prospects for future implementations. PMID:19906694

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types

PubMed Central

Howe, E.A.; de Souza, A.; Lahr, D.L.; Chatwin, S.; Montgomery, P.; Alexander, B.R.; Nguyen, D.-T.; Cruz, Y.; Stonich, D.A.; Walzer, G.; Rose, J.T.; Picard, S.C.; Liu, Z.; Rose, J.N.; Xiang, X.; Asiedu, J.; Durkin, D.; Levine, J.; Yang, J.J.; Schürer, S.C.; Braisted, J.C.; Southall, N.; Southern, M.R.; Chung, T.D.Y.; Brudz, S.; Tanega, C.; Schreiber, S.L.; Bittker, J.A.; Guha, R.; Clemons, P.A.

2015-01-01

BARD, the BioAssay Research Database (https://bard.nih.gov/) is a public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions. Data published through the BARD application program interface (API) can be accessed by researchers using web-based query tools or a desktop client. Third-party developers wishing to create new tools can use the API to produce stand-alone tools or new plug-ins that can be integrated into BARD. The entire BARD suite of tools therefore supports three classes of researcher: those who wish to publish data, those who wish to mine data for testable hypotheses, and those in the developer community who wish to build tools that leverage this carefully curated chemical biology resource. PMID:25477388

SU-E-T-220: A Web-Based Research System for Outcome Analysis of NSCLC Treated with SABR.

PubMed

Le, A; Yang, Y; Michalski, D; Heron, D; Huq, M

2012-06-01

To establish a web-based software system, an electronic patient record (ePR), to consolidate and evaluate clinical data, dose delivery and treatment outcomes for non small cell lung cancer (NSCLC) patients treated with hypofractionated stereotactic ablative radiation therapy (SABR) across institutions. The new trend of information technology in medical imaging and informatics is towards the development of an electronic patient record (ePR), in which all health and medical information of each patient are organized under the patient's name and identification number. The system has been developed using the Wamp Server, a package of Apache web server, PHP and MySQL database to facilitate patient data input and management, and evaluation of patient clinical data and dose delivery across institution using web technology. The data of each patient to be recorded in the database include pre-treatment clinical data, treatment plan in DICOM-RT format and follow-up data. The pre-treatment data include demographics data, pathology condition, cancer staging. The follow-up data include the survival status, local tumor control condition and toxicity. The clinical data are entered to the system through the web page while the treatment plan data will be imported from the treatment planning system (TPS) using DICOM communication. The collection of data of NSCLC patients treated with SABR stored in the ePR is always accessible and can be retrieved and processed in the future. The core of the ePR is the database which integrates all patient data in one location. The web-based DICOM RT ePR system utilizes the current state-of-the-art medical informatics approach to investigate the combination and consolidation of patient data and outcome results. This will allow clinically-driven data mining for dose distributions and resulting treatment outcome in connection with biological modeling of the treatment parameters to quantify the efficacy of SABR in treating NSCLC patients. © 2012 American Association of Physicists in Medicine.

Prototype and Evaluation of AutoHelp: A Case-based, Web-accessible Help Desk System for EOSDIS

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.; Thurman, David A.

1999-01-01

AutoHelp is a case-based, Web-accessible help desk for users of the EOSDIS. Its uses a combination of advanced computer and Web technologies, knowledge-based systems tools, and cognitive engineering to offload the current, person-intensive, help desk facilities at the DAACs. As a case-based system, AutoHelp starts with an organized database of previous help requests (questions and answers) indexed by a hierarchical category structure that facilitates recognition by persons seeking assistance. As an initial proof-of-concept demonstration, a month of email help requests to the Goddard DAAC were analyzed and partially organized into help request cases. These cases were then categorized to create a preliminary case indexing system, or category structure. This category structure allows potential users to identify or recognize categories of questions, responses, and sample cases similar to their needs. Year one of this research project focused on the development of a technology demonstration. User assistance 'cases' are stored in an Oracle database in a combination of tables linking prototypical questions with responses and detailed examples from the email help requests analyzed to date. When a potential user accesses the AutoHelp system, a Web server provides a Java applet that displays the category structure of the help case base organized by the needs of previous users. When the user identifies or requests a particular type of assistance, the applet uses Java database connectivity (JDBC) software to access the database and extract the relevant cases. The demonstration will include an on-line presentation of how AutoHelp is currently structured. We will show how a user might request assistance via the Web interface and how the AutoHelp case base provides assistance. The presentation will describe the DAAC data collection, case definition, and organization to date, as well as the AutoHelp architecture. It will conclude with the year 2 proposal to more fully develop the case base, the user interface (including the category structure), interface with the current DAAC Help System, the development of tools to add new cases, and user testing and evaluation at (perhaps) the Goddard DAAC.

Cloud/web mapping and geoprocessing services - Intelligently linking geoinformation

NASA Astrophysics Data System (ADS)

Veenendaal, Bert; Brovelli, Maria Antonia; Wu, Lixin

2016-04-01

We live in a world that is alive with information and geographies. "Everything happens somewhere" (Tosta, 2001). This reality is being exposed in the digital earth technologies providing a multi-dimensional, multi-temporal and multi-resolution model of the planet, based on the needs of diverse actors: from scientists to decision makers, communities and citizens (Brovelli et al., 2015). We are building up a geospatial information infrastructure updated in real time thanks to mobile, positioning and sensor observations. Users can navigate, not only through space but also through time, to access historical data and future predictions based on social and/or environmental models. But how do we find the information about certain geographic locations or localities when it is scattered in the cloud and across the web of data behind a diversity of databases, web services and hyperlinked pages? We need to be able to link geoinformation together in order to integrate it, make sense of it, and use it appropriately for managing the world and making decisions.