United states national land cover data base development? 1992-2001 and beyond

USGS Publications Warehouse

Yang, L.

2008-01-01

An accurate, up-to-date and spatially-explicate national land cover database is required for monitoring the status and trends of the nation's terrestrial ecosystem, and for managing and conserving land resources at the national scale. With all the challenges and resources required to develop such a database, an innovative and scientifically sound planning must be in place and a partnership be formed among users from government agencies, research institutes and private sectors. In this paper, we summarize major scientific and technical issues regarding the development of the NLCD 1992 and 2001. Experiences and lessons learned from the project are documented with regard to project design, technical approaches, accuracy assessment strategy, and projecti imiplementation.Future improvements in developing next generation NLCD beyond 2001 are suggested, including: 1) enhanced satellite data preprocessing in correction of atmospheric and adjacency effect and the topographic normalization; 2) improved classification accuracy through comprehensive and consistent training data and new algorithm development; 3) multi-resolution and multi-temporal database targeting major land cover changes and land cover database updates; 4) enriched database contents by including additional biophysical parameters and/or more detailed land cover classes through synergizing multi-sensor, multi-temporal, and multi-spectral satellite data and ancillary data, and 5) transform the NLCD project into a national land cover monitoring program. ?? 2008 IEEE.

Lake Pontchartrain Basin: bottom sediments and related environmental resources

USGS Publications Warehouse

Manheim, Frank T.; Hayes, Laura

2002-01-01

Lake Pontchartrain is the largest estuary southern Louisiana. It is an important recreational, commercial, and environmental resource for New Orleans and southwestern Louisiana. This publication is part of a 5-year cooperative program led by the USGS on the geological framework and sedimentary processes of the Lake Pontchartrain Basin.This presentation is divided into two main parts:- Scientific Research and Assessments- Multimedia Tools and Regional ResourcesThe scientific sections include historical information on the area; shipboard, field, and remote sensing studies; and a comprehensive sediment database with geological and chemical discussions of the region.The multimedia and resources sections include Geographic Information System (GIS) tools and data, a video demonstrating vibracore sampling techniques in Lake Pontchartrain, and abstracts from four Basics of the Basin symposia.

A multidisciplinary database for global distribution

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

Wolfe, P.J.

The issue of selenium toxicity in the environment has been documented in the scientific literature for over 50 years. Recent studies reveal a complex connection between selenium and human and animal populations. This article introduces a bibliographic citation database on selenium in the environment developed for global distribution via the Internet by the University of Wyoming Libraries. The database incorporates material from commercial sources, print abstracts, indexes, and U.S. government literature, resulting in a multidisciplinary resource. Relevant disciplines include, biology, medicine, veterinary science, botany, chemistry, geology, pollution, aquatic sciences, ecology, and others. It covers the years 1985-1996 for most subjectmore » material, with additional years being added as resources permit.« less

The Marshall Islands Data Management Program

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

Stoker, A.C.; Conrado, C.L.

1995-09-01

This report is a resource document of the methods and procedures used currently in the Data Management Program of the Marshall Islands Dose Assessment and Radioecology Project. Since 1973, over 60,000 environmental samples have been collected. Our program includes relational database design, programming and maintenance; sample and information management; sample tracking; quality control; and data entry, evaluation and reduction. The usefulness of scientific databases involves careful planning in order to fulfill the requirements of any large research program. Compilation of scientific results requires consolidation of information from several databases, and incorporation of new information as it is generated. The successmore » in combining and organizing all radionuclide analysis, sample information and statistical results into a readily accessible form, is critical to our project.« less

The Protein Information Resource: an integrated public resource of functional annotation of proteins

PubMed Central

Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

2002-01-01

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

An international aerospace information system: A cooperative opportunity

NASA Technical Reports Server (NTRS)

Cotter, Gladys A.; Blados, Walter R.

1992-01-01

Scientific and technical information (STI) is a valuable resource which represents the results of large investments in research and development (R&D), and the expertise of a nation. NASA and its predecessor organizations have developed and managed the preeminent aerospace information system. We see information and information systems changing and becoming more international in scope. In Europe, consistent with joint R&D programs and a view toward a united Europe, we have seen the emergence of a European Aerospace Database concept. In addition, the development of aeronautics and astronautics in individual nations have also lead to initiatives for national aerospace databases. Considering recent technological developments in information science and technology, as well as the reality of scarce resources in all nations, it is time to reconsider the mutually beneficial possibilities offered by cooperation and international resource sharing. The new possibilities offered through cooperation among the various aerospace database efforts toward an international aerospace database initiative which can optimize the cost/benefit equation for all participants are considered.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

PubMed Central

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A.; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A.; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R.R.; Kasukawa, Takeya; Kawaji, Hideya

2017-01-01

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. PMID:27794045

Outreach and online training services at the Saccharomyces Genome Database.

PubMed

MacPherson, Kevin A; Starr, Barry; Wong, Edith D; Dalusag, Kyla S; Hellerstedt, Sage T; Lang, Olivia W; Nash, Robert S; Skrzypek, Marek S; Engel, Stacia R; Cherry, J Michael

2017-01-01

The Saccharomyces Genome Database (SGD; www.yeastgenome.org ), the primary genetics and genomics resource for the budding yeast S. cerevisiae , provides free public access to expertly curated information about the yeast genome and its gene products. As the central hub for the yeast research community, SGD engages in a variety of social outreach efforts to inform our users about new developments, promote collaboration, increase public awareness of the importance of yeast to biomedical research, and facilitate scientific discovery. Here we describe these various outreach methods, from networking at scientific conferences to the use of online media such as blog posts and webinars, and include our perspectives on the benefits provided by outreach activities for model organism databases. http://www.yeastgenome.org. © The Author(s) 2017. Published by Oxford University Press.

USE OF LANDSCAPE SCIENCE FRO ENVIRONMENTAL ASSESSMENT PILOT STUDY

EPA Science Inventory

Landscape metrics or indicators are calculated by combining various scientific databases using technologies from geographic information systems. These metrics facilitate the understanding that events that might occur in one ecosystem or resource can affect the conditions of many ...

WorldWideScience.org: the global science gateway.

PubMed

Fitzpatrick, Roberta Bronson

2009-10-01

WorldWideScience.org is a Web-based global gateway connecting users to both national and international scientific databases and portals. This column will provide background information on the resource as well as introduce basic searching practices for users.

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.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

PubMed

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kasukawa, Takeya; Kawaji, Hideya

2017-01-04

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India

PubMed Central

Meetei, Potshangbam Angamba; Singh, Pankaj; Nongdam, Potshangbam; Prabhu, N Prakash; Rathore, RS; Vindal, Vaibhav

2012-01-01

The North-East region of India is one of the twelve mega biodiversity region, containing many rare and endangered species. A curated database of medicinal and aromatic plants from the regions called NeMedPlant is developed. The database contains traditional, scientific and medicinal information about plants and their active constituents, obtained from scholarly literature and local sources. The database is cross-linked with major biochemical databases and analytical tools. The integrated database provides resource for investigations into hitherto unexplored medicinal plants and serves to speed up the discovery of natural productsbased drugs. Availability The database is available for free at http://bif.uohyd.ac.in/nemedplant/orhttp://202.41.85.11/nemedplant/ PMID:22419844

XML-based information system for planetary sciences

NASA Astrophysics Data System (ADS)

Carraro, F.; Fonte, S.; Turrini, D.

2009-04-01

EuroPlaNet (EPN in the following) has been developed by the planetological community under the "Sixth Framework Programme" (FP6 in the following), the European programme devoted to the improvement of the European research efforts through the creation of an internal market for science and technology. The goal of the EPN programme is the creation of a European network aimed to the diffusion of data produced by space missions dedicated to the study of the Solar System. A special place within the EPN programme is that of I.D.I.S. (Integrated and Distributed Information Service). The main goal of IDIS is to offer to the planetary science community a user-friendly access to the data and information produced by the various types of research activities, i.e. Earth-based observations, space observations, modeling, theory and laboratory experiments. During the FP6 programme IDIS development consisted in the creation of a series of thematic nodes, each of them specialized in a specific scientific domain, and a technical coordination node. The four thematic nodes are the Atmosphere node, the Plasma node, the Interiors & Surfaces node and the Small Bodies & Dust node. The main task of the nodes have been the building up of selected scientific cases related with the scientific domain of each node. The second work done by EPN nodes have been the creation of a catalogue of resources related to their main scientific theme. Both these efforts have been used as the basis for the development of the main IDIS goal, i.e. the integrated distributed service. An XML-based data model have been developed to describe resources using meta-data and to store the meta-data within an XML-based database called eXist. A search engine has been then developed in order to allow users to search resources within the database. Users can select the resource type and can insert one or more values or can choose a value among those present in a list, depending on selected resource. The system searches for all the resources containing the inserted values within the resources descriptions. An important facility of the IDIS search system is the multi-node search capability. This is due to the capacity of eXist to make queries on remote databases. This allows the system to show all resources which satisfy the search criteria on local node and to show how many resources are found on remote nodes, giving also a link to open the results page on remote nodes. During FP7 the development of the IDIS system will have the main goal to make the service Virtual Observatory compliant.

Unification - An international aerospace information issue

NASA Technical Reports Server (NTRS)

Cotter, Gladys A.; Lahr, Thomas F.

1992-01-01

Scientific and Technical Information (STI) represents the results of large investments in research and development (R&D) and the expertise of a nation and is a valuable resource. For more than four decades, NASA and its predecessor organizations have developed and managed the preeminent aerospace information system. NASA obtains foreign materials through its international exchange relationships, continually increasing the comprehensiveness of the NASA Aerospace Database (NAD). The NAD is de facto the international aerospace database. This paper reviews current NASA goals and activities with a view toward maintaining compatibility among international aerospace information systems, eliminating duplication of effort, and sharing resources through international cooperation wherever possible.

Research mapping in North Sumatra based on Scopus

NASA Astrophysics Data System (ADS)

Nasution, M. K. M.; Sitepu, R.; Rosmayati; Bakti, D.; Hardi, S. M.

2018-02-01

Research is needed to improve the capacity of human resources to manage natural resources for human well-being. Research is done by institutions such as universities or research institutions, but the research picture related to human welfare interests is not easy to obtain. If research can be proven through scientific publications, scientific research publication databases can be used to view research behaviour. Research mapping in North Sumatra needs to be done to see the suitability of research conducted with development needs in North Sumatra, and as a presentation is the Universitas Sumatera Utara which shows that research conducted has 60% strength, especially in the exact sciences.

Resource physiology of conifers: Acquisition, allocation, and utilization

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

Smith, W.K.; Hinckley, T.M.

1995-03-01

This book focuses on a synthetic view of the resource physiology of conifer trees with an emphasis on developing a perspective that can integrate across the biological hierarchy. This objective is in concert with more scientific goals of maintaining biological diversity and the sustainability of forest systems. The preservation of coniferous forest ecosystems is a major concern today. This volume deals with the topics of resource acquisition, allocation, and utilization in conifers. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

Dam Removal Information Portal (DRIP)—A map-based resource linking scientific studies and associated geospatial information about dam removals

USGS Publications Warehouse

Duda, Jeffrey J.; Wieferich, Daniel J.; Bristol, R. Sky; Bellmore, J. Ryan; Hutchison, Vivian B.; Vittum, Katherine M.; Craig, Laura; Warrick, Jonathan A.

2016-08-18

The removal of dams has recently increased over historical levels due to aging infrastructure, changing societal needs, and modern safety standards rendering some dams obsolete. Where possibilities for river restoration, or improved safety, exceed the benefits of retaining a dam, removal is more often being considered as a viable option. Yet, as this is a relatively new development in the history of river management, science is just beginning to guide our understanding of the physical and ecological implications of dam removal. Ultimately, the “lessons learned” from previous scientific studies on the outcomes dam removal could inform future scientific understanding of ecosystem outcomes, as well as aid in decision-making by stakeholders. We created a database visualization tool, the Dam Removal Information Portal (DRIP), to display map-based, interactive information about the scientific studies associated with dam removals. Serving both as a bibliographic source as well as a link to other existing databases like the National Hydrography Dataset, the derived National Dam Removal Science Database serves as the foundation for a Web-based application that synthesizes the existing scientific studies associated with dam removals. Thus, using the DRIP application, users can explore information about completed dam removal projects (for example, their location, height, and date removed), as well as discover sources and details of associated of scientific studies. As such, DRIP is intended to be a dynamic collection of scientific information related to dams that have been removed in the United States and elsewhere. This report describes the architecture and concepts of this “metaknowledge” database and the DRIP visualization tool.

Fostering Education and Research Goals Through Partnerships Between Academic Programs and Geoinformatics Projects

NASA Astrophysics Data System (ADS)

Block, K. A.; Lehnert, K. A.; Johansson, A. K.; Herzberg, C. T.; Stern, R. J.; Bloomer, S.; Gerard-Little, P.; Paul, M.; Raye, U.; Sou, N.

2007-12-01

Geoinformatics resources are indispensable tools for researchers and educators at the forefront of geoscience. One example is PetDB (http://www.petdb.org) which serves as a data resource and reference in a broad suite of studies of the solid earth and is cited in over 160 peer-reviewed articles. The ongoing success of geochemical and petrological database projects, such as PetDB, SedDB, and the EarthChem Deep Lithosphere dataset depends on addressing disciplinary interest and scientific need. A new generation of scientists who understand and utilize online data resources therefore possess a unique advantage over researchers with limited experience using online databases in that they can help shape the way the resources evolve. In an effort to foment awareness and further research goals, students and faculty from the University of Texas at Dallas, Rutgers University, and Columbia University have partnered with researchers at the Lamont-Doherty Earth Observatory to provide training in the use and development of geochemical databases to undergraduate and graduate students. Student internships lasting between 6 weeks and two months consisted of familiarization with relational databases at every level. Internships were developed to extend and apply students' prior knowledge to the development of data resources, to nurture interest in geochemistry and petrology, and to encourage students into pursuing graduate studies by engaging them in current scientific topics. Students were mentored one-on-one and assigned to data compilation in specific topics with the intent of providing background in the literature that can be used in future research papers. Outcomes of the internships include the development of a new petrological dataset of samples from the Central Atlantic Magmatic Province (CAMP), expansion of a database of mantle xenoliths (EarthChem Deep Lithosphere Dataset) that will serve as a major component to a doctoral dissertation, and the development of a classification for mantle peridotites. These efforts are expected to have a significant impact on long-standing research issues and will provide insight into the processes involving the breakup of Pangea, the influence of large igneous provinces on mass extinctions, and the evolution of the North American lithospheric mantle.

A public database of macromolecular diffraction experiments.

PubMed

Grabowski, Marek; Langner, Karol M; Cymborowski, Marcin; Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Zimmerman, Matthew D; Elsliger, Marc André; Burley, Stephen K; Minor, Wladek

2016-11-01

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.

An Innovative Infrastructure with a Universal Geo-Spatiotemporal Data Representation Supporting Cost-Effective Integration of Diverse Earth Science Data

NASA Technical Reports Server (NTRS)

Rilee, Michael Lee; Kuo, Kwo-Sen

2017-01-01

The SpatioTemporal Adaptive Resolution Encoding (STARE) is a unifying scheme encoding geospatial and temporal information for organizing data on scalable computing/storage resources, minimizing expensive data transfers. STARE provides a compact representation that turns set-logic functions into integer operations, e.g. conditional sub-setting, taking into account representative spatiotemporal resolutions of the data in the datasets. STARE geo-spatiotemporally aligns data placements of diverse data on massive parallel resources to maximize performance. Automating important scientific functions (e.g. regridding) and computational functions (e.g. data placement) allows scientists to focus on domain-specific questions instead of expending their efforts and expertise on data processing. With STARE-enabled automation, SciDB (Scientific Database) plus STARE provides a database interface, reducing costly data preparation, increasing the volume and variety of interoperable data, and easing result sharing. Using SciDB plus STARE as part of an integrated analysis infrastructure dramatically eases combining diametrically different datasets.

A Unique Digital Electrocardiographic Repository for the Development of Quantitative Electrocardiography and Cardiac Safety: The Telemetric and Holter ECG Warehouse (THEW)

PubMed Central

Couderc, Jean-Philippe

2010-01-01

The sharing of scientific data reinforces open scientific inquiry; it encourages diversity of analysis and opinion while promoting new research and facilitating the education of next generations of scientists. In this article, we present an initiative for the development of a repository containing continuous electrocardiographic information and their associated clinical information. This information is shared with the worldwide scientific community in order to improve quantitative electrocardiology and cardiac safety. First, we present the objectives of the initiative and its mission. Then, we describe the resources available in this initiative following three components: data, expertise and tools. The Data available in the Telemetric and Holter ECG Warehouse (THEW) includes continuous ECG signals and associated clinical information. The initiative attracted various academic and private partners whom expertise covers a large list of research arenas related to quantitative electrocardiography; their contribution to the THEW promotes cross-fertilization of scientific knowledge, resources, and ideas that will advance the field of quantitative electrocardiography. Finally, the tools of the THEW include software and servers to access and review the data available in the repository. To conclude, the THEW is an initiative developed to benefit the scientific community and to advance the field of quantitative electrocardiography and cardiac safety. It is a new repository designed to complement the existing ones such as Physionet, the AHA-BIH Arrhythmia Database, and the CSE database. The THEW hosts unique datasets from clinical trials and drug safety studies that, so far, were not available to the worldwide scientific community. PMID:20863512

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

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

Lu, P.Y.; Wassom, J.S.

Scientific and technological developments bring unprecedented stress to our environment. Society has to predict the results of potential health risks from technologically based actions that may have serious, far-reaching consequences. The potential for error in making such predictions or assessment is great and multiplies with the increasing size and complexity of the problem being studied. Because of this, the availability and use of reliable data is the key to any successful forecasting effort. Scientific research and development generate new data and information. Much of the scientific data being produced daily is stored in computers for subsequent analysis. This situation providesmore » both an invaluable resource and an enormous challenge. With large amounts of government funds being devoted to health and environmental research programs and with maintenance of our living environment at stake, we must make maximum use of the resulting data to forecast and avert catastrophic effects. Along with the readily available. The most efficient means of obtaining the data necessary for assessing the health effects of chemicals is to utilize applications include the toxicology databases and information files developed at ORNL. To make most efficient use of the data/information that has already been prepared, attention and resources should be directed toward projects that meticulously evaluate the available data/information and create specialized peer-reviewed value-added databases. Such projects include the National Library of Medicine`s Hazardous Substances Data Bank, and the U.S. Air Force Installation Restoration Toxicology Guide. These and similar value-added toxicology databases were developed at ORNL and are being maintained and updated. These databases and supporting information files, as well as some data evaluation techniques are discussed in this paper with special focus on how they are used to assess potential health effects of environmental agents. 19 refs., 5 tabs.« less

[Open access to academic scholarship as a public policy resource: a study of the Capes database on Brazilian theses and dissertations].

PubMed

da Silva Rosa, Teresa; Carneiro, Maria José

2010-12-01

Access to scientific knowledge is a valuable resource than can inform and validate positions taken in formulating public policy. But access to this knowledge can be challenging, given the diversity and breadth of available scholarship. Communication between the fields of science and of politics requires the dissemination of scholarship and access to it. We conducted a study using an open-access search tool in order to map existent knowledge on a specific topic: agricultural contributions to the preservation of biodiversity. The present article offers a critical view of access to the information available through the Capes database on Brazilian theses and dissertations.

On Establishing Big Data Wave Breakwaters with Analytics (Invited)

NASA Astrophysics Data System (ADS)

Riedel, M.

2013-12-01

The Research Data Alliance Big Data Analytics (RDA-BDA) Interest Group seeks to develop community based recommendations on feasible data analytics approaches to address scientific community needs of utilizing large quantities of data. RDA-BDA seeks to analyze different scientific domain applications and their potential use of various big data analytics techniques. A systematic classification of feasible combinations of analysis algorithms, analytical tools, data and resource characteristics and scientific queries will be covered in these recommendations. These combinations are complex since a wide variety of different data analysis algorithms exist (e.g. specific algorithms using GPUs of analyzing brain images) that need to work together with multiple analytical tools reaching from simple (iterative) map-reduce methods (e.g. with Apache Hadoop or Twister) to sophisticated higher level frameworks that leverage machine learning algorithms (e.g. Apache Mahout). These computational analysis techniques are often augmented with visual analytics techniques (e.g. computational steering on large-scale high performance computing platforms) to put the human judgement into the analysis loop or new approaches with databases that are designed to support new forms of unstructured or semi-structured data as opposed to the rather tradtional structural databases (e.g. relational databases). More recently, data analysis and underpinned analytics frameworks also have to consider energy footprints of underlying resources. To sum up, the aim of this talk is to provide pieces of information to understand big data analytics in the context of science and engineering using the aforementioned classification as the lighthouse and as the frame of reference for a systematic approach. This talk will provide insights about big data analytics methods in context of science within varios communities and offers different views of how approaches of correlation and causality offer complementary methods to advance in science and engineering today. The RDA Big Data Analytics Group seeks to understand what approaches are not only technically feasible, but also scientifically feasible. The lighthouse Goal of the RDA Big Data Analytics Group is a classification of clever combinations of various Technologies and scientific applications in order to provide clear recommendations to the scientific community what approaches are technicalla and scientifically feasible.

Databases and Web Tools for Cancer Genomics Study

PubMed Central

Yang, Yadong; Dong, Xunong; Xie, Bingbing; Ding, Nan; Chen, Juan; Li, Yongjun; Zhang, Qian; Qu, Hongzhu; Fang, Xiangdong

2015-01-01

Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community. PMID:25707591

NASA's SMD Cross-Forum Resources for Supporting Scientist Engagement in Education and Public Outreach Activities

NASA Astrophysics Data System (ADS)

Buxner, S.; Cobabe-Ammann, E. A.; Hsu, B. C.; Sharma, M.; Peticolas, L. M.; Schwerin, T. G.; Shipp, S. S.; Smith, D.

2012-12-01

Sharing the excitement of ongoing scientific discoveries is an important aspect of scientific activity for researchers. Directly engaging scientists in education and public outreach (E/PO) activities has the benefit of directly connecting the public to those who engage in scientific activities. A shortage of training in education methods, public speaking, and working with various public audiences increases barriers to engaging scientists in these types in E/PO activities. NASA's Science Mission Directorate (SMD) Education and Public forums (astrophysics, earth science, heliophysics, and planetary science) support scientists currently involved in E/PO and who are interested in becoming involved in E/PO through a variety of avenues. Over the past three years, the forums have developed a variety of resources to help engage scientists in education and public outreach. We will showcase the following resources developed through the SMD E/PO cross-forum efforts: Professional development resources for writing NASA SMD E/PO proposals (webinars and other online tools), ongoing professional development at scientific conferences to increase scientist engagement in E/PO activities, toolkits for scientists interested in best practices in E/PO (online guides for K-12 education and public outreach), toolkits to inform scientists of science education resources developed within each scientific thematic community, EarthSpace (a community web space where instructors can find and share about teaching space and earth sciences in the undergraduate classroom, including class materials news and funding opportunities, and the latest education research, http://www.lpi.usra.edu/earthspace/), thematic resources for teaching about SMD science topics, and an online database of scientists interested in connecting with education programs. Learn more about the Forum and find resources at http://smdepo.org/.

An intermediary's perspective of online databases for local governments

NASA Technical Reports Server (NTRS)

Jack, R. F.

1984-01-01

Numerous public administration studies have indicated that local government agencies for a variety of reasons lack access to comprehensive information resources; furthermore, such entities are often unwilling or unable to share information regarding their own problem-solving innovations. The NASA/University of Kentucky Technology Applications Program devotes a considerable effort to providing scientific and technical information and assistance to local agencies, relying on its access to over 500 distinct online databases offered by 20 hosts. The author presents a subjective assessment, based on his own experiences, of several databases which may prove useful in obtaining information for this particular end-user community.

New drug information resources for pharmacists at the National Library of Medicine.

PubMed

Knoben, James E; Phillips, Steven J

2014-01-01

To provide an overview of selected drug information-related databases of the National Library of Medicine (NLM), with a focus on newer resources that support the professional information needs of pharmacists and other health care providers. NLM, which is the world's largest medical library, provides an array of bibliographic, factual, and evidence-based drug, herbal remedy, and dietary supplement information resources. Five of the more recently introduced online resources include areas of particular importance to pharmacists, including a repository of current product labeling/package inserts, with automated search links to associated information resources; a portal to drug information that allows pharmacists to search multiple databases simultaneously and link to related medication and health care information resources; authoritative information on the effects of medications, herbal remedies, and dietary supplements in nursing infants and their mothers; comprehensive information, including a case registry, on the potential for liver toxicity due to drugs, herbal remedies, and dietary supplements; and a pill identification system with two intuitive search methodologies. NLM provides several clinical-scientific drug information resources that are particularly useful in meeting the professional information needs of pharmacists.

Databases, Repositories, and Other Data Resources in Structural Biology.

PubMed

Zheng, Heping; Porebski, Przemyslaw J; Grabowski, Marek; Cooper, David R; Minor, Wladek

2017-01-01

Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

Technology for the Organic Chemist: Three Exploratory Modules

ERIC Educational Resources Information Center

Esteb, John J.; McNulty, LuAnne M.; Magers, John; Morgan, Paul; Wilson, Anne M.

2010-01-01

The ability to use computer-based technology is an essential skill set for students majoring in chemistry. This exercise details the introduction of appropriate uses for this technology in the organic chemistry series. The incorporation of chemically appropriate online resources (module 1), scientific databases (module 2), and the use of a…

Orthographic and Phonological Neighborhood Databases across Multiple Languages.

PubMed

Marian, Viorica

2017-01-01

The increased globalization of science and technology and the growing number of bilinguals and multilinguals in the world have made research with multiple languages a mainstay for scholars who study human function and especially those who focus on language, cognition, and the brain. Such research can benefit from large-scale databases and online resources that describe and measure lexical, phonological, orthographic, and semantic information. The present paper discusses currently-available resources and underscores the need for tools that enable measurements both within and across multiple languages. A general review of language databases is followed by a targeted introduction to databases of orthographic and phonological neighborhoods. A specific focus on CLEARPOND illustrates how databases can be used to assess and compare neighborhood information across languages, to develop research materials, and to provide insight into broad questions about language. As an example of how using large-scale databases can answer questions about language, a closer look at neighborhood effects on lexical access reveals that not only orthographic, but also phonological neighborhoods can influence visual lexical access both within and across languages. We conclude that capitalizing upon large-scale linguistic databases can advance, refine, and accelerate scientific discoveries about the human linguistic capacity.

The Resource Identification Initiative: a cultural shift in publishing.

PubMed

Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S; Haendel, Melissa A; Kennedy, David N; Hill, Sean; Hof, Patrick R; Martone, Maryann E; Pols, Maaike; Tan, Serena C; Washington, Nicole; Zudilova-Seinstra, Elena; Vasilevsky, Nicole

2016-01-01

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, that is, reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.

The Resource Identification Initiative: A Cultural Shift in Publishing.

PubMed

Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S; Haendel, Melissa A; Kennedy, David N; Hill, Sean; Hof, Patrick R; Martone, Maryann E; Pols, Maaike; Tan, Serena C; Washington, Nicole; Zudilova-Seinstra, Elena; Vasilevsky, Nicole

2016-01-01

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their articles prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central Web portal (http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine-readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 articles have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40, with RRIDs appearing in 62 different journals to date. Here we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources. © 2015 Wiley Periodicals, Inc.

The Resource Identification Initiative: A cultural shift in publishing

PubMed Central

Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S; Haendel, Melissa A; Kennedy, David N; Hill, Sean; Hof, Patrick R; Martone, Maryann E; Pols, Maaike; Tan, Serena S; Washington, Nicole; Zudilova-Seinstra, Elena; Vasilevsky, Nicole

2016-01-01

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as “How did other studies use resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e. software and databases). RRIDs are assigned by an authoritative database, for example a model organism database, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal (http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources. PMID:26589523

The Resource Identification Initiative: A Cultural Shift in Publishing.

PubMed

Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S; Haendel, Melissa A; Kennedy, David N; Hill, Sean; Hof, Patrick R; Martone, Maryann E; Pols, Maaike; Tan, Serena S; Washington, Nicole; Zudilova-Seinstra, Elena; Vasilevsky, Nicole

2016-04-01

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example a model organism database, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources ). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

PubMed

Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

2016-01-01

Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016. Published by Oxford University Press.

The PMDB Protein Model Database

PubMed Central

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

Oceans of Data: In what ways can learning research inform the development of electronic interfaces and tools for use by students accessing large scientific databases?

NASA Astrophysics Data System (ADS)

Krumhansl, R. A.; Foster, J.; Peach, C. L.; Busey, A.; Baker, I.

2012-12-01

The practice of science and engineering is being revolutionized by the development of cyberinfrastructure for accessing near real-time and archived observatory data. Large cyberinfrastructure projects have the potential to transform the way science is taught in high school classrooms, making enormous quantities of scientific data available, giving students opportunities to analyze and draw conclusions from many kinds of complex data, and providing students with experiences using state-of-the-art resources and techniques for scientific investigations. However, online interfaces to scientific data are built by scientists for scientists, and their design can significantly impede broad use by novices. Knowledge relevant to the design of student interfaces to complex scientific databases is broadly dispersed among disciplines ranging from cognitive science to computer science and cartography and is not easily accessible to designers of educational interfaces. To inform efforts at bridging scientific cyberinfrastructure to the high school classroom, Education Development Center, Inc. and the Scripps Institution of Oceanography conducted an NSF-funded 2-year interdisciplinary review of literature and expert opinion pertinent to making interfaces to large scientific databases accessible to and usable by precollege learners and their teachers. Project findings are grounded in the fundamentals of Cognitive Load Theory, Visual Perception, Schemata formation and Universal Design for Learning. The Knowledge Status Report (KSR) presents cross-cutting and visualization-specific guidelines that highlight how interface design features can address/ ameliorate challenges novice high school students face as they navigate complex databases to find data, and construct and look for patterns in maps, graphs, animations and other data visualizations. The guidelines present ways to make scientific databases more broadly accessible by: 1) adjusting the cognitive load imposed by the user interface and visualizations so that it doesn't exceed the amount of information the learner can actively process; 2) drawing attention to important features and patterns; and 3) enabling customization of visualizations and tools to meet the needs of diverse learners.

Netlib services and resources

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

Browne, S.V.; Green, S.C.; Moore, K.

1994-04-01

The Netlib repository, maintained by the University of Tennessee and Oak Ridge National Laboratory, contains freely available software, documents, and databases of interest to the numerical, scientific computing, and other communities. This report includes both the Netlib User`s Guide and the Netlib System Manager`s Guide, and contains information about Netlib`s databases, interfaces, and system implementation. The Netlib repository`s databases include the Performance Database, the Conferences Database, and the NA-NET mail forwarding and Whitepages Databases. A variety of user interfaces enable users to access the Netlib repository in the manner most convenient and compatible with their networking capabilities. These interfaces includemore » the Netlib email interface, the Xnetlib X Windows client, the netlibget command-line TCP/IP client, anonymous FTP, anonymous RCP, and gopher.« less

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.

PubMed

Bousfield, David; McEntyre, Johanna; Velankar, Sameer; Papadatos, George; Bateman, Alex; Cochrane, Guy; Kim, Jee-Hyub; Graef, Florian; Vartak, Vid; Alako, Blaise; Blomberg, Niklas

2016-01-01

Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry.  We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications.

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources

PubMed Central

Bousfield, David; McEntyre, Johanna; Velankar, Sameer; Papadatos, George; Bateman, Alex; Cochrane, Guy; Kim, Jee-Hyub; Graef, Florian; Vartak, Vid; Alako, Blaise; Blomberg, Niklas

2016-01-01

Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry.  We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications. PMID:27092246

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

PubMed Central

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. PMID:25158685

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.

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

Science.gov: gateway to government science information.

PubMed

Fitzpatrick, Roberta Bronson

2010-01-01

Science.gov is a portal to more than 40 scientific databases and 200 million pages of science information via a single query. It connects users to science information and research results from the U.S. government. This column will provide readers with an overview of the resource, as well as basic search hints.

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.

The electronic Rothamsted Archive (e-RA), an online resource for data from the Rothamsted long-term experiments.

PubMed

Perryman, Sarah A M; Castells-Brooke, Nathalie I D; Glendining, Margaret J; Goulding, Keith W T; Hawkesford, Malcolm J; Macdonald, Andy J; Ostler, Richard J; Poulton, Paul R; Rawlings, Christopher J; Scott, Tony; Verrier, Paul J

2018-05-15

The electronic Rothamsted Archive, e-RA (www.era.rothamsted.ac.uk) provides a permanent managed database to both securely store and disseminate data from Rothamsted Research's long-term field experiments (since 1843) and meteorological stations (since 1853). Both historical and contemporary data are made available via this online database which provides the scientific community with access to a unique continuous record of agricultural experiments and weather measured since the mid-19 th century. Qualitative information, such as treatment and management practices, plans and soil information, accompanies the data and are made available on the e-RA website. e-RA was released externally to the wider scientific community in 2013 and this paper describes its development, content, curation and the access process for data users. Case studies illustrate the diverse applications of the data, including its original intended purposes and recent unforeseen applications. Usage monitoring demonstrates the data are of increasing interest. Future developments, including adopting FAIR data principles, are proposed as the resource is increasingly recognised as a unique archive of data relevant to sustainable agriculture, agroecology and the environment.

HoPaCI-DB: host-Pseudomonas and Coxiella interaction database

PubMed Central

Bleves, Sophie; Dunger, Irmtraud; Walter, Mathias C.; Frangoulidis, Dimitrios; Kastenmüller, Gabi; Voulhoux, Romé; Ruepp, Andreas

2014-01-01

Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database (http://mips.helmholtz-muenchen.de/HoPaCI/) of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches. PMID:24137008

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

PubMed

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

PubMed Central

Vizcaíno, Juan Antonio; Foster, Joseph M.; Martens, Lennart

2010-01-01

Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and NCBI Peptidome. In this review the capabilities of each of these will be described, paying special attention to four key properties: data types stored, applicable data submission strategies, supported formats, and available data mining and visualization tools. Additionally, the data contents from model organisms will be enumerated for each resource. There are other valuable smaller and/or more specialized repositories but they will not be covered in this review. Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced. PMID:20615486

PaperBLAST: Text Mining Papers for Information about Homologs

DOE PAGES

Price, Morgan N.; Arkin, Adam P.

2017-08-15

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quicklymore » finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.« less

PaperBLAST: Text Mining Papers for Information about Homologs

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

Price, Morgan N.; Arkin, Adam P.

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quicklymore » finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.« less

PaperBLAST: Text Mining Papers for Information about Homologs

PubMed Central

Arkin, Adam P.

2017-01-01

ABSTRACT Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST’s database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions. PMID:28845458

PaperBLAST: Text Mining Papers for Information about Homologs.

PubMed

Price, Morgan N; Arkin, Adam P

2017-01-01

Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST's database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins' functions.

Rapid Scientific Promotion of Scientific Productions in Stem Cells According to The Indexed Papers in The ISI (web of knowledge).

PubMed

Alijani, Rahim

2015-01-01

In recent years emphasis has been placed on evaluation studies and the publication of scientific papers in national and international journals. In this regard the publication of scientific papers in journals in the Institute for Scientific Information (ISI) database is highly recommended. The evaluation of scientific output via articles in journals indexed in the ISI database will enable the Iranian research authorities to allocate and organize research budgets and human resources in a way that maximises efficient science production. The purpose of the present paper is to publish a general and valid view of science production in the field of stem cells. In this research, outputs in the field of stem cell research are evaluated by survey research, the method of science assessment called Scientometrics in this branch of science. A total of 1528 documents was extracted from the ISI database and analysed using descriptive statistics software in Excel. The results of this research showed that 1528 papers in the stem cell field in the Web of Knowledge database were produced by Iranian researchers. The top ten Iranian researchers in this field have produced 936 of these papers, equivalent to 61.3% of the total. Among the top ten, Soleimani M. has occupied the first place with 181 papers. Regarding international scientific participation, Iranian researchers have cooperated to publish papers with researchers from 50 countries. Nearly 32% (452 papers) of the total research output in this field has been published in the top 10 journals. These results show that a small number of researchers have published the majority of papers in the stem cell field. International participation in this field of research unacceptably low. Such participation provides the opportunity to import modern science and international experience into Iran. This not only causes scientific growth, but also improves the research and enhances opportunities for employment and professional development. Iranian scientific outputs from stem cell research should not be limited to only a few specific journals.

United States Food and Drug Administration and Department of Defense shelf-life extension program of pharmaceutical products: progress and promise.

PubMed

Khan, Saeed R; Kona, Ravikanth; Faustino, Patrick J; Gupta, Abhay; Taylor, Jeb S; Porter, Donna A; Khan, Mansoor

2014-05-01

The Department of Defense (DoD)-United States Food and Drug Administration (FDA) shelf-life extension program (SLEP) was established in 1986 through an intra-agency agreement between the DoD and the FDA to extend the shelf life of product nearing expiry. During the early stages of development, special attention was paid to program operation, labeling requirements, and the cost benefits associated with this program. In addition to the substantial cost benefits, the program also provides the FDA's Center for Drug Evaluation and Research with significant scientific understanding and pharmaceutical resource. As a result of this unique resource, numerous regulatory research opportunities to improve public health present themselves from this distinctive scientific database, which includes examples of products shelf life, their long-term stability issues, and various physical and chemical tests to identify such failures. The database also serves as a scientific resource for mechanistic understanding and identification of test failures leading to the development of new formulations or more robust packaging. It has been recognized that SLEP is very important in maintaining both national security and public welfare by confirming that the stockpiled pharmaceutical products meet quality standards after the "expiration date" assigned by the sponsor. SLEP research is an example of regulatory science that is needed to best ensure product performance past the original shelf life. The objective of this article is to provide a brief history and background and most importantly the public health benefits of the SLEP. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

A unique linkage of administrative and clinical registry databases to expand analytic possibilities in pediatric heart transplantation research.

PubMed

Godown, Justin; Thurm, Cary; Dodd, Debra A; Soslow, Jonathan H; Feingold, Brian; Smith, Andrew H; Mettler, Bret A; Thompson, Bryn; Hall, Matt

2017-12-01

Large clinical, research, and administrative databases are increasingly utilized to facilitate pediatric heart transplant (HTx) research. Linking databases has proven to be a robust strategy across multiple disciplines to expand the possible analyses that can be performed while leveraging the strengths of each dataset. We describe a unique linkage of the Scientific Registry of Transplant Recipients (SRTR) database and the Pediatric Health Information System (PHIS) administrative database to provide a platform to assess resource utilization in pediatric HTx. All pediatric patients (1999-2016) who underwent HTx at a hospital enrolled in the PHIS database were identified. A linkage was performed between the SRTR and PHIS databases in a stepwise approach using indirect identifiers. To determine the feasibility of using these linked data to assess resource utilization, total and post-HTx hospital costs were assessed. A total of 3188 unique transplants were identified as being present in both databases and amenable to linkage. Linkage of SRTR and PHIS data was successful in 3057 (95.9%) patients, of whom 2896 (90.8%) had complete cost data. Median total and post-HTx hospital costs were $518,906 (IQR $324,199-$889,738), and $334,490 (IQR $235,506-$498,803) respectively with significant differences based on patient demographics and clinical characteristics at HTx. Linkage of the SRTR and PHIS databases is feasible and provides an invaluable tool to assess resource utilization. Our analysis provides contemporary cost data for pediatric HTx from the largest US sample reported to date. It also provides a platform for expanded analyses in the pediatric HTx population. Copyright © 2017 Elsevier Inc. All rights reserved.

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.

PubMed

Riviere, Guillaume; Klopp, Christophe; Ibouniyamine, Nabihoudine; Huvet, Arnaud; Boudry, Pierre; Favrel, Pascal

2015-12-02

The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries. The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

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.

Western Mineral and Environmental Resources Science Center--providing comprehensive earth science for complex societal issues

USGS Publications Warehouse

Frank, David G.; Wallace, Alan R.; Schneider, Jill L.

2010-01-01

Minerals in the environment and products manufactured from mineral materials are all around us and we use and come into contact with them every day. They impact our way of life and the health of all that lives. Minerals are critical to the Nation's economy and knowing where future mineral resources will come from is important for sustaining the Nation's economy and national security. The U.S. Geological Survey (USGS) Mineral Resources Program (MRP) provides scientific information for objective resource assessments and unbiased research results on mineral resource potential, production and consumption statistics, as well as environmental consequences of mining. The MRP conducts this research to provide information needed for land planners and decisionmakers about where mineral commodities are known and suspected in the earth's crust and about the environmental consequences of extracting those commodities. As part of the MRP scientists of the Western Mineral and Environmental Resources Science Center (WMERSC or 'Center' herein) coordinate the development of national, geologic, geochemical, geophysical, and mineral-resource databases and the migration of existing databases to standard models and formats that are available to both internal and external users. The unique expertise developed by Center scientists over many decades in response to mineral-resource-related issues is now in great demand to support applications such as public health research and remediation of environmental hazards that result from mining and mining-related activities. Western Mineral and Environmental Resources Science Center Results of WMERSC research provide timely and unbiased analyses of minerals and inorganic materials to (1) improve stewardship of public lands and resources; (2) support national and international economic and security policies; (3) sustain prosperity and improve our quality of life; and (4) protect and improve public health, safety, and environmental quality. The MRP supports approximately 40 USGS research specialists who utilize cooperative agreements with universities, industry, and other governmental agencies to support their collaborative research and information exchange. Scientists of the WMERSC study how and where non-fuel mineral resources form and are concentrated in the earth's crust, where mineral resources might be found in the future, and how mineral materials interact with the environment to affect human and ecosystem health. Natural systems (ecosystems) are complex - our understanding of how ecosystems operate requires collecting and synthesizing large amounts of geologic, geochemical, biologic, hydrologic, and meteorological information. Scientists in the Center strive to understand the interplay of various processes and how they affect the structure, composition, and health of ecosystems. Such understanding, which is then summarized in publicly available reports, is used to address and solve a wide variety of issues that are important to society and the economy. WMERSC scientists have extensive national and international experience in these scientific specialties and capabilities - they have collaborated with many Federal, State, and local agencies; with various private sector organizations; as well as with foreign countries and organizations. Nearly every scientific and societal challenge requires a different combination of scientific skills and capabilities. With their breadth of scientific specialties and capabilities, the scientists of the WMERSC can provide scientifically sound approaches to a wide range of societal challenges and issues. The following sections describe examples of important issues that have been addressed by scientists in the Center, the methods employed, and the relevant conclusions. New directions are inevitable as societal needs change over time. Scientists of the WMERSC have a diverse set of skills and capabilities and are proficient in the collection and integration of

MememxGATE: Unearthing Latent Content Features for Improved Search and Relevancy Ranking Across Scientific Literature

NASA Astrophysics Data System (ADS)

Wilson, B. D.; McGibbney, L. J.; Mattmann, C. A.; Ramirez, P.; Joyce, M.; Whitehall, K. D.

2015-12-01

Quantifying scientific relevancy is of increasing importance to NASA and the research community. Scientific relevancy may be defined by mapping the impacts of a particular NASA mission, instrument, and/or retrieved variables to disciplines such as climate predictions, natural hazards detection and mitigation processes, education, and scientific discoveries. Related to relevancy, is the ability to expose data with similar attributes. This in turn depends upon the ability for us to extract latent, implicit document features from scientific data and resources and make them explicit, accessible and useable for search activities amongst others. This paper presents MemexGATE; a server side application, command line interface and computing environment for running large scale metadata extraction, general architecture text engineering, document classification and indexing tasks over document resources such as social media streams, scientific literature archives, legal documentation, etc. This work builds on existing experiences using MemexGATE (funded, developed and validated through the DARPA Memex Progrjam PI Mattmann) for extracting and leveraging latent content features from document resources within the Materials Research domain. We extend the software functionality capability to the domain of scientific literature with emphasis on the expansion of gazetteer lists, named entity rules, natural language construct labeling (e.g. synonym, antonym, hyponym, etc.) efforts to enable extraction of latent content features from data hosted by wide variety of scientific literature vendors (AGU Meeting Abstract Database, Springer, Wiley Online, Elsevier, etc.) hosting earth science literature. Such literature makes both implicit and explicit references to NASA datasets and relationships between such concepts stored across EOSDIS DAAC's hence we envisage that a significant part of this effort will also include development and understanding of relevancy signals which can ultimately be utilized for improved search and relevancy ranking across scientific literature.

The Resource Identification Initiative: A cultural shift in publishing

PubMed Central

Brush, Matthew; Grethe, Jeffery S.; Haendel, Melissa A; Kennedy, David N.; Hill, Sean; Hof, Patrick R.; Martone, Maryann E.; Pols, Maaike; Tan, Serena C.; Washington, Nicole; Zudilova‐Seinstra, Elena; Vasilevsky, Nicole

2016-01-01

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as “How did other studies use resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their articles prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example, a model organism database for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central Web portal (http://scicrunch.org/resources). RRIDs meet three key criteria: they are machine‐readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 articles have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40, with RRIDs appearing in 62 different journals to date. Here we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post‐pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources. J. Comp. Neurol. 524:8–22, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc. PMID:26599696

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

PubMed

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Fossil Calibration Database-A New Resource for Divergence Dating.

PubMed

Ksepka, Daniel T; Parham, James F; Allman, James F; Benton, Michael J; Carrano, Matthew T; Cranston, Karen A; Donoghue, Philip C J; Head, Jason J; Hermsen, Elizabeth J; Irmis, Randall B; Joyce, Walter G; Kohli, Manpreet; Lamm, Kristin D; Leehr, Dan; Patané, Josés L; Polly, P David; Phillips, Matthew J; Smith, N Adam; Smith, Nathan D; Van Tuinen, Marcel; Ware, Jessica L; Warnock, Rachel C M

2015-09-01

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the database. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

PubMed Central

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry BF; Tipton, Keith F

2007-01-01

Background We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. Description The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at . The data are available for download as SQL and XML files via FTP. Conclusion ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List. PMID:17662133

FCDD: A Database for Fruit Crops Diseases.

PubMed

Chauhan, Rupal; Jasrai, Yogesh; Pandya, Himanshu; Chaudhari, Suman; Samota, Chand Mal

2014-01-01

Fruit Crops Diseases Database (FCDD) requires a number of biotechnology and bioinformatics tools. The FCDD is a unique bioinformatics resource that compiles information about 162 details on fruit crops diseases, diseases type, its causal organism, images, symptoms and their control. The FCDD contains 171 phytochemicals from 25 fruits, their 2D images and their 20 possible sequences. This information has been manually extracted and manually verified from numerous sources, including other electronic databases, textbooks and scientific journals. FCDD is fully searchable and supports extensive text search. The main focus of the FCDD is on providing possible information of fruit crops diseases, which will help in discovery of potential drugs from one of the common bioresource-fruits. The database was developed using MySQL. The database interface is developed in PHP, HTML and JAVA. FCDD is freely available. http://www.fruitcropsdd.com/

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.

Monitoring of IaaS and scientific applications on the Cloud using the Elasticsearch ecosystem

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Guarise, A.; Lusso, S.; Masera, M.; Vallero, S.

2015-05-01

The private Cloud at the Torino INFN computing centre offers IaaS services to different scientific computing applications. The infrastructure is managed with the OpenNebula cloud controller. The main stakeholders of the facility are a grid Tier-2 site for the ALICE collaboration at LHC, an interactive analysis facility for the same experiment and a grid Tier-2 site for the BES-III collaboration, plus an increasing number of other small tenants. Besides keeping track of the usage, the automation of dynamic allocation of resources to tenants requires detailed monitoring and accounting of the resource usage. As a first investigation towards this, we set up a monitoring system to inspect the site activities both in terms of IaaS and applications running on the hosted virtual instances. For this purpose we used the Elasticsearch, Logstash and Kibana stack. In the current implementation, the heterogeneous accounting information is fed to different MySQL databases and sent to Elasticsearch via a custom Logstash plugin. For the IaaS metering, we developed sensors for the OpenNebula API. The IaaS level information gathered through the API is sent to the MySQL database through an ad-hoc developed RESTful web service, which is also used for other accounting purposes. Concerning the application level, we used the Root plugin TProofMonSenderSQL to collect accounting data from the interactive analysis facility. The BES-III virtual instances used to be monitored with Zabbix, as a proof of concept we also retrieve the information contained in the Zabbix database. Each of these three cases is indexed separately in Elasticsearch. We are now starting to consider dismissing the intermediate level provided by the SQL database and evaluating a NoSQL option as a unique central database for all the monitoring information. We setup a set of Kibana dashboards with pre-defined queries in order to monitor the relevant information in each case. In this way we have achieved a uniform monitoring interface for both the IaaS and the scientific applications, mostly leveraging off-the-shelf tools.

Computing through Scientific Abstractions in SysBioPS

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

Chin, George; Stephan, Eric G.; Gracio, Deborah K.

2004-10-13

Today, biologists and bioinformaticists have a tremendous amount of computational power at their disposal. With the availability of supercomputers, burgeoning scientific databases and digital libraries such as GenBank and PubMed, and pervasive computational environments such as the Grid, biologists have access to a wealth of computational capabilities and scientific data at hand. Yet, the rapid development of computational technologies has far exceeded the typical biologist’s ability to effectively apply the technology in their research. Computational sciences research and development efforts such as the Biology Workbench, BioSPICE (Biological Simulation Program for Intra-Cellular Evaluation), and BioCoRE (Biological Collaborative Research Environment) are importantmore » in connecting biologists and their scientific problems to computational infrastructures. On the Computational Cell Environment and Heuristic Entity-Relationship Building Environment projects at the Pacific Northwest National Laboratory, we are jointly developing a new breed of scientific problem solving environment called SysBioPSE that will allow biologists to access and apply computational resources in the scientific research context. In contrast to other computational science environments, SysBioPSE operates as an abstraction layer above a computational infrastructure. The goal of SysBioPSE is to allow biologists to apply computational resources in the context of the scientific problems they are addressing and the scientific perspectives from which they conduct their research. More specifically, SysBioPSE allows biologists to capture and represent scientific concepts and theories and experimental processes, and to link these views to scientific applications, data repositories, and computer systems.« less

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

PubMed Central

2010-01-01

Background Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License. PMID:20587024

Cumulative exergy extraction from the natural environment (CEENE): a comprehensive life cycle impact assessment method for resource accounting.

PubMed

Dewulf, J; Bösch, M E; De Meester, B; Van der Vorst, G; Van Langenhove, H; Hellweg, S; Huijbregts, M A J

2007-12-15

The objective of the paper is to establish a comprehensive resource-based life cycle impact assessment (LCIA) method which is scientifically sound and that enables to assess all kinds of resources that are deprived from the natural ecosystem, all quantified on one single scale, free of weighting factors. The method is based on the exergy concept. Consistent exergy data on fossils, nuclear and metal ores, minerals, air, water, land occupation, and renewable energy sources were elaborated, with well defined system boundaries. Based on these data, the method quantifies the exergy "taken away" from natural ecosystems, and is thus called the cumulative exergy extraction from the natural environment (CEENE). The acquired data set was coupled with a state-of-the art life cycle inventory database, ecoinvent. In this way, the method is able to quantitatively distinguish eight categories of resources withdrawn from the natural environment: renewable resources, fossil fuels, nuclear energy, metal ores, minerals, water resources, land resources, and atmospheric resources. Third, the CEENE method is illustrated for a number of products that are available in ecoinvent, and results are compared with common resource oriented LCIA methods. The application to the materials in the ecoinvent database showed that fossil resources and land use are of particular importance with regard to the total CEENE score, although the other resource categories may also be significant.

Cooperative Project To Develop a Database of Discipline-Specific Workbook Exercises for Agricultural and Biological Engineering, Entomology, and Biological Sciences Courses.

ERIC Educational Resources Information Center

Ellsbury, Susan H.; And Others

A two-part text, "Science Resources: A Self-Paced Instructional Workbook," was designed to provide science students at Mississippi State University with: (1) instruction on basic library usage and reference tools common to most scientific disciplines; (2) materials adapted to specific disciplines; and (3) services available to them from the…

The electronic Rothamsted Archive (e-RA), an online resource for data from the Rothamsted long-term experiments

PubMed Central

Perryman, Sarah A. M.; Castells-Brooke, Nathalie I. D.; Glendining, Margaret J.; Goulding, Keith W. T.; Hawkesford, Malcolm J.; Macdonald, Andy J.; Ostler, Richard J.; Poulton, Paul R.; Rawlings, Christopher J.; Scott, Tony; Verrier, Paul J.

2018-01-01

The electronic Rothamsted Archive, e-RA (www.era.rothamsted.ac.uk) provides a permanent managed database to both securely store and disseminate data from Rothamsted Research’s long-term field experiments (since 1843) and meteorological stations (since 1853). Both historical and contemporary data are made available via this online database which provides the scientific community with access to a unique continuous record of agricultural experiments and weather measured since the mid-19th century. Qualitative information, such as treatment and management practices, plans and soil information, accompanies the data and are made available on the e-RA website. e-RA was released externally to the wider scientific community in 2013 and this paper describes its development, content, curation and the access process for data users. Case studies illustrate the diverse applications of the data, including its original intended purposes and recent unforeseen applications. Usage monitoring demonstrates the data are of increasing interest. Future developments, including adopting FAIR data principles, are proposed as the resource is increasingly recognised as a unique archive of data relevant to sustainable agriculture, agroecology and the environment. PMID:29762552

DataHub: Knowledge-based data management for data discovery

NASA Astrophysics Data System (ADS)

Handley, Thomas H.; Li, Y. Philip

1993-08-01

Currently available database technology is largely designed for business data-processing applications, and seems inadequate for scientific applications. The research described in this paper, the DataHub, will address the issues associated with this shortfall in technology utilization and development. The DataHub development is addressing the key issues in scientific data management of scientific database models and resource sharing in a geographically distributed, multi-disciplinary, science research environment. Thus, the DataHub will be a server between the data suppliers and data consumers to facilitate data exchanges, to assist science data analysis, and to provide as systematic approach for science data management. More specifically, the DataHub's objectives are to provide support for (1) exploratory data analysis (i.e., data driven analysis); (2) data transformations; (3) data semantics capture and usage; analysis-related knowledge capture and usage; and (5) data discovery, ingestion, and extraction. Applying technologies that vary from deductive databases, semantic data models, data discovery, knowledge representation and inferencing, exploratory data analysis techniques and modern man-machine interfaces, DataHub will provide a prototype, integrated environement to support research scientists' needs in multiple disciplines (i.e. oceanography, geology, and atmospheric) while addressing the more general science data management issues. Additionally, the DataHub will provide data management services to exploratory data analysis applications such as LinkWinds and NCSA's XIMAGE.

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.

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

Preserving science for the ages--USGS data rescue

USGS Publications Warehouse

Wippich, Carol

2012-01-01

The U.S. Geological Survey (USGS) is a steward for over 130 years of rich, diverse natural science and information resources. We document one-of-a-kind observations of natural phenomena and cultural impacts on our changing world. In order for society to deal with national and global trends, the USGS must enable access and use of legacy, inaccessible information by including these data in our digital archives and databases. The USGS has conducted scientific assessments on the quality and quantity of the Nation's water resources, provided access to geospatial and natural resource data, and conducted multi-purpose natural science studies. All of these have generated records that need to be accessible and integrated in order to be examined for new information and interpretations that were never intended by the original collector. The Federal Records Act of 1950 mandates that the USGS preserve Federal records containing evidence of the agency's organization, functions, policies, decisions, procedures, and essential transactions. At the USGS, the goal of Open Government is to improve and increase access to scientific information. Therefore, it is incumbent upon the USGS to preserve, make available, and provide accountability for the data that it creates from our scientific projects.

Web resources for rare auto-inflammatory diseases: towards a common patient registry.

PubMed

Touitou, Isabelle; Hentgen, Véronique; Koné-Paut, Isabelle

2009-06-01

To review information resources on rare auto-inflammatory disorders (AIDs) for use by health care professionals, focusing particularly on patient registries. Using relevant key words, we surveyed the websites of several scientific societies of immunology, paediatrics and rheumatology, as well as Pubmed and specialized databases for AIDs. The Internet provides a wide variety of information related to AIDs. Moreover, several other initiatives have been undertaken to create new resources for professionals. We reviewed six patient registries for rare AIDs, taking a special interest in the submission questionnaire. We revealed a wide overlap between the items used in the questionnaires, whereas the currently available registries appeared inappropriate for AIDs patients with complex or undefined diagnosis. AIDs share common clinical features, pathophysiological pathways and therapeutic approaches. Although several resources are now available for rare AIDs, a unique and dedicated site gathering all aspects of these diseases as a whole is still lacking, i.e. covering research as well as the needs of AIDs patients and health care professionals. Our study thus advocates a merging of existing patient registries or the creation of a common database.

e-MIR2: a public online inventory of medical informatics resources.

PubMed

de la Calle, Guillermo; García-Remesal, Miguel; Nkumu-Mbomio, Nelida; Kulikowski, Casimir; Maojo, Victor

2012-08-02

Over the past years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for the Medical Informatics (MI) field, so that locating and accessing them currently remains a difficult and time-consuming task. We have created a repository of MI resources from the scientific literature, providing free access to its contents through a web-based service. We define informatics resources as all those elements that constitute, serve to define or are used by informatics systems, ranging from architectures or development methodologies to terminologies, vocabularies, databases or tools. Relevant information describing the resources is automatically extracted from manuscripts published in top-ranked MI journals. We used a pattern matching approach to detect the resources' names and their main features. Detected resources are classified according to three different criteria: functionality, resource type and domain. To facilitate these tasks, we have built three different classification schemas by following a novel approach based on folksonomies and social tagging. We adopted the terminology most frequently used by MI researchers in their publications to create the concepts and hierarchical relationships belonging to the classification schemas. The classification algorithm identifies the categories associated with resources and annotates them accordingly. The database is then populated with this data after manual curation and validation. We have created an online repository of MI resources to assist researchers in locating and accessing the most suitable resources to perform specific tasks. The database contains 609 resources at the time of writing and is available at http://www.gib.fi.upm.es/eMIR2. We are continuing to expand the number of available resources by taking into account further publications as well as suggestions from users and resource developers.

The NASA ADS Abstract Service and the Distributed Astronomy Digital Library [and] Project Soup: Comparing Evaluations of Digital Collection Efforts [and] Cross-Organizational Access Management: A Digital Library Authentication and Authorization Architecture [and] BibRelEx: Exploring Bibliographic Databases by Visualization of Annotated Content-based Relations [and] Semantics-Sensitive Retrieval for Digital Picture Libraries [and] Encoded Archival Description: An Introduction and Overview.

ERIC Educational Resources Information Center

Kurtz, Michael J.; Eichorn, Guenther; Accomazzi, Alberto; Grant, Carolyn S.; Demleitner, Markus; Murray, Stephen S.; Jones, Michael L. W.; Gay, Geri K.; Rieger, Robert H.; Millman, David; Bruggemann-Klein, Anne; Klein, Rolf; Landgraf, Britta; Wang, James Ze; Li, Jia; Chan, Desmond; Wiederhold, Gio; Pitti, Daniel V.

1999-01-01

Includes six articles that discuss a digital library for astronomy; comparing evaluations of digital collection efforts; cross-organizational access management of Web-based resources; searching scientific bibliographic databases based on content-based relations between documents; semantics-sensitive retrieval for digital picture libraries; and…

Validating crash locations for quantitative spatial analysis: a GIS-based approach.

PubMed

Loo, Becky P Y

2006-09-01

In this paper, the spatial variables of the crash database in Hong Kong from 1993 to 2004 are validated. The proposed spatial data validation system makes use of three databases (the crash, road network and district board databases) and relies on GIS to carry out most of the validation steps so that the human resource required for manually checking the accuracy of the spatial data can be enormously reduced. With the GIS-based spatial data validation system, it was found that about 65-80% of the police crash records from 1993 to 2004 had correct road names and district board information. In 2004, the police crash database contained about 12.7% mistakes for road names and 9.7% mistakes for district boards. The situation was broadly comparable to the United Kingdom. However, the results also suggest that safety researchers should carefully validate spatial data in the crash database before scientific analysis.

The design and implementation of the immune epitope database and analysis resource

PubMed Central

Peters, Bjoern; Sidney, John; Bourne, Phil; Bui, Huynh-Hoa; Buus, Soeren; Doh, Grace; Fleri, Ward; Kronenberg, Mitch; Kubo, Ralph; Lund, Ole; Nemazee, David; Ponomarenko, Julia V.; Sathiamurthy, Muthu; Schoenberger, Stephen P.; Stewart, Scott; Surko, Pamela; Way, Scott; Wilson, Steve; Sette, Alessandro

2016-01-01

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, “The Immune Epitope Database and Analysis Resource.” We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide. PMID:15895191

e-MIR2: a public online inventory of medical informatics resources

PubMed Central

2012-01-01

Background Over the past years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for the Medical Informatics (MI) field, so that locating and accessing them currently remains a difficult and time-consuming task. Description We have created a repository of MI resources from the scientific literature, providing free access to its contents through a web-based service. We define informatics resources as all those elements that constitute, serve to define or are used by informatics systems, ranging from architectures or development methodologies to terminologies, vocabularies, databases or tools. Relevant information describing the resources is automatically extracted from manuscripts published in top-ranked MI journals. We used a pattern matching approach to detect the resources’ names and their main features. Detected resources are classified according to three different criteria: functionality, resource type and domain. To facilitate these tasks, we have built three different classification schemas by following a novel approach based on folksonomies and social tagging. We adopted the terminology most frequently used by MI researchers in their publications to create the concepts and hierarchical relationships belonging to the classification schemas. The classification algorithm identifies the categories associated with resources and annotates them accordingly. The database is then populated with this data after manual curation and validation. Conclusions We have created an online repository of MI resources to assist researchers in locating and accessing the most suitable resources to perform specific tasks. The database contains 609 resources at the time of writing and is available at http://www.gib.fi.upm.es/eMIR2. We are continuing to expand the number of available resources by taking into account further publications as well as suggestions from users and resource developers. PMID:22857741

The Neotoma Paleoecology Database: An International Community-Curated Resource for Paleoecological and Paleoenvironmental Data

NASA Astrophysics Data System (ADS)

Williams, J. W.; Grimm, E. C.; Ashworth, A. C.; Blois, J.; Charles, D. F.; Crawford, S.; Davis, E.; Goring, S. J.; Graham, R. W.; Miller, D. A.; Smith, A. J.; Stryker, M.; Uhen, M. D.

2017-12-01

The Neotoma Paleoecology Database supports global change research at the intersection of geology and ecology by providing a high-quality, community-curated data repository for paleoecological data. These data are widely used to study biological responses and feedbacks to past environmental change at local to global scales. The Neotoma data model is flexible and can store multiple kinds of fossil, biogeochemical, or physical variables measured from sedimentary archives. Data additions to Neotoma are growing and include >3.5 million observations, >16,000 datasets, and >8,500 sites. Dataset types include fossil pollen, vertebrates, diatoms, ostracodes, macroinvertebrates, plant macrofossils, insects, testate amoebae, geochronological data, and the recently added organic biomarkers, stable isotopes, and specimen-level data. Neotoma data can be found and retrieved in multiple ways, including the Explorer map-based interface, a RESTful Application Programming Interface, the neotoma R package, and digital object identifiers. Neotoma has partnered with the Paleobiology Database to produce a common data portal for paleobiological data, called the Earth Life Consortium. A new embargo management is designed to allow investigators to put their data into Neotoma and then make use of Neotoma's value-added services. Neotoma's distributed scientific governance model is flexible and scalable, with many open pathways for welcoming new members, data contributors, stewards, and research communities. As the volume and variety of scientific data grow, community-curated data resources such as Neotoma have become foundational infrastructure for big data science.

Groundwater modeling in integrated water resources management--visions for 2020.

PubMed

Refsgaard, Jens Christian; Højberg, Anker Lajer; Møller, Ingelise; Hansen, Martin; Søndergaard, Verner

2010-01-01

Groundwater modeling is undergoing a change from traditional stand-alone studies toward being an integrated part of holistic water resources management procedures. This is illustrated by the development in Denmark, where comprehensive national databases for geologic borehole data, groundwater-related geophysical data, geologic models, as well as a national groundwater-surface water model have been established and integrated to support water management. This has enhanced the benefits of using groundwater models. Based on insight gained from this Danish experience, a scientifically realistic scenario for the use of groundwater modeling in 2020 has been developed, in which groundwater models will be a part of sophisticated databases and modeling systems. The databases and numerical models will be seamlessly integrated, and the tasks of monitoring and modeling will be merged. Numerical models for atmospheric, surface water, and groundwater processes will be coupled in one integrated modeling system that can operate at a wide range of spatial scales. Furthermore, the management systems will be constructed with a focus on building credibility of model and data use among all stakeholders and on facilitating a learning process whereby data and models, as well as stakeholders' understanding of the system, are updated to currently available information. The key scientific challenges for achieving this are (1) developing new methodologies for integration of statistical and qualitative uncertainty; (2) mapping geological heterogeneity and developing scaling methodologies; (3) developing coupled model codes; and (4) developing integrated information systems, including quality assurance and uncertainty information that facilitate active stakeholder involvement and learning.

IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data

PubMed Central

Kaas, Quentin; Ruiz, Manuel; Lefranc, Marie-Paule

2004-01-01

IMGT/3Dstructure-DB and IMGT/Structural-Query are a novel 3D structure database and a new tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system®, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools. IMGT/3Dstructure-DB data are described according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY concepts. IMGT/3Dstructure-DB provides IMGT gene and allele identification of IG, TR and MHC proteins with known 3D structures, domain delimitations, amino acid positions according to the IMGT unique numbering and renumbered coordinate flat files. Moreover IMGT/3Dstructure-DB provides 2D graphical representations (or Collier de Perles) and results of contact analysis. The IMGT/StructuralQuery tool allows search of this database based on specific structural characteristics. IMGT/3Dstructure-DB and IMGT/StructuralQuery are freely available at http://imgt.cines.fr. PMID:14681396

Geospatial characteristics of Florida's coastal and offshore environments: Administrative and political boundaries and offshore sand resources

USGS Publications Warehouse

Demopoulos, Amanda W.J.; Foster, Ann M.; Jones, Michal L.; Gualtieri, Daniel J.

2011-01-01

The Geospatial Characteristics Geopdf of Florida's Coastal and Offshore Environments is a comprehensive collection of geospatial data describing the political and natural resources of Florida. This interactive map provides spatial information on bathymetry, sand resources, military areas, marine protected areas, cultural resources, locations of submerged cables, and shipping routes. The map should be useful to coastal resource managers and others interested in the administrative and political boundaries of Florida's coastal and offshore region. In particular, as oil and gas explorations continue to expand, the map may be used to explore information regarding sensitive areas and resources in the State of Florida. Users of this geospatial database will find that they have access to synthesized information in a variety of scientific disciplines concerning Florida's coastal zone. This powerful tool provides a one-stop assembly of data that can be tailored to fit the needs of many natural resource managers.

bioNerDS: exploring bioinformatics’ database and software use through literature mining

PubMed Central

2013-01-01

Background Biology-focused databases and software define bioinformatics and their use is central to computational biology. In such a complex and dynamic field, it is of interest to understand what resources are available, which are used, how much they are used, and for what they are used. While scholarly literature surveys can provide some insights, large-scale computer-based approaches to identify mentions of bioinformatics databases and software from primary literature would automate systematic cataloguing, facilitate the monitoring of usage, and provide the foundations for the recovery of computational methods for analysing biological data, with the long-term aim of identifying best/common practice in different areas of biology. Results We have developed bioNerDS, a named entity recogniser for the recovery of bioinformatics databases and software from primary literature. We identify such entities with an F-measure ranging from 63% to 91% at the mention level and 63-78% at the document level, depending on corpus. Not attaining a higher F-measure is mostly due to high ambiguity in resource naming, which is compounded by the on-going introduction of new resources. To demonstrate the software, we applied bioNerDS to full-text articles from BMC Bioinformatics and Genome Biology. General mention patterns reflect the remit of these journals, highlighting BMC Bioinformatics’s emphasis on new tools and Genome Biology’s greater emphasis on data analysis. The data also illustrates some shifts in resource usage: for example, the past decade has seen R and the Gene Ontology join BLAST and GenBank as the main components in bioinformatics processing. Abstract Conclusions We demonstrate the feasibility of automatically identifying resource names on a large-scale from the scientific literature and show that the generated data can be used for exploration of bioinformatics database and software usage. For example, our results help to investigate the rate of change in resource usage and corroborate the suspicion that a vast majority of resources are created, but rarely (if ever) used thereafter. bioNerDS is available at http://bionerds.sourceforge.net/. PMID:23768135

The value of protein structure classification information-Surveying the scientific literature

DOE PAGES

Fox, Naomi K.; Brenner, Steven E.; Chandonia, John -Marc

2015-08-27

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from themore » resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings.« less

The value of protein structure classification information-Surveying the scientific literature

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

Fox, Naomi K.; Brenner, Steven E.; Chandonia, John -Marc

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from themore » resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings.« less

Computer network access to scientific information systems for minority universities

NASA Astrophysics Data System (ADS)

Thomas, Valerie L.; Wakim, Nagi T.

1993-08-01

The evolution of computer networking technology has lead to the establishment of a massive networking infrastructure which interconnects various types of computing resources at many government, academic, and corporate institutions. A large segment of this infrastructure has been developed to facilitate information exchange and resource sharing within the scientific community. The National Aeronautics and Space Administration (NASA) supports both the development and the application of computer networks which provide its community with access to many valuable multi-disciplinary scientific information systems and on-line databases. Recognizing the need to extend the benefits of this advanced networking technology to the under-represented community, the National Space Science Data Center (NSSDC) in the Space Data and Computing Division at the Goddard Space Flight Center has developed the Minority University-Space Interdisciplinary Network (MU-SPIN) Program: a major networking and education initiative for Historically Black Colleges and Universities (HBCUs) and Minority Universities (MUs). In this paper, we will briefly explain the various components of the MU-SPIN Program while highlighting how, by providing access to scientific information systems and on-line data, it promotes a higher level of collaboration among faculty and students and NASA scientists.

Kalium: a database of potassium channel toxins from scorpion venom.

PubMed

Kuzmenkov, Alexey I; Krylov, Nikolay A; Chugunov, Anton O; Grishin, Eugene V; Vassilevski, Alexander A

2016-01-01

Kalium (http://kaliumdb.org/) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.Database URL:http://kaliumdb.org/. © The Author(s) 2016. Published by Oxford University Press.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

Tools and data services registry: a community effort to document bioinformatics resources

PubMed Central

Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil; Chmura, Piotr; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; Booth, Tim; Bretaudeau, Anthony; Brezovsky, Jan; Casadio, Rita; Cesareni, Gianni; Coppens, Frederik; Cornell, Michael; Cuccuru, Gianmauro; Davidsen, Kristian; Vedova, Gianluca Della; Dogan, Tunca; Doppelt-Azeroual, Olivia; Emery, Laura; Gasteiger, Elisabeth; Gatter, Thomas; Goldberg, Tatyana; Grosjean, Marie; Grüning, Björn; Helmer-Citterich, Manuela; Ienasescu, Hans; Ioannidis, Vassilios; Jespersen, Martin Closter; Jimenez, Rafael; Juty, Nick; Juvan, Peter; Koch, Maximilian; Laibe, Camille; Li, Jing-Woei; Licata, Luana; Mareuil, Fabien; Mičetić, Ivan; Friborg, Rune Møllegaard; Moretti, Sebastien; Morris, Chris; Möller, Steffen; Nenadic, Aleksandra; Peterson, Hedi; Profiti, Giuseppe; Rice, Peter; Romano, Paolo; Roncaglia, Paola; Saidi, Rabie; Schafferhans, Andrea; Schwämmle, Veit; Smith, Callum; Sperotto, Maria Maddalena; Stockinger, Heinz; Vařeková, Radka Svobodová; Tosatto, Silvio C.E.; de la Torre, Victor; Uva, Paolo; Via, Allegra; Yachdav, Guy; Zambelli, Federico; Vriend, Gert; Rost, Burkhard; Parkinson, Helen; Løngreen, Peter; Brunak, Søren

2016-01-01

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools. PMID:26538599

[Health-related scientific and technological capabilities and university-industry research collaboration].

PubMed

Britto, Jorge; Vargas, Marco Antônio; Gadelha, Carlos Augusto Grabois; Costa, Laís Silveira

2012-12-01

To examine recent developments in health-related scientific capabilities, the impact of lines of incentives on reducing regional scientific imbalances, and university-industry research collaboration in Brazil. Data were obtained from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brazilian National Council for Scientific and Technological Development) databases for the years 2000 to 2010. There were assessed indicators of resource mobilization, research network structuring, and knowledge transfer between science and industry initiatives. Based on the regional distribution map of health-related scientific and technological capabilities there were identified patterns of scientific capabilities and science-industry collaboration. There was relative spatial deconcentration of health research groups and more than 6% of them worked in six areas of knowledge areas: medicine, collective health, dentistry, veterinary medicine, ecology and physical education. Lines of incentives that were adopted from 2000 to 2009 contributed to reducing regional scientific imbalances and improving preexisting capabilities or, alternatively, encouraging spatial decentralization of these capabilities. Health-related scientific and technological capabilities remain highly spatially concentrated in Brazil and incentive policies have contributed to reduce to some extent these imbalances.

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.

Research and development of web oriented remote sensing image publication system based on Servlet technique

NASA Astrophysics Data System (ADS)

Juanle, Wang; Shuang, Li; Yunqiang, Zhu

2005-10-01

According to the requirements of China National Scientific Data Sharing Program (NSDSP), the research and development of web oriented RS Image Publication System (RSIPS) is based on Java Servlet technique. The designing of RSIPS framework is composed of 3 tiers, which is Presentation Tier, Application Service Tier and Data Resource Tier. Presentation Tier provides user interface for data query, review and download. For the convenience of users, visual spatial query interface is included. Served as a middle tier, Application Service Tier controls all actions between users and databases. Data Resources Tier stores RS images in file and relationship databases. RSIPS is developed with cross platform programming based on Java Servlet tools, which is one of advanced techniques in J2EE architecture. RSIPS's prototype has been developed and applied in the geosciences clearinghouse practice which is among the experiment units of NSDSP in China.

Locating grey literature on communication disorders.

PubMed

Shpilko, Inna

2005-01-01

This article provides an overview of selected Web-based resources containing grey literature in the area of communication disorders. It is geared to practitioners, researchers, students, and consumers seeking reliable, freely available scientific information. Grey (or gray) literature has been defined as "that which is produced on all levels of government, academics, business, and industry in print and electronic formats, but which is not controlled by commercial publishers."1 This paper reviews various general reference sources potentially containing grey literature on communication disorders. This review includes identification of the methods specialists in this field use to obtain this valuable, yet often overlooked, literature. Access points and search tools for identifying grey literature on communication disorders are recommended. Commercial databases containing grey literature are not included. Conclusions presented in this article are considered complementary to traditionally published information resources on communication disorders, such as scholarly journals, online databases, etc.

A study on literature obsolescence and core journals' cost-benefit in citations of the 'Scientific Medical Journal of Ahwaz'.

PubMed

Zare-Farashbandi, Firoozeh; Mohammadi, Parastoo Parsaei

2014-01-01

One of the methods of identifying core and popular resources is by citation evaluation. Using citation evaluation, the librarians of the Acquisition Department can use quantitative methods to indentify core and popular resources among numerous information resources and make serious savings in the library's budget, by acquiring these core resources and eliminating useless ones. The aim of this study is assessing literature obsolescence and core journals' cost-benefit in citations of the 'Scientific Medical Journal of Ahwaz'. This study is a descriptive and cross-sectional survey that uses citation analysis. Sampling is objective sampling from all documents from years 1364 (1985) to 1385 (2006), and the population comprises of 6342 citations of the articles published in 'Scientific Medical Journal of Ahwaz'. Data collection is done through referring to the original documents and the data is analyzed using the Excel software, and for descriptive and analytical statistics the cost-benefit formula and Bradford law formula are used. Findings showed that the average citation for each document in the 'Scientific Medical Journal of Ahwaz' was 15.81. The average citation to international sources was 14.37, and the average citation to national sources was 1.44. The literature obsolescence of Farsi documents in this study was 15 years, while it was equal to 20 years for English documents. The highly cited Farsi journals were (sorted based on citation in descending order): 'Scientific Medical Journal of Ahwaz', 'Daroudarman', 'Nabz,' and 'Journal of Medical School, Shahid Beheshti University of Medical Sciences'. The highly cited English journals were (sorted based on citation in descending order): 'Pediatrics', 'The New England Journal of Medicine', 'Gastroenterology' and 'Medicine'. All of these four journals are part of the ISI database and have good impact factors in the Journal Citation Reports (JCR). Also their cost-benefit was reasonable based on the frequency of their use. The authors of the investigated journal were more inclined to use international references. The resources used by the authors of this journal are relatively obsolete and the authors ought to use more up-to-date resources. The subscription for high citation English and Farsi journals is still available in this university. Also the authors of this journal have used accredited ISI journals as their resource, which is a sign of the credibility for the 'Scientific Medical Journal of Ahwaz'.

Scientific Data Services -- A High-Performance I/O System with Array Semantics

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

Wu, Kesheng; Byna, Surendra; Rotem, Doron

2011-09-21

As high-performance computing approaches exascale, the existing I/O system design is having trouble keeping pace in both performance and scalability. We propose to address this challenge by adopting database principles and techniques in parallel I/O systems. First, we propose to adopt an array data model because many scientific applications represent their data in arrays. This strategy follows a cardinal principle from database research, which separates the logical view from the physical layout of data. This high-level data model gives the underlying implementation more freedom to optimize the physical layout and to choose the most effective way of accessing the data.more » For example, knowing that a set of write operations is working on a single multi-dimensional array makes it possible to keep the subarrays in a log structure during the write operations and reassemble them later into another physical layout as resources permit. While maintaining the high-level view, the storage system could compress the user data to reduce the physical storage requirement, collocate data records that are frequently used together, or replicate data to increase availability and fault-tolerance. Additionally, the system could generate secondary data structures such as database indexes and summary statistics. We expect the proposed Scientific Data Services approach to create a “live” storage system that dynamically adjusts to user demands and evolves with the massively parallel storage hardware.« less

Science center capabilities to monitor and investigate Michigan’s water resources, 2016

USGS Publications Warehouse

Giesen, Julia A.; Givens, Carrie E.

2016-09-06

Michigan faces many challenges related to water resources, including flooding, drought, water-quality degradation and impairment, varying water availability, watershed-management issues, stormwater management, aquatic-ecosystem impairment, and invasive species. Michigan’s water resources include approximately 36,000 miles of streams, over 11,000 inland lakes, 3,000 miles of shoreline along the Great Lakes (MDEQ, 2016), and groundwater aquifers throughout the State.The U.S. Geological Survey (USGS) works in cooperation with local, State, and other Federal agencies, as well as tribes and universities, to provide scientific information used to manage the water resources of Michigan. To effectively assess water resources, the USGS uses standardized methods to operate streamgages, water-quality stations, and groundwater stations. The USGS also monitors water quality in lakes and reservoirs, makes periodic measurements along rivers and streams, and maintains all monitoring data in a national, quality-assured, hydrologic database.The USGS in Michigan investigates the occurrence, distribution, quantity, movement, and chemical and biological quality of surface water and groundwater statewide. Water-resource monitoring and scientific investigations are conducted statewide by USGS hydrologists, hydrologic technicians, biologists, and microbiologists who have expertise in data collection as well as various scientific specialties. A support staff consisting of computer-operations and administrative personnel provides the USGS the functionality to move science forward. Funding for USGS activities in Michigan comes from local and State agencies, other Federal agencies, direct Federal appropriations, and through the USGS Cooperative Matching Funds, which allows the USGS to partially match funding provided by local and State partners.This fact sheet provides an overview of the USGS current (2016) capabilities to monitor and study Michigan’s vast water resources. More information regarding projects by the Michigan Water Science Center (MI WSC) is available at http://mi.water.usgs.gov/.

Standardized description of scientific evidence using the Evidence Ontology (ECO)

PubMed Central

Chibucos, Marcus C.; Mungall, Christopher J.; Balakrishnan, Rama; Christie, Karen R.; Huntley, Rachael P.; White, Owen; Blake, Judith A.; Lewis, Suzanna E.; Giglio, Michelle

2014-01-01

The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org PMID:25052702

The Sequenced Angiosperm Genomes and Genome Databases.

PubMed

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

The Sequenced Angiosperm Genomes and Genome Databases

PubMed Central

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology. PMID:29706973

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 knowledge base for tracking the impact of genomics on population health.

PubMed

Yu, Wei; Gwinn, Marta; Dotson, W David; Green, Ridgely Fisk; Clyne, Mindy; Wulf, Anja; Bowen, Scott; Kolor, Katherine; Khoury, Muin J

2016-12-01

We created an online knowledge base (the Public Health Genomics Knowledge Base (PHGKB)) to provide systematically curated and updated information that bridges population-based research on genomics with clinical and public health applications. Weekly horizon scanning of a wide variety of online resources is used to retrieve relevant scientific publications, guidelines, and commentaries. After curation by domain experts, links are deposited into Web-based databases. PHGKB currently consists of nine component databases. Users can search the entire knowledge base or search one or more component databases directly and choose options for customizing the display of their search results. PHGKB offers researchers, policy makers, practitioners, and the general public a way to find information they need to understand the complicated landscape of genomics and population health.Genet Med 18 12, 1312-1314.

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

Wojick, D E; Warnick, W L; Carroll, B C

With the United States federal government spending billions annually for research and development, ways to increase the productivity of that research can have a significant return on investment. The process by which science knowledge is spread is called diffusion. It is therefore important to better understand and measure the benefits of this diffusion of knowledge. In particular, it is important to understand whether advances in Internet searching can speed up the diffusion of scientific knowledge and accelerate scientific progress despite the fact that the vast majority of scientific information resources continue to be held in deep web databases that manymore » search engines cannot fully access. To address the complexity of the search issue, the term global discovery is used for the act of searching across heterogeneous environments and distant communities. This article discusses these issues and describes research being conducted by the Office of Scientific and Technical Information (OSTI).« less

Ophthalmology and vision science research: part 5: surfing or sieving--using literature databases wisely.

PubMed

Sherwin, Trevor; Gilhotra, Amardeep K

2006-02-01

Literature databases are an ever-expanding resource available to the field of medical sciences. Understanding how to use such databases efficiently is critical for those involved in research. However, for the uninitiated, getting started is a major hurdle to overcome and for the occasional user, the finer points of database searching remain an unacquired skill. In the fifth and final article in this series aimed at those embarking on ophthalmology and vision science research, we look at how the beginning researcher can start to use literature databases and, by using a stepwise approach, how they can optimize their use. This instructional paper gives a hypothetical example of a researcher writing a review article and how he or she acquires the necessary scientific literature for the article. A prototype search of the Medline database is used to illustrate how even a novice might swiftly acquire the skills required for a medium-level search. It provides examples and key tips that can increase the proficiency of the occasional user. Pitfalls of database searching are discussed, as are the limitations of which the user should be aware.

EMMA—mouse mutant resources for the international scientific community

PubMed Central

Wilkinson, Phil; Sengerova, Jitka; Matteoni, Raffaele; Chen, Chao-Kung; Soulat, Gaetan; Ureta-Vidal, Abel; Fessele, Sabine; Hagn, Michael; Massimi, Marzia; Pickford, Karen; Butler, Richard H.; Marschall, Susan; Mallon, Ann-Marie; Pickard, Amanda; Raspa, Marcello; Scavizzi, Ferdinando; Fray, Martin; Larrigaldie, Vanessa; Leyritz, Johan; Birney, Ewan; Tocchini-Valentini, Glauco P.; Brown, Steve; Herault, Yann; Montoliu, Lluis; de Angelis, Martin Hrabé; Smedley, Damian

2010-01-01

The laboratory mouse is the premier animal model for studying human disease and thousands of mutants have been identified or produced, most recently through gene-specific mutagenesis approaches. High throughput strategies by the International Knockout Mouse Consortium (IKMC) are producing mutants for all protein coding genes. Generating a knock-out line involves huge monetary and time costs so capture of both the data describing each mutant alongside archiving of the line for distribution to future researchers is critical. The European Mouse Mutant Archive (EMMA) is a leading international network infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. Additionally EMMA is one of four repositories involved in the IKMC, and therefore the current figure of 1700 archived lines will rise markedly. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org. PMID:19783817

Data structures and organisation: Special problems in scientific applications

NASA Astrophysics Data System (ADS)

Read, Brian J.

1989-12-01

In this paper we discuss and offer answers to the following questions: What, really, are the benifits of databases in physics? Are scientific databases essentially different from conventional ones? What are the drawbacks of a commercial database management system for use with scientific data? Do they outweigh the advantages? Do databases systems have adequate graphics facilities, or is a separate graphics package necessary? SQL as a standard language has deficiencies, but what are they for scientific data in particular? Indeed, is the relational model appropriate anyway? Or, should we turn to object oriented databases?

Mental health economics: insights from Brazil.

PubMed

Cruz, Luciane; Lima, Ana Flavia Da Silva; Graeff-Martins, Ana; Maia, Carlos Renato Moreira; Ziegelmann, Patricia; Miguel, Sandoro; Fleck, Marcelo; Polanczyk, Carisi

2013-04-01

As the responsibility and demand on health care grows and resources do not increase at the same pace, the healthcare system has been forced to reconsider the benefits and costs of their actions, to ensure a rational and effective decision-making process regarding the adoption of interventions and allocation of resources. Cost-effectiveness (CE) studies represent one of the basic tools to achieve this goal. To present the current state of Health Technology Assessment (HTA) and health economics in mental health in Brazil and its importance to the decision-making process. Descriptive paper on HTA and health economics in Brazil. Databases from government and universities as well as some scientific databases to assess the information are presented. Economic analysis to evaluate interventions in mental health care is a relatively recent addition to the field of health economics; in Brazil, it is also considered a topic within Epidemiology research area. There have been an increased number of studies developed in high-income countries. However, there are fewer CE studies in low- and middle-income ones. Psychiatric disorders represent a significant burden in developing countries, where resources devoted to health care are even scarcer.

MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

PubMed Central

Montague, Elizabeth; Stanberry, Larissa; Higdon, Roger; Janko, Imre; Lee, Elaine; Anderson, Nathaniel; Choiniere, John; Stewart, Elizabeth; Yandl, Gregory; Broomall, William; Kolker, Natali

2014-01-01

Abstract Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding. PMID:24910945

The value of protein structure classification information—Surveying the scientific literature

PubMed Central

Fox, Naomi K.; Brenner, Steven E.

2015-01-01

ABSTRACT The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:26313554

An Innovative Infrastructure with a Universal Geo-spatiotemporal Data Representation Supporting Cost-effective Integration of Diverse Earth Science Data

NASA Astrophysics Data System (ADS)

Kuo, K. S.; Rilee, M. L.

2017-12-01

Existing pathways for bringing together massive, diverse Earth Science datasets for integrated analyses burden end users with data packaging and management details irrelevant to their domain goals. The major data repositories focus on archival, discovery, and dissemination of products (files) in a standardized manner. End-users must download and then adapt these files using local resources and custom methods before analysis can proceed. This reduces scientific or other domain productivity, as scarce resources and expertise must be diverted to data processing. The Spatio-Temporal Adaptive Resolution Encoding (STARE) is a unifying scheme encoding geospatial and temporal information for organizing data on scalable computing/storage resources, minimizing expensive data transfers. STARE provides a compact representation that turns set-logic functions, e.g. conditional subsetting, into integer operations, that takes into account representative spatiotemporal resolutions of the data in the datasets, which is needed for data placement alignment of geo-spatiotemporally diverse data on massive parallel resources. Automating important scientific functions (e.g. regridding) and computational functions (e.g. data placement) allows scientists to focus on domain specific questions instead of expending their expertise on data processing. While STARE is not tied to any particular computing technology, we have used STARE for visualization and the SciDB array database to analyze Earth Science data on a 28-node compute cluster. STARE's automatic data placement and coupling of geometric and array indexing allows complicated data comparisons to be realized as straightforward database operations like "join." With STARE-enabled automation, SciDB+STARE provides a database interface, reducing costly data preparation, increasing the volume and variety of integrable data, and easing result sharing. Using SciDB+STARE as part of an integrated analysis infrastructure, we demonstrate the dramatic ease of combining diametrically different datasets, i.e. gridded (NMQ radar) vs. spacecraft swath (TRMM). SciDB+STARE is an important step towards a computational infrastructure for integrating and sharing diverse, complex Earth Science data and science products derived from them.

Exploring Antarctic Land Surface Temperature Extremes Using Condensed Anomaly Databases

NASA Astrophysics Data System (ADS)

Grant, Glenn Edwin

Satellite observations have revolutionized the Earth Sciences and climate studies. However, data and imagery continue to accumulate at an accelerating rate, and efficient tools for data discovery, analysis, and quality checking lag behind. In particular, studies of long-term, continental-scale processes at high spatiotemporal resolutions are especially problematic. The traditional technique of downloading an entire dataset and using customized analysis code is often impractical or consumes too many resources. The Condensate Database Project was envisioned as an alternative method for data exploration and quality checking. The project's premise was that much of the data in any satellite dataset is unneeded and can be eliminated, compacting massive datasets into more manageable sizes. Dataset sizes are further reduced by retaining only anomalous data of high interest. Hosting the resulting "condensed" datasets in high-speed databases enables immediate availability for queries and exploration. Proof of the project's success relied on demonstrating that the anomaly database methods can enhance and accelerate scientific investigations. The hypothesis of this dissertation is that the condensed datasets are effective tools for exploring many scientific questions, spurring further investigations and revealing important information that might otherwise remain undetected. This dissertation uses condensed databases containing 17 years of Antarctic land surface temperature anomalies as its primary data. The study demonstrates the utility of the condensate database methods by discovering new information. In particular, the process revealed critical quality problems in the source satellite data. The results are used as the starting point for four case studies, investigating Antarctic temperature extremes, cloud detection errors, and the teleconnections between Antarctic temperature anomalies and climate indices. The results confirm the hypothesis that the condensate databases are a highly useful tool for Earth Science analyses. Moreover, the quality checking capabilities provide an important method for independent evaluation of dataset veracity.

The role of patent and non-patent databases in patent research in universities

NASA Astrophysics Data System (ADS)

Tolstaya, A. M.; Suslina, I. V.; Tolstaya, P. M.

2017-01-01

This studies deal with the description and systematization of the popular patent retrieval resources. The importance of the non-patent information when conducting patent research for the intellectual property created in educational and scientific activity of the university is highlighted. The differences in the patent and non-patent information are found out. Based on the databases` analysis the authors conducted the patent research on "Wireless endoscopic capsules" (development of the NRNU MEPhI). This study can be used to facilitate the university work on the new product development in order to improve the efficiency of the process of the commercialization of the intellectual activity results, including the entering the international market.

Cardiac CT and MRI for congenital heart disease in Asian countries: recent trends in publication based on a scientific database.

PubMed

Tsai, I-Chen; Goo, Hyun Woo

2013-06-01

In the past 12 years, during the process of imaging congenital heart disease (CHD), Asian doctors have not only made every effort to adhere to established magnetic resonance imaging (MRI) protocols as in Western countries, but also have developed Computed tomography (CT) as an alternative problem-solving technique. Databases have shown that Asian doctors were more inclined to utilize CT than MRI in evaluating CHD. Articles in the literature focusing on CT have been cited more frequently than articles on MRI. Additionally, several repeatedly cited CT articles have become seminal papers in this field. The database reflects a trend suggesting that Asian doctors actively adapt to new techniques and flexibly develop unique strategies to overcome limitations caused by the relatively limited resources often available to them.

Assessing availability of scientific journals, databases, and health library services in Canadian health ministries: a cross-sectional study.

PubMed

Léon, Grégory; Ouimet, Mathieu; Lavis, John N; Grimshaw, Jeremy; Gagnon, Marie-Pierre

2013-03-21

Evidence-informed health policymaking logically depends on timely access to research evidence. To our knowledge, despite the substantial political and societal pressure to enhance the use of the best available research evidence in public health policy and program decision making, there is no study addressing availability of peer-reviewed research in Canadian health ministries. To assess availability of (1) a purposive sample of high-ranking scientific journals, (2) bibliographic databases, and (3) health library services in the fourteen Canadian health ministries. From May to October 2011, we conducted a cross-sectional survey among librarians employed by Canadian health ministries to collect information relative to availability of scientific journals, bibliographic databases, and health library services. Availability of scientific journals in each ministry was determined using a sample of 48 journals selected from the 2009 Journal Citation Reports (Sciences and Social Sciences Editions). Selection criteria were: relevance for health policy based on scope note information about subject categories and journal popularity based on impact factors. We found that the majority of Canadian health ministries did not have subscription access to key journals and relied heavily on interlibrary loans. Overall, based on a sample of high-ranking scientific journals, availability of journals through interlibrary loans, online and print-only subscriptions was estimated at 63%, 28% and 3%, respectively. Health Canada had a 2.3-fold higher number of journal subscriptions than that of the provincial ministries' average. Most of the organisations provided access to numerous discipline-specific and multidisciplinary databases. Many organisations provided access to the library resources described through library partnerships or consortia. No professionally led health library environment was found in four out of fourteen Canadian health ministries (i.e. Manitoba Health, Northwest Territories Department of Health and Social Services, Nunavut Department of Health and Social Services and Yukon Department of Health and Social Services). There is inequity in availability of peer-reviewed research in the fourteen Canadian health ministries. This inequity could present a problem, as each province and territory is responsible for formulating and implementing evidence-informed health policies and services for the benefit of its population.

Assessing availability of scientific journals, databases, and health library services in Canadian health ministries: a cross-sectional study

PubMed Central

2013-01-01

Background Evidence-informed health policymaking logically depends on timely access to research evidence. To our knowledge, despite the substantial political and societal pressure to enhance the use of the best available research evidence in public health policy and program decision making, there is no study addressing availability of peer-reviewed research in Canadian health ministries. Objectives To assess availability of (1) a purposive sample of high-ranking scientific journals, (2) bibliographic databases, and (3) health library services in the fourteen Canadian health ministries. Methods From May to October 2011, we conducted a cross-sectional survey among librarians employed by Canadian health ministries to collect information relative to availability of scientific journals, bibliographic databases, and health library services. Availability of scientific journals in each ministry was determined using a sample of 48 journals selected from the 2009 Journal Citation Reports (Sciences and Social Sciences Editions). Selection criteria were: relevance for health policy based on scope note information about subject categories and journal popularity based on impact factors. Results We found that the majority of Canadian health ministries did not have subscription access to key journals and relied heavily on interlibrary loans. Overall, based on a sample of high-ranking scientific journals, availability of journals through interlibrary loans, online and print-only subscriptions was estimated at 63%, 28% and 3%, respectively. Health Canada had a 2.3-fold higher number of journal subscriptions than that of the provincial ministries’ average. Most of the organisations provided access to numerous discipline-specific and multidisciplinary databases. Many organisations provided access to the library resources described through library partnerships or consortia. No professionally led health library environment was found in four out of fourteen Canadian health ministries (i.e. Manitoba Health, Northwest Territories Department of Health and Social Services, Nunavut Department of Health and Social Services and Yukon Department of Health and Social Services). Conclusions There is inequity in availability of peer-reviewed research in the fourteen Canadian health ministries. This inequity could present a problem, as each province and territory is responsible for formulating and implementing evidence-informed health policies and services for the benefit of its population. PMID:23514333

Scientifically supported mental health intervention in schools: meeting accountability demands with an online resource.

PubMed

Powers, Joelle D

2012-01-01

Legislation has been passed that holds schools increasingly accountable for the proficiency of all students, including those with mental health problems. A critical obstacle impeding the ability of schools to effectively support students is the lack of access to quick, pre-screened, and organized information about scientifically-supported interventions that effectively address youth mental health problems. A new mental health best practices database was developed and made available online that provides access to free and user-friendly information about evidence-based interventions for use in schools. School staff will be better able to meet accountability demands of legislation and to effectively respond to student mental health problems.

usSEABED: Gulf of Mexico and Caribbean (Puerto Rico and U.S. Virgin Islands) offshore surficial sediment data release

USGS Publications Warehouse

Buczkowski, Brian J.; Reid, Jane A.; Jenkins, Chris J.; Reid, Jamey M.; Williams, S. Jeffress; Flocks, James G.

2006-01-01

Over the past 50 years there has been an explosion in scientific interest, research effort and information gathered on the geologic sedimentary character of the United States continental margin. Data and information from thousands of publications have greatly increased our scientific understanding of the geologic origins of the shelf surface but rarely have those data been combined and integrated. This publication is the first release of the Gulf of Mexico and Caribbean (Puerto Rico and U.S. Virgin Islands) coastal and offshore data from the usSEABED database. The report contains a compilation of published and previously unpublished sediment texture and other geologic data about the sea floor from diverse sources. usSEABED is an innovative database system developed to bring assorted data together in a unified database. The dbSEABED system is used to process the data. Examples of maps displaying attributes such as grain size and sediment color are included. This database contains information that is a scientific foundation for the USGS Marine Aggregate Resources and Processes Assessment and Benthic Habitats projects, and will be useful to the marine science community for other studies of the Gulf of Mexico and Caribbean continental margins. This publication is divided into ten sections: Home, Introduction, Content, usSEABED (data), dbSEABED (processing), Data Catalog, References, Contacts, Acknowledgments and Frequently Asked Questions. Use the navigation bar on the left to navigate to specific sections of this report. Underlined topics throughout the publication are links to more information. Links to specific and detailed information on processing and those to pages outside this report will open in a new browser window.

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.

Planetary In Situ Resource Utilization: 2000-2004

NASA Technical Reports Server (NTRS)

2004-01-01

This custom bibliography from the NASA Scientific and Technical Information Program lists a sampling of records found in the NASA Aeronautics and Space Database. The scope of this topic includes technologies for ultimately enabling us to "cut the cord" with Earth for space logistics. This area of focus is one of the enabling technologies as defined by NASA s Report of the President s Commission on Implementation of United States Space Exploration Policy, published in June 2004.

Analysing patent landscapes in plant biotechnology and new plant breeding techniques.

PubMed

Parisi, Claudia; Rodríguez-Cerezo, Emilio; Thangaraj, Harry

2013-02-01

This article aims to inform the reader of the importance of searching patent landscapes in plant biotechnology and the use of basic tools to perform a patent search. The recommendations for a patent search strategy are illustrated with the specific example of zinc finger nuclease technology for genetic engineering in plants. Within this scope, we provide a general introduction to searching using two online and free-access patent databases esp@cenet and PatentScope. The essential features of the two databases, and their functionality is described, together with short descriptions to enable the reader to understand patents, searching, their content, patent families, and their territorial scope. We mostly stress the value of patent searching for mining scientific, rather than legal information. Search methods through the use of keywords and patent codes are elucidated together with suggestions about how to search with or combine codes with keywords and we also comment on limitations of each method. We stress the importance of patent literature to complement more mainstream scientific literature, and the relative complexities and difficulties in searching patents compared to the latter. A parallel online resource where we describe detailed search exercises is available through reference for those intending further exploration. In essence this is aimed at a novice patent searcher who may want to examine accessory patent literature to complement knowledge gained from mainstream journal resources.

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

A Distributed Web-based Solution for Ionospheric Model Real-time Management, Monitoring, and Short-term Prediction

NASA Astrophysics Data System (ADS)

Kulchitsky, A.; Maurits, S.; Watkins, B.

2006-12-01

With the widespread availability of the Internet today, many people can monitor various scientific research activities. It is important to accommodate this interest providing on-line access to dynamic and illustrative Web-resources, which could demonstrate different aspects of ongoing research. It is especially important to explain and these research activities for high school and undergraduate students, thereby providing more information for making decisions concerning their future studies. Such Web resources are also important to clarify scientific research for the general public, in order to achieve better awareness of research progress in various fields. Particularly rewarding is dissemination of information about ongoing projects within Universities and research centers to their local communities. The benefits of this type of scientific outreach are mutual, since development of Web-based automatic systems is prerequisite for many research projects targeting real-time monitoring and/or modeling of natural conditions. Continuous operation of such systems provide ongoing research opportunities for the statistically massive validation of the models, as well. We have developed a Web-based system to run the University of Alaska Fairbanks Polar Ionospheric Model in real-time. This model makes use of networking and computational resources at the Arctic Region Supercomputing Center. This system was designed to be portable among various operating systems and computational resources. Its components can be installed across different computers, separating Web servers and computational engines. The core of the system is a Real-Time Management module (RMM) written Python, which facilitates interactions of remote input data transfers, the ionospheric model runs, MySQL database filling, and PHP scripts for the Web-page preparations. The RMM downloads current geophysical inputs as soon as they become available at different on-line depositories. This information is processed to provide inputs for the next ionospheic model time step and then stored in a MySQL database as the first part of the time-specific record. The RMM then performs synchronization of the input times with the current model time, prepares a decision on initialization for the next model time step, and monitors its execution. Then, as soon as the model completes computations for the next time step, RMM visualizes the current model output into various short-term (about 1-2 hours) forecasting products and compares prior results with available ionospheric measurements. The RMM places prepared images into the MySQL database, which can be located on a different computer node, and then proceeds to the next time interval continuing the time-loop. The upper-level interface of this real-time system is the a PHP-based Web site (http://www.arsc.edu/SpaceWeather/new). This site provides general information about the Earth polar and adjacent mid-latitude ionosphere, allows for monitoring of the current developments and short-term forecasts, and facilitates access to the comparisons archive stored in the database.

DMTB: the magnetotactic bacteria database

NASA Astrophysics Data System (ADS)

Pan, Y.; Lin, W.

2012-12-01

Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

The Biomolecular Crystallization Database Version 4: expanded content and new features.

PubMed

Tung, Michael; Gallagher, D Travis

2009-01-01

The Biological Macromolecular Crystallization Database (BMCD) has been a publicly available resource since 1988, providing a curated archive of information on crystal growth for proteins and other biological macromolecules. The BMCD content has recently been expanded to include 14 372 crystal entries. The resource continues to be freely available at http://xpdb.nist.gov:8060/BMCD4. In addition, the software has been adapted to support the Java-based Lucene query language, enabling detailed searching over specific parameters, and explicit search of parameter ranges is offered for five numeric variables. Extensive tools have been developed for import and handling of data from the RCSB Protein Data Bank. The updated BMCD is called version 4.02 or BMCD4. BMCD4 entries have been expanded to include macromolecule sequence, enabling more elaborate analysis of relations among protein properties, crystal-growth conditions and the geometric and diffraction properties of the crystals. The BMCD version 4.02 contains greatly expanded content and enhanced search capabilities to facilitate scientific analysis and design of crystal-growth strategies.

Information And Data-Sharing Plan of IPY China Activity

NASA Astrophysics Data System (ADS)

Zhang, X.; Cheng, W.

2007-12-01

Polar Data-Sharing is an effective resolution to global system and polar science problems and to interdisciplinary and sustainable study, as well as an important means to deal with IPY scientific heritages and realize IPY goals. Corresponding to IPY Data-Sharing policies, Information and Data-Sharing Plan was listed in five sub-plans of IPY Chinese Programme launched in March, 2007,they are Scientific research program of the Prydz Bay, Amery Ice Shelf and Dome A transects(short title:'PANDA'), the Arctic Scientific Research Expedition Plan, International Cooperation Plan, Information and Data-Sharing Plan, Education and Outreach. China, since the foundation of Antarctic Zhongshan Station in 1989, has carried out systematic scientific expeditions and researches in Larsemann Hills, Prydz Bay and the neighbouring sea areas, organized 14 Prydz Bay oceanographic investigations, 3 Amery Ice Shelf expeditions, 4 Grove Mountains expeditions and 5 inland ice cap scientific expeditions. 2 comprehensive oceanographic investigations in the Arctic Ocean were conducted in 1999 and 2003, acquired a large amount of data and samples in PANDA section and fan areas of Pacific Ocean in the Arctic Ocean. A mechanism of basic data submitting ,sharing and archiving has been gradually set up since 2000. Presently, Polar Science Database and Polar Sample Resource Sharing Platform of China with the aim of sharing polar data and samples has been initially established and began to provide sharing service to domestic and oversea users. According to IPY Chinese Activity, 2 scientific expeditions in the Arctic Ocean, 3 in the South Ocean, 2 at Amery Ice Shelf, 1 on Grove Mountains and 2 inland ice cap expeditions on Dome A will be carried out during IPY period. According to the experiences accumulated in the past and the jobs in the future, the Information and Data- Sharing Plan, during 2007-2010, will save, archive, and provide exchange and sharing services upon the data obtained by scientific expeditions on the site of IPY Chinese Programme. Meanwhile, focusing on areas in east Antarctic Dome A-Grove Mountain-Zhongshan Station-Amery Ice Shelf-Prydz Bay Section and the fan areas of Pacific Ocean in the Arctic Ocean, the Plan will also collect and integrate IPY data and historical data and establish database of PANDA Section and the Arctic Ocean. The details are as follows: On the basis of integrating the observed data acquired during the expeditions of China, the Plan will, adopting portal technology, develop 5 subject databases (English version included):(1) Database of Zhongshan Station- Dome A inner land ice cap section;(2) Database of interaction of ocean-ice-atmosphere-ice shelf in east Antarctica;(3) Database of geological and glaciological advance and retreat evolvement in Grove Mountains; (4) Database of Solar Terrestrial Physics at Zhongshan Station; (5) Oceanographic database of fan area of Pacific Ocean in the Arctic Ocean. CN-NADC of PRIC is the institute which assumes the responsibility for the Plan, specifically, it coordinates and organizes the operation of the Plan which includes data management, developing the portal of data and information sharing, and international exchanges. The specific assignments under the Plan will be carried out by research institutes under CAS (Chinese Academy of Sciences), SOA ( State Oceanic Administration), State Bureau of Surveying and Mapping and Ministry of Education.

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/.

Role for protein–protein interaction databases in human genetics

PubMed Central

Pattin, Kristine A; Moore, Jason H

2010-01-01

Proteomics and the study of protein–protein interactions are becoming increasingly important in our effort to understand human diseases on a system-wide level. Thanks to the development and curation of protein-interaction databases, up-to-date information on these interaction networks is accessible and publicly available to the scientific community. As our knowledge of protein–protein interactions increases, it is important to give thought to the different ways that these resources can impact biomedical research. In this article, we highlight the importance of protein–protein interactions in human genetics and genetic epidemiology. Since protein–protein interactions demonstrate one of the strongest functional relationships between genes, combining genomic data with available proteomic data may provide us with a more in-depth understanding of common human diseases. In this review, we will discuss some of the fundamentals of protein interactions, the databases that are publicly available and how information from these databases can be used to facilitate genome-wide genetic studies. PMID:19929610

Towards Monitoring-as-a-service for Scientific Computing Cloud applications using the ElasticSearch ecosystem

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Guarise, A.; Lusso, S.; Masera, M.; Vallero, S.

2015-12-01

The INFN computing centre in Torino hosts a private Cloud, which is managed with the OpenNebula cloud controller. The infrastructure offers Infrastructure-as-a-Service (IaaS) and Platform-as-a-Service (PaaS) services to different scientific computing applications. The main stakeholders of the facility are a grid Tier-2 site for the ALICE collaboration at LHC, an interactive analysis facility for the same experiment and a grid Tier-2 site for the BESIII collaboration, plus an increasing number of other small tenants. The dynamic allocation of resources to tenants is partially automated. This feature requires detailed monitoring and accounting of the resource usage. We set up a monitoring framework to inspect the site activities both in terms of IaaS and applications running on the hosted virtual instances. For this purpose we used the ElasticSearch, Logstash and Kibana (ELK) stack. The infrastructure relies on a MySQL database back-end for data preservation and to ensure flexibility to choose a different monitoring solution if needed. The heterogeneous accounting information is transferred from the database to the ElasticSearch engine via a custom Logstash plugin. Each use-case is indexed separately in ElasticSearch and we setup a set of Kibana dashboards with pre-defined queries in order to monitor the relevant information in each case. For the IaaS metering, we developed sensors for the OpenNebula API. The IaaS level information gathered through the API is sent to the MySQL database through an ad-hoc developed RESTful web service. Moreover, we have developed a billing system for our private Cloud, which relies on the RabbitMQ message queue for asynchronous communication to the database and on the ELK stack for its graphical interface. The Italian Grid accounting framework is also migrating to a similar set-up. Concerning the application level, we used the Root plugin TProofMonSenderSQL to collect accounting data from the interactive analysis facility. The BESIII virtual instances used to be monitored with Zabbix, as a proof of concept we also retrieve the information contained in the Zabbix database. In this way we have achieved a uniform monitoring interface for both the IaaS and the scientific applications, mostly leveraging off-the-shelf tools. At present, we are working to define a model for monitoring-as-a-service, based on the tools described above, which the Cloud tenants can easily configure to suit their specific needs.

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.

The ERESE Project: Interfacing with the ERDA Digital Archive and ERR Reference Database in EarthRef.org

NASA Astrophysics Data System (ADS)

Koppers, A. A.; Staudigel, H.; Mills, H.; Keller, M.; Wallace, A.; Bachman, N.; Helly, J.; Helly, M.; Miller, S. P.; Massell Symons, C.

2004-12-01

To bridge the gap between Earth science teachers, librarians, scientists and data archive managers, we have started the ERESE project that will create, archive and make available "Enduring Resources in Earth Science Education" through information technology (IT) portals. In the first phase of this National Science Digital Library (NSDL) project, we are focusing on the development of these ERESE resources for middle and high school teachers to be used in lesson plans with "plate tectonics" and "magnetics" as their main theme. In this presentation, we will show how these new ERESE resources are being generated, how they can be uploaded via online web wizards, how they are archived, how we make them available via the EarthRef.org Digital Archive (ERDA) and Reference Database (ERR), and how they relate to the SIOExplorer database containing data objects for all seagoing cruises carried out by the Scripps Institution of Oceanography. The EarthRef.org web resource uses the vision of a "general description" of the Earth as a geological system to provide an IT infrastructure for the Earth sciences. This emphasizes the marriage of the "scientific process" (and its results) with an educational cyber-infrastructure for teaching Earth sciences, on any level, from middle school to college and graduate levels. Eight different databases reside under EarthRef.org from which ERDA holds any digital object that has been uploaded by other scientists, teachers and students for free, while the ERR holds more than 80,000 publications. For more than 1,500 of these publications, this latter database makes available for downloading JPG/PDF images of the abstracts, data tables, methods and appendices, together with their digitized contents in Microsoft Word and Excel format. Both holdings are being used to store the ERESE objects that are being generated by a group of undergraduate students majoring in Environmental Systems (ESYS) program at the UCSD with an emphasis on the Earth Sciences. These students perform library and internet research in order to design and generate these "Enduring Resources in Earth Science Education" that they test by closely interacting with the research faculty at the Scripps Institution of Oceanography. Typical ERESE resources can be diagrams, model cartoons, maps, data sets for analyses, and glossary items and essays to explain certain Earth Science concepts and are ready to be used in the classroom.

Geologic map of the eastern half of the Vail 30' x 60' quadrangle, Eagle, Summit, and Grand Counties, Colorado

USGS Publications Warehouse

Kellogg, Karl S.; Shroba, Ralph R.; Premo, Wayne R.; Bryant, Bruce

2011-01-01

The map is intended as a database for a variety of land-use and scientific purposes, including (1) assessment of geologically stable building sites, (2) planning for road and highway construction, (3) assessment of groundwater resources, (4) assessment of mineral resources, (5) determining geologic-hazard potential (flooding, landslide, rockfall, and seismic risk), (6) evaluating the structure of the northern Rio Grande rift in the Blue River valley, (7) improvement in understanding of the sedimentary section, which spans the period from the Cambrian to the Holocene, and (8) new insights into the geologic history of the Proterozoic basement rocks, including a number of new radiometric dates.

Profile and scientific production of CNPq researchers in cardiology.

PubMed

Oliveira, Eduardo Araujo de; Ribeiro, Antonio Luiz Pinho; Quirino, Isabel Gomes; Oliveira, Maria Christina Lopes; Martelli, Daniella Reis; Lima, Leonardo Santos; Colosimo, Enrico Antonio; Lopes, Thais Junqueira; Silva, Ana Cristina Simões; Martelli, Hercílio

2011-09-01

Systematic assessments of the scientific production can optimize resource allocation and increase research productivity in Brazil. The aim of this study was to evaluate the profile and scientific production of researchers in the field of Cardiology who have fellowship in Medicine provided by the Conselho Nacional de Desenvolvimento Científico e Tecnológico. The curriculum Lattes of 33 researchers with active fellowships from 2006 to 2008 were included in the analysis. The variables of interest were: gender, affiliation, tutoring of undergraduate, masters and PhD students, and scientific production and its impact. : There was predominance of males (72.7%) and of fellowship level 2 (56.4%). Three states of the Federation were responsible for 94% of the researchers: SP (28; 71.8%), RS (4; 10.3%), e RJ (3; 9.1%). Four institutions are responsible for about 82% of researchers: USP (13; 39.4%), UNESP (5; 15.2%), UFRGS (4; 12.1%) e UNIFESP (3; 9.1%). During all academic careers, the researchers published 2.958 journal articles, with a mean of 89 articles per researcher. Of total, 55% and 75% were indexed at Web of Science and Scopus databases, respectively. The researchers received a total of 19648 citations at the database Web of Science, with a median of 330 citations per researcher (IQ = 198-706). The average number of citations per article was 13.5 citations (SD = 11.6). Our study has shown that researchers in the field of cardiology have a relevant scientific production. The knowledge of the profile of researchers in the field of Cardiology will probably enable effective strategies to qualitatively improve the scientific output of Brazilian researchers.

[Interagency collaboration in Spanish scientific production in nursing: social network analysis].

PubMed

Almero-Canet, Amparo; López-Ferrer, Mayte; Sales-Orts, Rafael

2013-01-01

The objectives of this paper are to analyze the Spanish scientific production in nursing, define its temporal evolution, its geographical and institutional distribution, and observe the interinstitutional collaboration. We analyze a comprehensive sample of Spanish scientific production in the nursing area extracted from the multidisciplinary database SciVerse Scopus. The nursing scientific production grows along time. The collaboration rate is 3.7 authors per paper and 61% of the authors only publish one paper. Barcelona and Madrid are the provinces with highest number of authors. Most belong to the hospitalary environment, followed closely by authors belonging to the university. The most institutions that collaborate, sharing authorship of articles are: University of Barcelona, Autonomous University of Barcelona and Clinic Hospital of Barcelona. The nursing scientific production has been increasing since her incorporation at the university. The collaboration rate found is higher than found for other papers. It shows a low decrease of occasional authors. It discusses the outlook of scientific collaboration in nursing in Spain, at the level of institutions by co-authorship of papers, through a network graph. It observes their distribution, importance and interactions or lack thereof. There is a strong need to use international databases for research, care and teaching, in addition to the national specialized information resources. Professionals are encouraged to normalization of the paper's signature, both, surnames and institutions to which they belong. It confirms the limited cooperation with foreign institutions, although there is an increasing trend of collaboration between Spanish authors in this discipline. It is observed, clearly defined three interinstitutional collaboration patterns. Copyright © 2012 Elsevier España, S.L. All rights reserved.

THE CELL CENTERED DATABASE PROJECT: AN UPDATE ON BUILDING COMMUNITY RESOURCES FOR MANAGING AND SHARING 3D IMAGING DATA

PubMed Central

Martone, Maryann E.; Tran, Joshua; Wong, Willy W.; Sargis, Joy; Fong, Lisa; Larson, Stephen; Lamont, Stephan P.; Gupta, Amarnath; Ellisman, Mark H.

2008-01-01

Databases have become integral parts of data management, dissemination and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D and 4D structural and protein distribution information from confocal, multiphoton and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the five years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data. PMID:18054501

Design and development of a geo-referenced database to radionuclides in food

NASA Astrophysics Data System (ADS)

Nascimento, L. M. E.; Ferreira, A. C. M.; Gonzalez, S. A.

2018-03-01

The primary purpose of the range of activities concerning the info management of the environmental assessment is to provide to scientific community an improved access to environmental data, as well as to support the decision making loop, in case of contamination events due either to accidental or intentional causes. In recent years, geotechnologies became a key reference in environmental research and monitoring, since they deliver an efficient data retrieval and subsequent processing about natural resources. This study aimed at the development of a georeferenced database (SIGLARA – SIstema Georeferenciado Latino Americano de Radionuclídeos em Alimentos), designed to radioactivity in food data storage, available in three languages (Spanish, Portuguese and English), employing free software[l].

Chandra monitoring, trends, and response

NASA Astrophysics Data System (ADS)

Spitzbart, Brad D.; Wolk, Scott J.; Isobe, Takashi

2002-12-01

The Chandra X-ray Observatory was launched in July, 1999 and has yielded extraordinary scientific results. Behind the scenes, our Monitoring and Trends Analysis (MTA) system has proven to be a valuable resource. With three years worth of on-orbit data, we have available a vast array of both telescope diagnostic information and analysis of scientific data to access Observatory performance. As part of Chandra's Science Operations Team (SOT), the primary goal of MTA is to provide tools for effective decision making leading to the most efficient production of quality science output from the Observatory. We occupy a middle ground between flight operations, chiefly concerned with the health and safety of the spacecraft, and validation and verification, concerned with the scientific validity of the data taken and whether or not they fulfill the observer's requirements. In that role we provide and receive support from systems engineers, instrument experts, operations managers, and scientific users. MTA tools, products, and services include real-time monitoring and alert generation for the most mission critical components, long term trending of all spacecraft systems, detailed analysis of various subsystems for life expectancy or anomaly resolution, and creating and maintaining a large SQL database of relevant information. This is accomplished through the use of a wide variety of input data sources and flexible, accessible programming and analysis techniques. This paper will discuss the overall design of the system, its evolution and the resources available.

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

Production and distribution of scientific and technical databases - Comparison among Japan, US and Europe

NASA Astrophysics Data System (ADS)

Onodera, Natsuo; Mizukami, Masayuki

This paper estimates several quantitative indice on production and distribution of scientific and technical databases based on various recent publications and attempts to compare the indice internationally. Raw data used for the estimation are brought mainly from the Database Directory (published by MITI) for database production and from some domestic and foreign study reports for database revenues. The ratio of the indice among Japan, US and Europe for usage of database is similar to those for general scientific and technical activities such as population and R&D expenditures. But Japanese contributions to production, revenue and over-countory distribution of databases are still lower than US and European countries. International comparison of relative database activities between public and private sectors is also discussed.

Biocuration at the Saccharomyces genome database.

PubMed

Skrzypek, Marek S; Nash, Robert S

2015-08-01

Saccharomyces Genome Database is an online resource dedicated to managing information about the biology and genetics of the model organism, yeast (Saccharomyces cerevisiae). This information is derived primarily from scientific publications through a process of human curation that involves manual extraction of data and their organization into a comprehensive system of knowledge. This system provides a foundation for further analysis of experimental data coming from research on yeast as well as other organisms. In this review we will demonstrate how biocuration and biocurators add a key component, the biological context, to our understanding of how genes, proteins, genomes and cells function and interact. We will explain the role biocurators play in sifting through the wealth of biological data to incorporate and connect key information. We will also discuss the many ways we assist researchers with their various research needs. We hope to convince the reader that manual curation is vital in converting the flood of data into organized and interconnected knowledge, and that biocurators play an essential role in the integration of scientific information into a coherent model of the cell. © 2015 Wiley Periodicals, Inc.

Biocuration at the Saccharomyces Genome Database

PubMed Central

Skrzypek, Marek S.; Nash, Robert S.

2015-01-01

Saccharomyces Genome Database is an online resource dedicated to managing information about the biology and genetics of the model organism, yeast (Saccharomyces cerevisiae). This information is derived primarily from scientific publications through a process of human curation that involves manual extraction of data and their organization into a comprehensive system of knowledge. This system provides a foundation for further analysis of experimental data coming from research on yeast as well as other organisms. In this review we will demonstrate how biocuration and biocurators add a key component, the biological context, to our understanding of how genes, proteins, genomes and cells function and interact. We will explain the role biocurators play in sifting through the wealth of biological data to incorporate and connect key information. We will also discuss the many ways we assist researchers with their various research needs. We hope to convince the reader that manual curation is vital in converting the flood of data into organized and interconnected knowledge, and that biocurators play an essential role in the integration of scientific information into a coherent model of the cell. PMID:25997651

NIST Gas Hydrate Research Database and Web Dissemination Channel.

PubMed

Kroenlein, K; Muzny, C D; Kazakov, A; Diky, V V; Chirico, R D; Frenkel, M; Sloan, E D

2010-01-01

To facilitate advances in application of technologies pertaining to gas hydrates, a freely available data resource containing experimentally derived information about those materials was developed. This work was performed by the Thermodynamic Research Center (TRC) paralleling a highly successful database of thermodynamic and transport properties of molecular pure compounds and their mixtures. Population of the gas-hydrates database required development of guided data capture (GDC) software designed to convert experimental data and metadata into a well organized electronic format, as well as a relational database schema to accommodate all types of numerical and metadata within the scope of the project. To guarantee utility for the broad gas hydrate research community, TRC worked closely with the Committee on Data for Science and Technology (CODATA) task group for Data on Natural Gas Hydrates, an international data sharing effort, in developing a gas hydrate markup language (GHML). The fruits of these efforts are disseminated through the NIST Sandard Reference Data Program [1] as the Clathrate Hydrate Physical Property Database (SRD #156). A web-based interface for this database, as well as scientific results from the Mallik 2002 Gas Hydrate Production Research Well Program [2], is deployed at http://gashydrates.nist.gov.

usSEABED: Pacific coast (California, Oregon, Washington) offshore surficial-sediment data release

USGS Publications Warehouse

Reid, Jane A.; Reid, Jamey M.; Jenkins, Chris J.; Zimmermann, Mark; Williams, S. Jeffress; Field, Michael E.

2006-01-01

Over the past 50 years there has been an explosion in scientific interest, research effort, and information gathered on the geologic sedimentary character of the continental margin of the United States. Data and information from thousands of publications have greatly increased our scientific understanding of the geologic origins of the margin surface but rarely have those data been combined and integrated. This publication is the first release of the Pacific coast data from the usSEABED database. The report contains a compilation of published and unpublished sediment texture and other geologic data about the sea floor from diverse sources. usSEABED is an innovative database system developed to unify assorted data, with the data processed by the dbSEABED system. Examples of maps displaying attributes such as grain size and sediment color are included. This database contains information that is a scientific foundation for the U.S. Geological Survey (USGS) Sea floor Mapping and Benthic Habitats project and the Marine Aggregate Resources and Processes assessment project, and will be useful to the marine science community for other studies of the Pacific coast continental margin. The publication is divided into 10 sections: Home, Introduction, Content, usSEABED (data), dbSEABED (processing), Data Catalog, References, Contacts, Acknowledgments, and Frequently Asked Questions. Use the navigation bar on the left to navigate to specific sections of this report. Underlined topics throughout the publication are links to more information. Links to specific and detailed information on processing and to those to pages outside this report will open in a new browser window.

Using PeptideAtlas, SRMAtlas and PASSEL – Comprehensive Resources for discovery and targeted proteomics

PubMed Central

Kusebauch, Ulrike; Deutsch, Eric W.; Campbell, David S.; Sun, Zhi; Farrah, Terry; Moritz, Robert L.

2014-01-01

PeptideAtlas, SRMAtlas and PASSEL are web-accessible resources to support discovery and targeted proteomics research. PeptideAtlas is a multi-species compendium of shotgun proteomic data provided by the scientific community, SRMAtlas is a resource of high-quality, complete proteome SRM assays generated in a consistent manner for the targeted identification and quantification of proteins, and PASSEL is a repository that compiles and represents selected reaction monitoring data, all in an easy to use interface. The databases are generated from native mass spectrometry data files that are analyzed in a standardized manner including statistical validation of the results. Each resource offers search functionalities and can be queried by user defined constraints; the query results are provided in tables or are graphically displayed. PeptideAtlas, SRMAtlas and PASSEL are publicly available freely via the website http://www.peptideatlas.org. In this protocol, we describe the use of these resources, we highlight how to submit, search, collate and download data. PMID:24939129

NCI at Frederick Scientific Library Reintroduces Scientific Publications Database | Poster

Cancer.gov

A 20-year-old database of scientific publications by NCI at Frederick, FNLCR, and affiliated employees has gotten a significant facelift. Maintained by the Scientific Library, the redesigned database—which is linked from each of the Scientific Library’s web pages—offers features that were not available in previous versions, such as additional search limits and non-traditional metrics for scholarly and scientific publishing known as altmetrics.

A social-ecological database to advance research on infrastructure development impacts in the Brazilian Amazon.

PubMed

Tucker Lima, Joanna M; Valle, Denis; Moretto, Evandro Mateus; Pulice, Sergio Mantovani Paiva; Zuca, Nadia Lucia; Roquetti, Daniel Rondinelli; Beduschi, Liviam Elizabeth Cordeiro; Praia, Amanda Salles; Okamoto, Claudia Parucce Franco; da Silva Carvalhaes, Vinicius Leite; Branco, Evandro Albiach; Barbezani, Bruna; Labandera, Emily; Timpe, Kelsie; Kaplan, David

2016-08-30

Recognized as one of the world's most vital natural and cultural resources, the Amazon faces a wide variety of threats from natural resource and infrastructure development. Within this context, rigorous scientific study of the region's complex social-ecological system is critical to inform and direct decision-making toward more sustainable environmental and social outcomes. Given the Amazon's tightly linked social and ecological components and the scope of potential development impacts, effective study of this system requires an easily accessible resource that provides a broad and reliable data baseline. This paper brings together multiple datasets from diverse disciplines (including human health, socio-economics, environment, hydrology, and energy) to provide investigators with a variety of baseline data to explore the multiple long-term effects of infrastructure development in the Brazilian Amazon.

A social-ecological database to advance research on infrastructure development impacts in the Brazilian Amazon

PubMed Central

Tucker Lima, Joanna M.; Valle, Denis; Moretto, Evandro Mateus; Pulice, Sergio Mantovani Paiva; Zuca, Nadia Lucia; Roquetti, Daniel Rondinelli; Beduschi, Liviam Elizabeth Cordeiro; Praia, Amanda Salles; Okamoto, Claudia Parucce Franco; da Silva Carvalhaes, Vinicius Leite; Branco, Evandro Albiach; Barbezani, Bruna; Labandera, Emily; Timpe, Kelsie; Kaplan, David

2016-01-01

Recognized as one of the world’s most vital natural and cultural resources, the Amazon faces a wide variety of threats from natural resource and infrastructure development. Within this context, rigorous scientific study of the region’s complex social-ecological system is critical to inform and direct decision-making toward more sustainable environmental and social outcomes. Given the Amazon’s tightly linked social and ecological components and the scope of potential development impacts, effective study of this system requires an easily accessible resource that provides a broad and reliable data baseline. This paper brings together multiple datasets from diverse disciplines (including human health, socio-economics, environment, hydrology, and energy) to provide investigators with a variety of baseline data to explore the multiple long-term effects of infrastructure development in the Brazilian Amazon. PMID:27575915

Databases, Repositories and Other Data Resources in Structural Biology

PubMed Central

Zheng, Heping; Porebski, Przemyslaw J.; Grabowski, Marek; Cooper, David R.; Minor, Wladek

2017-01-01

Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and “meta” data with a high demand on data storage and manipulations. Primary data comes from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of existing biomedical studies. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) “Databases” and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, and be integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive “hubs” or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors. PMID:28573593

NCI at Frederick Scientific Library Reintroduces Scientific Publications Database | Poster

Cancer.gov

A 20-year-old database of scientific publications by NCI at Frederick, FNLCR, and affiliated employees has gotten a significant facelift. Maintained by the Scientific Library, the redesigned database—which is linked from each of the Scientific Library’s web pages—offers features that were not available in previous versions, such as additional search limits and non-traditional

The National Deep-Sea Coral and Sponge Database: A Comprehensive Resource for United States Deep-Sea Coral and Sponge Records

NASA Astrophysics Data System (ADS)

Dornback, M.; Hourigan, T.; Etnoyer, P.; McGuinn, R.; Cross, S. L.

2014-12-01

Research on deep-sea corals has expanded rapidly over the last two decades, as scientists began to realize their value as long-lived structural components of high biodiversity habitats and archives of environmental information. The NOAA Deep Sea Coral Research and Technology Program's National Database for Deep-Sea Corals and Sponges is a comprehensive resource for georeferenced data on these organisms in U.S. waters. The National Database currently includes more than 220,000 deep-sea coral records representing approximately 880 unique species. Database records from museum archives, commercial and scientific bycatch, and from journal publications provide baseline information with relatively coarse spatial resolution dating back as far as 1842. These data are complemented by modern, in-situ submersible observations with high spatial resolution, from surveys conducted by NOAA and NOAA partners. Management of high volumes of modern high-resolution observational data can be challenging. NOAA is working with our data partners to incorporate this occurrence data into the National Database, along with images and associated information related to geoposition, time, biology, taxonomy, environment, provenance, and accuracy. NOAA is also working to link associated datasets collected by our program's research, to properly archive them to the NOAA National Data Centers, to build a robust metadata record, and to establish a standard protocol to simplify the process. Access to the National Database is provided through an online mapping portal. The map displays point based records from the database. Records can be refined by taxon, region, time, and depth. The queries and extent used to view the map can also be used to download subsets of the database. The database, map, and website is already in use by NOAA, regional fishery management councils, and regional ocean planning bodies, but we envision it as a model that can expand to accommodate data on a global scale.

The Earth Science Women's Network (ESWN): A member-driven network approach to supporting women in the Geosciences

NASA Astrophysics Data System (ADS)

Hastings, M. G.; Kontak, R.; Adams, A. S.; Barnes, R. T.; Fischer, E. V.; Glessmer, M. S.; Holloway, T.; Marin-Spiotta, E.; Rodriguez, C.; Steiner, A. L.; Wiedinmyer, C.; Laursen, S. L.

2013-12-01

The Earth Science Women's Network (ESWN) is an organization of women geoscientists, many in the early stages of their careers. The mission of ESWN is to promote success in scientific careers by facilitating career development, community, informal mentoring and support, and professional collaborations. ESWN currently connects nearly 2000 women across the globe, and includes graduate students, postdoctoral scientists, tenure and non-tenure track faculty from diverse colleges and universities, program managers, and government, non-government and industry researchers. In 2009, ESWN received an NSF ADVANCE PAID award, with the primary goals to grow our membership to serve a wider section of the geosciences community, to design and administer career development workshops, to promote professional networking at scientific conferences, and to develop web resources to build connections, collaborations, and peer mentoring for and among women in the Earth Sciences. Now at the end of the grant, ESWN members have reported gains in a number of aspects of their personal and professional lives including: knowledge about career resources; a greater understanding of the challenges facing women in science and resources to overcome them; a sense of community and less isolation; greater confidence in their own career trajectories; professional collaborations; emotional support on a variety of issues; and greater engagement and retention in scientific careers. The new ESWN web center (www.ESWNonline.org), a major development supported by NSF ADVANCE and AGU, was created to facilitate communication and networking among our members. The web center offers a state-of-the-art social networking platform and features: 1) a public site offering information on ESWN, career resources for all early career scientists, and a 'members' spotlight' highlighting members' scientific and professional achievements; and 2) a password protected member area where users can personalize profiles, create and respond to discussions, and connect with other members. The new member area's archive of discussions and member database are searchable, providing better tools for targeted networking and collaboration.

Evaluation of HIV/AIDS prevention resources in Liberia: strategy and implications.

PubMed

Kennedy, Stephen B; Johnson, Knowlton; Harris, Albert O; Lincoln, Adams; Neace, William; Collins, David

2004-03-01

The purpose of this preliminary study was to assess the HIV/AIDS prevention needs, services, and resources in Liberia, including the readiness of local providers to conduct HIV/AIDS-related prevention programs based on a set of six key dimensions (prevention needs, knowledge, leadership, environment, risky behaviors, and resources). A valid self-administered qualitative-based health survey, based on a community readiness model, was utilized as the primary data collection source. A cross-sectional design that utilized a convenient sample of key informants such as health coordinators, program directors, and health administrator from both public and private HIV/AIDS-based organizations was used. Furthermore, an extensive review of the National Library of Medicine database of published articles from mid-1980 to 2002 was simultaneously conducted to gauge the extent of scientific publications on HIV/AIDS-related prevention services in Liberia. The findings from this study strongly suggest that Liberia is in a stage of vague awareness, as defined by the Tri-Ethnic Center community readiness framework, regarding HIV/AIDS-related activities, including a significant lack of HIV/AIDS-related resources and scientific publications. Accordingly, there is a critical need to acquire adequate resources and build capacity to implement effective HIV/AIDS-related prevention programming services in order to avert the negative public health consequences associated with HIV/AIDS, including the implementation of relevant evaluation and dissemination strategies. Most importantly, this model has the potential to be utilized in other resource-constraint settings, especially in the developing world, to assess prevention-related resources and programmatic readiness. This is the first published study to evaluate Liberia's HIV/AIDS prevention resources and to systematically document the extent and magnitude of the HIV/AIDS crises in the country.

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

Interoperability of GADU in using heterogeneous Grid resources for bioinformatics applications.

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

Sulakhe, D.; Rodriguez, A.; Wilde, M.

2008-03-01

Bioinformatics tools used for efficient and computationally intensive analysis of genetic sequences require large-scale computational resources to accommodate the growing data. Grid computational resources such as the Open Science Grid and TeraGrid have proved useful for scientific discovery. The genome analysis and database update system (GADU) is a high-throughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications. This paper describes the requirements for building an automated scalable system such as GADU that can run jobs on different Grids. The paper describes the resource-independent configuration of GADU using the Pegasus-based virtual datamore » system that makes high-throughput computational tools interoperable on heterogeneous Grid resources. The paper also highlights the features implemented to make GADU a gateway to computationally intensive bioinformatics applications on the Grid. The paper will not go into the details of problems involved or the lessons learned in using individual Grid resources as it has already been published in our paper on genome analysis research environment (GNARE) and will focus primarily on the architecture that makes GADU resource independent and interoperable across heterogeneous Grid resources.« less

Trends in the production of scientific data analysis resources.

PubMed

Hennessey, Jason; Georgescu, Constantin; Wren, Jonathan D

2014-01-01

As the amount of scientific data grows, peer-reviewed Scientific Data Analysis Resources (SDARs) such as published software programs, databases and web servers have had a strong impact on the productivity of scientific research. SDARs are typically linked to using an Internet URL, which have been shown to decay in a time-dependent fashion. What is less clear is whether or not SDAR-producing group size or prior experience in SDAR production correlates with SDAR persistence or whether certain institutions or regions account for a disproportionate number of peer-reviewed resources. We first quantified the current availability of over 26,000 unique URLs published in MEDLINE abstracts/titles over the past 20 years, then extracted authorship, institutional and ZIP code data. We estimated which URLs were SDARs by using keyword proximity analysis. We identified 23,820 non-archival URLs produced between 1996 and 2013, out of which 11,977 were classified as SDARs. Production of SDARs as measured with the Gini coefficient is more widely distributed among institutions (.62) and ZIP codes (.65) than scientific research in general, which tends to be disproportionately clustered within elite institutions (.91) and ZIPs (.96). An estimated one percent of institutions produced 68% of published research whereas the top 1% only accounted for 16% of SDARs. Some labs produced many SDARs (maximum detected = 64), but 74% of SDAR-producing authors have only published one SDAR. Interestingly, decayed SDARs have significantly fewer average authors (4.33 +/- 3.06), than available SDARs (4.88 +/- 3.59) (p < 8.32 × 10-4). Approximately 3.4% of URLs, as published, contain errors in their entry/format, including DOIs and links to clinical trials registry numbers. SDAR production is less dependent upon institutional location and resources, and SDAR online persistence does not seem to be a function of infrastructure or expertise. Yet, SDAR team size correlates positively with SDAR accessibility, suggesting a possible sociological factor involved. While a detectable URL entry error rate of 3.4% is relatively low, it raises the question of whether or not this is a general error rate that extends to additional published entities.

Internet Portal For A Distributed Management of Groundwater

NASA Astrophysics Data System (ADS)

Meissner, U. F.; Rueppel, U.; Gutzke, T.; Seewald, G.; Petersen, M.

The management of groundwater resources for the supply of German cities and sub- urban areas has become a matter of public interest during the last years. Negative headlines in the Rhein-Main-Area dealt with cracks in buildings as well as damaged woodlands and inundated agriculture areas as an effect of varying groundwater levels. Usually a holistic management of groundwater resources is not existent because of the complexity of the geological system, the large number of involved groups and their divergent interests and a lack of essential information. The development of a network- based information system for an efficient groundwater management was the target of the project: ?Grundwasser-Online?[1]. The management of groundwater resources has to take into account various hydro- geological, climatic, water-economical, chemical and biological interrelations [2]. Thus, the traditional approaches in information retrieval, which are characterised by a high personnel and time expenditure, are not sufficient. Furthermore, the efficient control of the groundwater cultivation requires a direct communication between the different water supply companies, the consultant engineers, the scientists, the govern- mental agencies and the public, by using computer networks. The presented groundwater information system consists of different components, especially for the collection, storage, evaluation and visualisation of groundwater- relevant information. Network-based technologies are used [3]. For the collection of time-dependant groundwater-relevant information, modern technologies of Mobile Computing have been analysed in order to provide an integrated approach in the man- agement of large groundwater systems. The aggregated information is stored within a distributed geo-scientific database system which enables a direct integration of simu- lation programs for the evaluation of interactions in groundwater systems. Thus, even a prognosis for the evolution of groundwater states can be given. In order to gener- ate reports automatically, technologies are utilised. The visualisation of geo-scientific databases in the internet considering their geographic reference is performed with internet map servers. According to the communication of the map server with the un- derlying geo-scientific database, it is necessary that the demanded data can be filtered interactively in the internet browser using chronological and logical criteria. With re- gard to public use the security aspects within the described distributed system are of 1 major importance. Therefore, security methods for the modelling of access rights in combination with digital signatures have been analysed and implemented in order to provide a secure data exchange and communication between the different partners in the network 2

Geology, Geochemistry, Geophysics, Mineral Occurrences and Mineral Resource Assessment for the Commonwealth of Puerto Rico

USGS Publications Warehouse

Bawiec, Walter J.

1998-01-01

The Commonwealth of Puerto Rico has been investigated over a very long period of time by earth scientists from many disciplines and with diverse objectives in the studies. This publication attempts to apply much of the geologic, geochemical, geophysical, and mineral occurrence information to a single objective focused on producing a mineral resource assessment for the Commonwealth of Puerto Rico. However, the value of this publication lies not within the results of the mineral resource assessment nor within the interactive PDF files which can be viewed on the screen, but within the geologic, geochemical, geophysical, and mineral occurrence digital map coverages and databases which can be used for their own unique applications. The mineral resource assessment of Puerto Rico represents compilation of several decades of mineral investigations and studies. These investigations have been the joint efforts of the U.S. Geological Survey, the Puerto Rico Department of Natural Resources, and the University of Puerto Rico. This report contains not only the mineral-resource assessment, but also much of the scientific evidence upon which the assessment was based.

Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge.

PubMed

Ningthoujam, Sanjoy Singh; Talukdar, Anupam Das; Potsangbam, Kumar Singh; Choudhury, Manabendra Dutta

2012-05-07

Major research contributions in ethnopharmacology have generated vast amount of data associated with medicinal plants. Computerized databases facilitate data management and analysis making coherent information available to researchers, planners and other users. Web-based databases also facilitate knowledge transmission and feed the circle of information exchange between the ethnopharmacological studies and public audience. However, despite the development of many medicinal plant databases, a lack of uniformity is still discernible. Therefore, it calls for defining a common standard to achieve the common objectives of ethnopharmacology. The aim of the study is to review the diversity of approaches in storing ethnopharmacological information in databases and to provide some minimal standards for these databases. Survey for articles on medicinal plant databases was done on the Internet by using selective keywords. Grey literatures and printed materials were also searched for information. Listed resources were critically analyzed for their approaches in content type, focus area and software technology. Necessity for rapid incorporation of traditional knowledge by compiling primary data has been felt. While citation collection is common approach for information compilation, it could not fully assimilate local literatures which reflect traditional knowledge. Need for defining standards for systematic evaluation, checking quality and authenticity of the data is felt. Databases focussing on thematic areas, viz., traditional medicine system, regional aspect, disease and phytochemical information are analyzed. Issues pertaining to data standard, data linking and unique identification need to be addressed in addition to general issues like lack of update and sustainability. In the background of the present study, suggestions have been made on some minimum standards for development of medicinal plant database. In spite of variations in approaches, existence of many overlapping features indicates redundancy of resources and efforts. As the development of global data in a single database may not be possible in view of the culture-specific differences, efforts can be given to specific regional areas. Existing scenario calls for collaborative approach for defining a common standard in medicinal plant database for knowledge sharing and scientific advancement. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

PubMed Central

Engel, Stacia R.; Cherry, J. Michael

2013-01-01

The first completed eukaryotic genome sequence was that of the yeast Saccharomyces cerevisiae, and the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the original model organism database. SGD remains the authoritative community resource for the S. cerevisiae reference genome sequence and its annotation, and continues to provide comprehensive biological information correlated with S. cerevisiae genes and their products. A diverse set of yeast strains have been sequenced to explore commercial and laboratory applications, and a brief history of those strains is provided. The publication of these new genomes has motivated the creation of new tools, and SGD will annotate and provide comparative analyses of these sequences, correlating changes with variations in strain phenotypes and protein function. We are entering a new era at SGD, as we incorporate these new sequences and make them accessible to the scientific community, all in an effort to continue in our mission of educating researchers and facilitating discovery. Database URL: http://www.yeastgenome.org/ PMID:23487186

The Cambridge Structural Database

PubMed Central

Groom, Colin R.; Bruno, Ian J.; Lightfoot, Matthew P.; Ward, Suzanna C.

2016-01-01

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface. PMID:27048719

The Cambridge Structural Database.

PubMed

Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

2016-04-01

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

LiverAtlas: a unique integrated knowledge database for systems-level research of liver and hepatic disease.

PubMed

Zhang, Yanqiong; Yang, Chunyuan; Wang, Shaochuang; Chen, Tao; Li, Mansheng; Wang, Xue; Li, Dongsheng; Wang, Kang; Ma, Jie; Wu, Songfeng; Zhang, Xueli; Zhu, Yunping; Wu, Jinsheng; He, Fuchu

2013-09-01

A large amount of liver-related physiological and pathological data exist in publicly available biological and bibliographic databases, which are usually far from comprehensive or integrated. Data collection, integration and mining processes pose a great challenge to scientific researchers and clinicians interested in the liver. To address these problems, we constructed LiverAtlas (http://liveratlas.hupo.org.cn), a comprehensive resource of biomedical knowledge related to the liver and various hepatic diseases by incorporating 53 databases. In the present version, LiverAtlas covers data on liver-related genomics, transcriptomics, proteomics, metabolomics and hepatic diseases. Additionally, LiverAtlas provides a wealth of manually curated information, relevant literature citations and cross-references to other databases. Importantly, an expert-confirmed Human Liver Disease Ontology, including relevant information for 227 types of hepatic disease, has been constructed and is used to annotate LiverAtlas data. Furthermore, we have demonstrated two examples of applying LiverAtlas data to identify candidate markers for hepatocellular carcinoma (HCC) at the systems level and to develop a systems biology-based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC differential diagnosis. LiverAtlas is the most comprehensive liver and hepatic disease resource, which helps biologists and clinicians to analyse their data at the systems level and will contribute much to the biomarker discovery and diagnostic performance enhancement for liver diseases. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Measuring the evolution and output of cross-disciplinary collaborations within the NCI Physical Sciences-Oncology Centers Network.

PubMed

Basner, Jodi E; Theisz, Katrina I; Jensen, Unni S; Jones, C David; Ponomarev, Ilya; Sulima, Pawel; Jo, Karen; Eljanne, Mariam; Espey, Michael G; Franca-Koh, Jonathan; Hanlon, Sean E; Kuhn, Nastaran Z; Nagahara, Larry A; Schnell, Joshua D; Moore, Nicole M

2013-12-01

Development of effective quantitative indicators and methodologies to assess the outcomes of cross-disciplinary collaborative initiatives has the potential to improve scientific program management and scientific output. This article highlights an example of a prospective evaluation that has been developed to monitor and improve progress of the National Cancer Institute Physical Sciences-Oncology Centers (PS-OC) program. Study data, including collaboration information, was captured through progress reports and compiled using the web-based analytic database: Interdisciplinary Team Reporting, Analysis, and Query Resource. Analysis of collaborations was further supported by data from the Thomson Reuters Web of Science database, MEDLINE database, and a web-based survey. Integration of novel and standard data sources was augmented by the development of automated methods to mine investigator pre-award publications, assign investigator disciplines, and distinguish cross-disciplinary publication content. The results highlight increases in cross-disciplinary authorship collaborations from pre- to post-award years among the primary investigators and confirm that a majority of cross-disciplinary collaborations have resulted in publications with cross-disciplinary content that rank in the top third of their field. With these evaluation data, PS-OC Program officials have provided ongoing feedback to participating investigators to improve center productivity and thereby facilitate a more successful initiative. Future analysis will continue to expand these methods and metrics to adapt to new advances in research evaluation and changes in the program.

The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Wiegers, Thomas C.; Murphy, Cynthia G.; Mattingly, Carolyn J.

2011-01-01

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators read the scientific literature and convert free-text information into a structured format using official nomenclature, integrating third party controlled vocabularies for chemicals, genes, diseases and organisms, and a novel controlled vocabulary for molecular interactions. Manual curation produces a robust, richly annotated dataset of highly accurate and detailed information. Currently, CTD describes over 349 000 molecular interactions between 6800 chemicals, 20 900 genes (for 330 organisms) and 4300 diseases that have been manually curated from over 25 400 peer-reviewed articles. This manually curated data are further integrated with other third party data (e.g. Gene Ontology, KEGG and Reactome annotations) to generate a wealth of toxicogenomic relationships. Here, we describe our approach to manual curation that uses a powerful and efficient paradigm involving mnemonic codes. This strategy allows biocurators to quickly capture detailed information from articles by generating simple statements using codes to represent the relationships between data types. The paradigm is versatile, expandable, and able to accommodate new data challenges that arise. We have incorporated this strategy into a web-based curation tool to further increase efficiency and productivity, implement quality control in real-time and accommodate biocurators working remotely. Database URL: http://ctd.mdibl.org PMID:21933848

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.

Making your database available through Wikipedia: the pros and cons.

PubMed

Finn, Robert D; Gardner, Paul P; Bateman, Alex

2012-01-01

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore.

PubMed

Ren, Jian; Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

2010-01-01

During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0).

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore

PubMed Central

Liu, Zexian; Gao, Xinjiao; Jin, Changjiang; Ye, Mingliang; Zou, Hanfa; Wen, Longping; Zhang, Zhaolei; Xue, Yu; Yao, Xuebiao

2010-01-01

During cell division/mitosis, a specific subset of proteins is spatially and temporally assembled into protein super complexes in three distinct regions, i.e. centrosome/spindle pole, kinetochore/centromere and midbody/cleavage furrow/phragmoplast/bud neck, and modulates cell division process faithfully. Although many experimental efforts have been carried out to investigate the characteristics of these proteins, no integrated database was available. Here, we present the MiCroKit database (http://microkit.biocuckoo.org) of proteins that localize in midbody, centrosome and/or kinetochore. We collected into the MiCroKit database experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. The current version of MiCroKit 3.0 provides detailed information for 1489 microkit proteins from seven model organisms, including Saccharomyces cerevisiae, Schizasaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, Mus musculus and Homo sapiens. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification. The online service of MiCroKit database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). PMID:19783819

Making your database available through Wikipedia: the pros and cons

PubMed Central

Finn, Robert D.; Gardner, Paul P.; Bateman, Alex

2012-01-01

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis. PMID:22144683

The international phosphate resource data base; development and maintenance

USGS Publications Warehouse

Bridges, Nancy J.

1983-01-01

The IPRDB (International Phosphate Resource Data Base) was developed to provide a single computerized source of geologic information about phosphate deposits worldwide. It is expected that this data base will encourage more thorough scientific analyses of phosphate deposits and assessments of undiscovered phosphate resources, and that methods of data collection and storage will be streamlined. Because the database was intended to serve as a repository for diverse and detailed data, a large amount of the early research effort was devoted to the design and development of the system. To date (1982), the file remains incomplete. All development work and file maintenance work on IPRDB was suspended as of October 1, 1982; this paper is intended to document the steps taken up to that date. The computer programs listed in the appendices were written specifically for the IPRDB phosbib file and are of limited future use.

Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R21 | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

Secondary Analysis and Integration of Existing Data to Elucidate the Genetic Architecture of Cancer Risk and Related Outcomes, R01 | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

This funding opportunity announcement (FOA) encourages applications that propose to conduct secondary data analysis and integration of existing datasets and database resources, with the ultimate aim to elucidate the genetic architecture of cancer risk and related outcomes. The goal of this initiative is to address key scientific questions relevant to cancer epidemiology by supporting the analysis of existing genetic or genomic datasets, possibly in combination with environmental, outcomes, behavioral, lifestyle, and molecular profiles data.

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.

PubMed

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bansal, Parit; Bridge, Alan J; Poux, Sylvain; Bougueleret, Lydie; Xenarios, Ioannis

2016-01-01

The Universal Protein Resource (UniProt, http://www.uniprot.org ) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.

Modernization and unification: Strategic goals for NASA STI program

NASA Technical Reports Server (NTRS)

Blados, W.; Cotter, Gladys A.

1993-01-01

Information is increasingly becoming a strategic resource in all societies and economies. The NASA Scientific and Technical Information (STI) Program has initiated a modernization program to address the strategic importance and changing characteristics of information. This modernization effort applies new technology to current processes to provide near-term benefits to the user. At the same time, we are developing a long-term modernization strategy designed to transition the program to a multimedia, global 'library without walls.' Notwithstanding this modernization program, it is recognized that no one information center can hope to collect all the relevant data. We see information and information systems changing and becoming more international in scope. We are finding that many nations are expending resources on national systems which duplicate each other. At the same time that this duplication exists, many useful sources of aerospace information are not being collected because of resource limitations. If nations cooperate to develop an international aerospace information system, resources can be used efficiently to cover expanded sources of information. We must consider forming a coalition to collect and provide access to disparate, multidisciplinary sources of information, and to develop standardized tools for documenting and manipulating this data and information. In view of recent technological developments in information science and technology, as well as the reality of scarce resources in all nations, it is time to explore the mutually beneficial possibilities offered by cooperation and international resource sharing. International resources need to be mobilized in a coordinated manner to move us towards this goal. This paper reviews the NASA modernization program and raises for consideration new possibilities for unification of the various aerospace database efforts toward a cooperative international aerospace database initiative that can optimize the cost/benefit equation for all participants.

ETDEWEB versus the World-Wide-Web: a specific database/web comparison

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

Cutler, Debbie

2010-06-28

A study was performed comparing user search results from the specialized scientific database on energy-related information, ETDEWEB, with search results from the internet search engines Google and Google Scholar. The primary objective of the study was to determine if ETDEWEB (the Energy Technology Data Exchange – World Energy Base) continues to bring the user search results that are not being found by Google and Google Scholar. As a multilateral information exchange initiative, ETDE’s member countries and partners contribute cost- and task-sharing resources to build the largest database of energy-related information in the world. As of early 2010, the ETDEWEB databasemore » has 4.3 million citations to world-wide energy literature. One of ETDEWEB’s strengths is its focused scientific content and direct access to full text for its grey literature (over 300,000 documents in PDF available for viewing from the ETDE site and over a million additional links to where the documents can be found at research organizations and major publishers globally). Google and Google Scholar are well-known for the wide breadth of the information they search, with Google bringing in news, factual and opinion-related information, and Google Scholar also emphasizing scientific content across many disciplines. The analysis compared the results of 15 energy-related queries performed on all three systems using identical words/phrases. A variety of subjects was chosen, although the topics were mostly in renewable energy areas due to broad international interest. Over 40,000 search result records from the three sources were evaluated. The study concluded that ETDEWEB is a significant resource to energy experts for discovering relevant energy information. For the 15 topics in this study, ETDEWEB was shown to bring the user unique results not shown by Google or Google Scholar 86.7% of the time. Much was learned from the study beyond just metric comparisons. Observations about the strengths of each system and factors impacting the search results are also shared along with background information and summary tables of the results. If a user knows a very specific title of a document, all three systems are helpful in finding the user a source for the document. But if the user is looking to discover relevant documents on a specific topic, each of the three systems will bring back a considerable volume of data, but quite different in focus. Google is certainly a highly-used and valuable tool to find significant ‘non-specialist’ information, and Google Scholar does help the user focus on scientific disciplines. But if a user’s interest is scientific and energy-specific, ETDEWEB continues to hold a strong position in the energy research, technology and development (RTD) information field and adds considerable value in knowledge discovery. (auth)« less

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.

PubMed

Bandrowski, A E; Cachat, J; Li, Y; Müller, H M; Sternberg, P W; Ciccarese, P; Clark, T; Marenco, L; Wang, R; Astakhov, V; Grethe, J S; Martone, M E

2012-01-01

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is 'hidden' from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community. DATABASE URL: http://neuinfo.org.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

PubMed Central

Bandrowski, A. E.; Cachat, J.; Li, Y.; Müller, H. M.; Sternberg, P. W.; Ciccarese, P.; Clark, T.; Marenco, L.; Wang, R.; Astakhov, V.; Grethe, J. S.; Martone, M. E.

2012-01-01

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is ‘hidden’ from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community. Database URL: http://neuinfo.org PMID:22434839

Anatomical entity mention recognition at literature scale

PubMed Central

Pyysalo, Sampo; Ananiadou, Sophia

2014-01-01

Motivation: Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to understanding the scientific literature. Despite extensive efforts to automatically analyze various aspects of biomedical text, there have been only few studies focusing on anatomical entities, and no dedicated methods for learning to automatically recognize anatomical entity mentions in free-form text have been introduced. Results: We present AnatomyTagger, a machine learning-based system for anatomical entity mention recognition. The system incorporates a broad array of approaches proposed to benefit tagging, including the use of Unified Medical Language System (UMLS)- and Open Biomedical Ontologies (OBO)-based lexical resources, word representations induced from unlabeled text, statistical truecasing and non-local features. We train and evaluate the system on a newly introduced corpus that substantially extends on previously available resources, and apply the resulting tagger to automatically annotate the entire open access scientific domain literature. The resulting analyses have been applied to extend services provided by the Europe PubMed Central literature database. Availability and implementation: All tools and resources introduced in this work are available from http://nactem.ac.uk/anatomytagger. Contact: sophia.ananiadou@manchester.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24162468

Research resources: curating the new eagle-i discovery system

PubMed Central

Vasilevsky, Nicole; Johnson, Tenille; Corday, Karen; Torniai, Carlo; Brush, Matthew; Segerdell, Erik; Wilson, Melanie; Shaffer, Chris; Robinson, David; Haendel, Melissa

2012-01-01

Development of biocuration processes and guidelines for new data types or projects is a challenging task. Each project finds its way toward defining annotation standards and ensuring data consistency with varying degrees of planning and different tools to support and/or report on consistency. Further, this process may be data type specific even within the context of a single project. This article describes our experiences with eagle-i, a 2-year pilot project to develop a federated network of data repositories in which unpublished, unshared or otherwise ‘invisible’ scientific resources could be inventoried and made accessible to the scientific community. During the course of eagle-i development, the main challenges we experienced related to the difficulty of collecting and curating data while the system and the data model were simultaneously built, and a deficiency and diversity of data management strategies in the laboratories from which the source data was obtained. We discuss our approach to biocuration and the importance of improving information management strategies to the research process, specifically with regard to the inventorying and usage of research resources. Finally, we highlight the commonalities and differences between eagle-i and similar efforts with the hope that our lessons learned will assist other biocuration endeavors. Database URL: www.eagle-i.net PMID:22434835

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

PubMed

Williams, Eleanor; Moore, Josh; Li, Simon W; Rustici, Gabriella; Tarkowska, Aleksandra; Chessel, Anatole; Leo, Simone; Antal, Bálint; Ferguson, Richard K; Sarkans, Ugis; Brazma, Alvis; Salas, Rafael E Carazo; Swedlow, Jason R

2017-08-01

Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links data from several imaging modalities, including high-content screening, super-resolution and time-lapse microscopy, digital pathology, public genetic or chemical databases, and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.

Exploration of options for publishing databases and supplemental material in society journals

USDA-ARS?s Scientific Manuscript database

As scientific information becomes increasingly more abundant, there is increasing interest among members of our societies to share databases. These databases have great value, for example, in providing long-term perspectives of various scientific problems and for use by modelers to extend the inform...

[Presence of the biomedical periodicals of Hungarian editions in international databases].

PubMed

Vasas, Lívia; Hercsel, Imréné

2006-01-15

Presence of the biomedical periodicals of Hungarian editions in international databases. The majority of Hungarian scientific results in medical and related sciences are published in scientific periodicals of foreign edition with high impact factor (IF) values, and they appear in international scientific literature in foreign languages. In this study the authors dealt with the presence and registered citation in international databases of those periodicals only, which had been published in Hungary and/or in cooperation with foreign publishing companies. The examination went back to year 1980 and covered a 25-year long period. 110 periodicals were selected for more detailed examination. The authors analyzed the situation of the current periodicals in the three most often visited databases (MEDLINE, EMBASE, Web of Science), and discovered, that the biomedical scientific periodicals of Hungarian interests were not represented with reasonable emphasis in the relevant international bibliographic databases. Because of the great number of data the scientific literature of medicine and related sciences could not be represented in its entirety, this publication, however, might give useful information for the inquirers, and call the attention of the competent people.

Tox-Database.net: a curated resource for data describing chemical triggered in vitro cardiac ion channels inhibition

PubMed Central

2012-01-01

Background Drugs safety issues are now recognized as being factors generating the most reasons for drug withdrawals at various levels of development and at the post-approval stage. Among them cardiotoxicity remains the main reason, despite the substantial effort put into in vitro and in vivo testing, with the main focus put on hERG channel inhibition as the hypothesized surrogate of drug proarrhythmic potency. The large interest in the IKr current has resulted in the development of predictive tools and informative databases describing a drug's susceptibility to interactions with the hERG channel, although there are no similar, publicly available sets of data describing other ionic currents driven by the human cardiomyocyte ionic channels, which are recognized as an overlooked drug safety target. Discussion The aim of this database development and publication was to provide a scientifically useful, easily usable and clearly verifiable set of information describing not only IKr (hERG), but also other human cardiomyocyte specific ionic channels inhibition data (IKs, INa, ICa). Summary The broad range of data (chemical space and in vitro settings) and the easy to use user interface makes tox-database.net a useful tool for interested scientists. Database URL http://tox-database.net. PMID:22947121

GANSEKI: JAMSTEC Deep Seafloor Rock Sample Database Emerging to the New Phase

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Ichiyama, Y.; Horikawa, H.; Sato, Y.; Soma, S.; Hanafusa, Y.

2013-12-01

Japan Agency for Marine-Earth Science and Technology (JAMSTEC) collects a lot of substantial samples as well as various geophysical data using its research vessels and submersibles. These samples and data, which are obtained by spending large amounts of human and physical resources, are precious wealth of the world scientific community. For the better use of these samples and data, it is important that they are utilized not only for initial purpose of each cruse but also for other general scientific and educational purposes of second-hand users. Based on the JAMSTEC data and sample handling policies [1], JAMSTEC has systematically stored samples and data obtained during research cruises, and provided them to domestic/foreign activities on research, education, and public relation. Being highly valued for second-hand usability, deep seafloor rock samples are one of the most important types of samples obtained by JAMSTEC, as oceanic biological samples and sediment core samples are. Rock samples can be utilized for natural history sciences and other various purposes; some of these purposes are connected to socially important issues such as earthquake mechanisms and mineral resource developments. Researchers and educators can access to JAMSTEC rock samples and associated data through 'GANSEKI [2]', the JAMSTEC Deep Seafloor Rock Sample Database. GANSEKI was established on the Internet in 2006 and its contents and functions have been continuously enriched and upgraded since then. GANSEKI currently provides 19 thousands of sample metadata, 9 thousands of collection inventory data and 18 thousands of geochemical data. Most of these samples are recovered from the North-western Pacific Ocean, although samples from other area are also included. The major update of GANSEKI held in May 2013 involved a replacement of database core system and a redesign of user interface. In the new GANSEKI, users can select samples easily and precisely using multi-index search, numerical constraints on geochemical data and thumbnail browsing of sample and thin-section photos. 'MyList' function allows users to organize, compare and download the data of selected samples. To develop a close network among online databases, the new GANSEKI allows multiple URL entries for individual samples. Now the curatorial staffs are working for maintaining references to other JAMSTEC databases such as 'DARWIN [3]' and 'J-EDI [4]'.

Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature.

PubMed

Ozyurt, Ibrahim Burak; Grethe, Jeffrey S; Martone, Maryann E; Bandrowski, Anita E

2016-01-01

The NIF Registry developed and maintained by the Neuroscience Information Framework is a cooperative project aimed at cataloging research resources, e.g., software tools, databases and tissue banks, funded largely by governments and available as tools to research scientists. Although originally conceived for neuroscience, the NIF Registry has over the years broadened in the scope to include research resources of general relevance to biomedical research. The current number of research resources listed by the Registry numbers over 13K. The broadening in scope to biomedical science led us to re-christen the NIF Registry platform as SciCrunch. The NIF/SciCrunch Registry has been cataloging the resource landscape since 2006; as such, it serves as a valuable dataset for tracking the breadth, fate and utilization of these resources. Our experience shows research resources like databases are dynamic objects, that can change location and scope over time. Although each record is entered manually and human-curated, the current size of the registry requires tools that can aid in curation efforts to keep content up to date, including when and where such resources are used. To address this challenge, we have developed an open source tool suite, collectively termed RDW: Resource Disambiguator for the (Web). RDW is designed to help in the upkeep and curation of the registry as well as in enhancing the content of the registry by automated extraction of resource candidates from the literature. The RDW toolkit includes a URL extractor from papers, resource candidate screen, resource URL change tracker, resource content change tracker. Curators access these tools via a web based user interface. Several strategies are used to optimize these tools, including supervised and unsupervised learning algorithms as well as statistical text analysis. The complete tool suite is used to enhance and maintain the resource registry as well as track the usage of individual resources through an innovative literature citation index honed for research resources. Here we present an overview of the Registry and show how the RDW tools are used in curation and usage tracking.

Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature

PubMed Central

Ozyurt, Ibrahim Burak; Grethe, Jeffrey S.; Martone, Maryann E.; Bandrowski, Anita E.

2016-01-01

The NIF Registry developed and maintained by the Neuroscience Information Framework is a cooperative project aimed at cataloging research resources, e.g., software tools, databases and tissue banks, funded largely by governments and available as tools to research scientists. Although originally conceived for neuroscience, the NIF Registry has over the years broadened in the scope to include research resources of general relevance to biomedical research. The current number of research resources listed by the Registry numbers over 13K. The broadening in scope to biomedical science led us to re-christen the NIF Registry platform as SciCrunch. The NIF/SciCrunch Registry has been cataloging the resource landscape since 2006; as such, it serves as a valuable dataset for tracking the breadth, fate and utilization of these resources. Our experience shows research resources like databases are dynamic objects, that can change location and scope over time. Although each record is entered manually and human-curated, the current size of the registry requires tools that can aid in curation efforts to keep content up to date, including when and where such resources are used. To address this challenge, we have developed an open source tool suite, collectively termed RDW: Resource Disambiguator for the (Web). RDW is designed to help in the upkeep and curation of the registry as well as in enhancing the content of the registry by automated extraction of resource candidates from the literature. The RDW toolkit includes a URL extractor from papers, resource candidate screen, resource URL change tracker, resource content change tracker. Curators access these tools via a web based user interface. Several strategies are used to optimize these tools, including supervised and unsupervised learning algorithms as well as statistical text analysis. The complete tool suite is used to enhance and maintain the resource registry as well as track the usage of individual resources through an innovative literature citation index honed for research resources. Here we present an overview of the Registry and show how the RDW tools are used in curation and usage tracking. PMID:26730820

Geochemical database of feed coal and coal combustion products (CCPs) from five power plants in the United States

USGS Publications Warehouse

Affolter, Ronald H.; Groves, Steve; Betterton, William J.; William, Benzel; Conrad, Kelly L.; Swanson, Sharon M.; Ruppert, Leslie F.; Clough, James G.; Belkin, Harvey E.; Kolker, Allan; Hower, James C.

2011-01-01

The principal mission of the U.S. Geological Survey (USGS) Energy Resources Program (ERP) is to (1) understand the processes critical to the formation, accumulation, occurrence, and alteration of geologically based energy resources; (2) conduct scientifically robust assessments of those resources; and (3) study the impacts of energy resource occurrence and (or) their production and use on both the environment and human health. The ERP promotes and supports research resulting in original, geology-based, non-biased energy information products for policy and decision makers, land and resource managers, other Federal and State agencies, the domestic energy industry, foreign governments, non-governmental groups, and academia. Investigations include research on the geology of oil, gas, and coal, and the impacts associated with energy resource occurrence, production, quality, and utilization. The ERP's focus on coal is to support investigations into current issues pertaining to coal production, beneficiation and (or) conversion, and the environmental impact of the coal combustion process and coal combustion products (CCPs). To accomplish these studies, the USGS combines its activities with other organizations to address domestic and international issues that relate to the development and use of energy resources.

Developing a Data Discovery Tool for Interdisciplinary Science: Leveraging a Web-based Mapping Application and Geosemantic Searching

NASA Astrophysics Data System (ADS)

Albeke, S. E.; Perkins, D. G.; Ewers, S. L.; Ewers, B. E.; Holbrook, W. S.; Miller, S. N.

2015-12-01

The sharing of data and results is paramount for advancing scientific research. The Wyoming Center for Environmental Hydrology and Geophysics (WyCEHG) is a multidisciplinary group that is driving scientific breakthroughs to help manage water resources in the Western United States. WyCEHG is mandated by the National Science Foundation (NSF) to share their data. However, the infrastructure from which to share such diverse, complex and massive amounts of data did not exist within the University of Wyoming. We developed an innovative framework to meet the data organization, sharing, and discovery requirements of WyCEHG by integrating both open and closed source software, embedded metadata tags, semantic web technologies, and a web-mapping application. The infrastructure uses a Relational Database Management System as the foundation, providing a versatile platform to store, organize, and query myriad datasets, taking advantage of both structured and unstructured formats. Detailed metadata are fundamental to the utility of datasets. We tag data with Uniform Resource Identifiers (URI's) to specify concepts with formal descriptions (i.e. semantic ontologies), thus allowing users the ability to search metadata based on the intended context rather than conventional keyword searches. Additionally, WyCEHG data are geographically referenced. Using the ArcGIS API for Javascript, we developed a web mapping application leveraging database-linked spatial data services, providing a means to visualize and spatially query available data in an intuitive map environment. Using server-side scripting (PHP), the mapping application, in conjunction with semantic search modules, dynamically communicates with the database and file system, providing access to available datasets. Our approach provides a flexible, comprehensive infrastructure from which to store and serve WyCEHG's highly diverse research-based data. This framework has not only allowed WyCEHG to meet its data stewardship requirements, but can provide a template for others to follow.

Comparison Study of Overlap among 21 Scientific Databases in Searching Pesticide Information.

ERIC Educational Resources Information Center

Meyer, Daniel E.; And Others

1983-01-01

Evaluates overlapping coverage of 21 scientific databases used in 10 online pesticide searches in an attempt to identify minimum number of databases needed to generate 90 percent of unique, relevant citations for given search. Comparison of searches combined under given pesticide usage (herbicide, fungicide, insecticide) is discussed. Nine…

Recent Developments of the GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Berthier, E.; Bolch, T.; Kargel, J. S.; Paul, F.; Racoviteanu, A.

2017-12-01

Earth's glaciers are shrinking almost without exception, leading to changes in water resources, timing of runoff, sea level, and hazard potential. Repeat mapping of glacier outlines, lakes, and glacier topography, along with glacial processes, is critically needed to understand how glaciers will react to a changing climate, and how those changes will impact humans. To understand the impacts and processes behind the observed changes, it is crucial to monitor glaciers through time by mapping their areal extent, snow lines, ice flow velocities, associated water bodies, and thickness changes. The glacier database of the Global Land Ice Measurements from Space (GLIMS) initiative is the only multi-temporal glacier database capable of tracking all these glacier measurements and providing them to the scientific community and broader public.Recent developments in GLIMS include improvements in the database and web applications and new activities in the international GLIMS community. The coverage of the GLIMS database has recently grown geographically and temporally by drawing on the Randolph Glacier Inventory (RGI) and other new data sets. The GLIMS database is globally complete, and approximately one third of glaciers have outlines from more than one time. New tools for visualizing and downloading GLIMS data in a choice of formats and data models have been developed, and a new data model for handling multiple glacier records through time while avoiding double-counting of glacier number or area is nearing completion. A GLIMS workshop was held in Boulder, Colorado this year to facilitate two-way communication with the greater community on future needs.The result of this work is a more complete and accurate glacier data repository that shows both the current state of glaciers on Earth and how they have changed in recent decades. Needs for future scientific and technical developments were identified and prioritized at the GLIMS Workshop, and are reported here.

An Overview of the Object Protocol Model (OPM) and the OPM Data Management Tools.

ERIC Educational Resources Information Center

Chen, I-Min A.; Markowitz, Victor M.

1995-01-01

Discussion of database management tools for scientific information focuses on the Object Protocol Model (OPM) and data management tools based on OPM. Topics include the need for new constructs for modeling scientific experiments, modeling object structures and experiments in OPM, queries and updates, and developing scientific database applications…

Importance of scientific resources among local public health practitioners.

PubMed

Fields, Robert P; Stamatakis, Katherine A; Duggan, Kathleen; Brownson, Ross C

2015-04-01

We examined the perceived importance of scientific resources for decision-making among local health department (LHD) practitioners in the United States. We used data from LHD practitioners (n = 849). Respondents ranked important decision-making resources, methods for learning about public health research, and academic journal use. We calculated descriptive statistics and used logistic regression to measure associations of individual and LHD characteristics with importance of scientific resources. Systematic reviews of scientific literature (24.7%) were most frequently ranked as important among scientific resources, followed by scientific reports (15.9%), general literature review articles (6.5%), and 1 or a few scientific studies (4.8%). Graduate-level education (adjusted odds ratios [AORs] = 1.7-3.5), larger LHD size (AORs = 2.0-3.5), and leadership support (AOR = 1.6; 95% confidence interval = 1.1, 2.3) were associated with a higher ranking of importance of scientific resources. Graduate training, larger LHD size, and leadership that supports a culture of evidence-based decision-making may increase the likelihood of practitioners viewing scientific resources as important. Targeting communication channels that practitioners view as important can also guide research dissemination strategies.

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

Nuclear Energy Infrastructure Database Description and User’s Manual

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

Heidrich, Brenden

In 2014, the Deputy Assistant Secretary for Science and Technology Innovation initiated the Nuclear Energy (NE)–Infrastructure Management Project by tasking the Nuclear Science User Facilities, formerly the Advanced Test Reactor National Scientific User Facility, to create a searchable and interactive database of all pertinent NE-supported and -related infrastructure. This database, known as the Nuclear Energy Infrastructure Database (NEID), is used for analyses to establish needs, redundancies, efficiencies, distributions, etc., to best understand the utility of NE’s infrastructure and inform the content of infrastructure calls. The Nuclear Science User Facilities developed the database by utilizing data and policy direction from amore » variety of reports from the U.S. Department of Energy, the National Research Council, the International Atomic Energy Agency, and various other federal and civilian resources. The NEID currently contains data on 802 research and development instruments housed in 377 facilities at 84 institutions in the United States and abroad. The effort to maintain and expand the database is ongoing. Detailed information on many facilities must be gathered from associated institutions and added to complete the database. The data must be validated and kept current to capture facility and instrumentation status as well as to cover new acquisitions and retirements. This document provides a short tutorial on the navigation of the NEID web portal at NSUF-Infrastructure.INL.gov.« less

Developing science gateways for drug discovery in a grid environment.

PubMed

Pérez-Sánchez, Horacio; Rezaei, Vahid; Mezhuyev, Vitaliy; Man, Duhu; Peña-García, Jorge; den-Haan, Helena; Gesing, Sandra

2016-01-01

Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources. To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

Editorial: Journal article reporting standards.

PubMed

Kazak, Anne E

2018-01-01

In this editorial, the author notes that this issue of American Psychologist features a pair of important articles related to newly updated standards for reporting research in psychology in scientific journals, covering both quantitative (Appelbaum et al., 2018) and qualitative (Levitt et al., 2018) research. The increasing breadth and complexity of research, and the importance of communicating it effectively, requires user-friendly resources that can be applied widely to scientific studies. These two articles are intended to serve that purpose, and to encourage thoroughness and accuracy in research reporting, for psychologists and other scientists in broader academic communities. The articles, known as the Journal Article Reporting Standards (JARS) reports, are based on the work of a task force appointed by the American Psychological Association (APA) Publications and Communications Board in 2015. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

IMGT, the international ImMunoGeneTics information system®

PubMed Central

Lefranc, Marie-Paule; Giudicelli, Véronique; Kaas, Quentin; Duprat, Elodie; Jabado-Michaloud, Joumana; Scaviner, Dominique; Ginestoux, Chantal; Clément, Oliver; Chaume, Denys; Lefranc, Gérard

2005-01-01

The international ImMunoGeneTics information system® (IMGT) (http://imgt.cines.fr), created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier II and CNRS) at Montpellier, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune systems (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT includes several sequence databases (IMGT/LIGM-DB, IMGT/PRIMER-DB, IMGT/PROTEIN-DB and IMGT/MHC-DB), one genome database (IMGT/GENE-DB) and one three-dimensional (3D) structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages (IMGT Marie-Paule page), and interactive tools. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow up of residual diseases) and therapeutical approaches (graft, immunotherapy and vaccinology). IMGT is freely available at http://imgt.cines.fr. PMID:15608269

Pathology as the enabler of human research.

PubMed

Crawford, James M; Tykocinski, Mark L

2005-09-01

Academic Pathology is a key player in human molecular science and in the powerful initiatives of the National Institutes of Health. Pathologists generate data crucial to virtually every molecular study of human tissue, and have the necessary skills and authority to oversee processing of human tissues for research analysis. We advocate that Academic Pathology is optimally positioned to drive the molecular revolution in study of human disease, through human tissue collection, analysis, and databasing. This can be achieved through playing a major role in human tissue procurement and management; establishing high-quality 'Pathology Resource Laboratories'; providing the scientific expertise for pathology data sharing; and recruiting and training physician scientists. Pathology should position itself to be the local institutional driver of technology implementation and development, by operating the resource laboratories, providing the expertise for technical and conceptual design of research projects, maintaining the databases that link molecular and morphological information on human tissues with the requisite clinical databases, providing education and mentorship of technology users, and nurturing new research through the development of preliminary data. We also consider that outstanding pathology journals are available for the publication of research emanating from such studies, to the benefit of the pathology profession as an academic enterprise. It is our earnest hope that Academic Pathology can play a leading role in the remarkable advances to be made as the 21st century unfolds.

Physicists Get INSPIREd: INSPIRE Project and Grid Applications

NASA Astrophysics Data System (ADS)

Klem, Jukka; Iwaszkiewicz, Jan

2011-12-01

INSPIRE is the new high-energy physics scientific information system developed by CERN, DESY, Fermilab and SLAC. INSPIRE combines the curated and trusted contents of SPIRES database with Invenio digital library technology. INSPIRE contains the entire HEP literature with about one million records and in addition to becoming the reference HEP scientific information platform, it aims to provide new kinds of data mining services and metrics to assess the impact of articles and authors. Grid and cloud computing provide new opportunities to offer better services in areas that require large CPU and storage resources including document Optical Character Recognition (OCR) processing, full-text indexing of articles and improved metrics. D4Science-II is a European project that develops and operates an e-Infrastructure supporting Virtual Research Environments (VREs). It develops an enabling technology (gCube) which implements a mechanism for facilitating the interoperation of its e-Infrastructure with other autonomously running data e-Infrastructures. As a result, this creates the core of an e-Infrastructure ecosystem. INSPIRE is one of the e-Infrastructures participating in D4Science-II project. In the context of the D4Science-II project, the INSPIRE e-Infrastructure makes available some of its resources and services to other members of the resulting ecosystem. Moreover, it benefits from the ecosystem via a dedicated Virtual Organization giving access to an array of resources ranging from computing and storage resources of grid infrastructures to data and services.

The Changing Face of Scientific Discourse: Analysis of Genomic and Proteomic Database Usage and Acceptance.

ERIC Educational Resources Information Center

Brown, Cecelia

2003-01-01

Discusses the growth in use and acceptance of Web-based genomic and proteomic databases (GPD) in scholarly communication. Confirms the role of GPD in the scientific literature cycle, suggests GPD are a storage and retrieval mechanism for molecular biology information, and recommends that existing models of scientific communication be updated to…

Prairie Resources

Science.gov Websites

Search Prairie Resources for Students Plant Database Plant Database Butterfly Info Butterfly Info Insects Insect Database Frogs Frog Info Bird Database Bird Database Online Prairie Data Online Prairie Data

Overview with methods and procedures of the U.S. Geological Survey mineral-resource assessment of the Sagebrush Focal Areas of Idaho, Montana, Nevada, Oregon, Utah, and Wyoming: Chapter A in Mineral resources of the Sagebrush Focal Areas of Idaho, Montana, Nevada, Oregon, Utah, and Wyoming

USGS Publications Warehouse

Day, Warren C.; Hammarstrom, Jane M.; Zientek, Michael L.; Frost, Thomas P.

2016-08-19

This report, chapter A of Scientific Investigations Report 2016–5089, provides an overview of the U.S. Geological Survey (USGS) Sagebrush Mineral-Resource Assessment (SaMiRA). The report also describes the methods, procedures, and voluminous fundamental reference information used throughout the assessment. Data from several major publicly available databases and other published sources were used to develop an understanding of the locatable, leaseable, and salable mineral resources of this vast area. This report describes the geologic, mineral-occurrence, geochemical, geophysical, remote-sensing, and Bureau of Land Management mineral-case-status data used for the assessment, along with the methods for evaluating locatable mineral-resource potential. The report also discusses energy-resource data (oil and gas, coal, and geothermal) used in the assessment. Appendixes include summary descriptive mineral-deposit models that provide the criteria necessary to assess for the pertinent locatable minerals and market-demand commodity profiles for locatable mineral commodities relevant to the project. Datasets used in the assessment are available as USGS data releases.

Resources for global risk assessment: the International Toxicity Estimates for Risk (ITER) and Risk Information Exchange (RiskIE) databases.

PubMed

Wullenweber, Andrea; Kroner, Oliver; Kohrman, Melissa; Maier, Andrew; Dourson, Michael; Rak, Andrew; Wexler, Philip; Tomljanovic, Chuck

2008-11-15

The rate of chemical synthesis and use has outpaced the development of risk values and the resolution of risk assessment methodology questions. In addition, available risk values derived by different organizations may vary due to scientific judgments, mission of the organization, or use of more recently published data. Further, each organization derives values for a unique chemical list so it can be challenging to locate data on a given chemical. Two Internet resources are available to address these issues. First, the International Toxicity Estimates for Risk (ITER) database (www.tera.org/iter) provides chronic human health risk assessment data from a variety of organizations worldwide in a side-by-side format, explains differences in risk values derived by different organizations, and links directly to each organization's website for more detailed information. It is also the only database that includes risk information from independent parties whose risk values have undergone independent peer review. Second, the Risk Information Exchange (RiskIE) is a database of in progress chemical risk assessment work, and includes non-chemical information related to human health risk assessment, such as training modules, white papers and risk documents. RiskIE is available at http://www.allianceforrisk.org/RiskIE.htm, and will join ITER on National Library of Medicine's TOXNET (http://toxnet.nlm.nih.gov/). Together, ITER and RiskIE provide risk assessors essential tools for easily identifying and comparing available risk data, for sharing in progress assessments, and for enhancing interaction among risk assessment groups to decrease duplication of effort and to harmonize risk assessment procedures across organizations.

A Brief Review of RNA–Protein Interaction Database Resources

PubMed Central

Yi, Ying; Zhao, Yue; Huang, Yan; Wang, Dong

2017-01-01

RNA–Protein interactions play critical roles in various biological processes. By collecting and analyzing the RNA–Protein interactions and binding sites from experiments and predictions, RNA–Protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. Here, we briefly review several widely used RNA–Protein interaction database resources developed in recent years to provide a guide of these databases. The content and major functions in databases are presented. The brief description of database helps users to quickly choose the database containing information they interested. In short, these RNA–Protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA–Protein interactions. PMID:29657278

The ERESE project: Bridging the gap between Digital Science Libraries and Education through Professional Development of Teachers and Database Development

NASA Astrophysics Data System (ADS)

Staudigel, H.; Helly, M.; Helly, J.; Koppers, A.; Massel-Symons, C.; Miller, S.

2004-12-01

The ERESE (Enduring Resources in Earth Science Education) project involves a close collaboration between teachers, librarians, educators, data archive managers and scientists in Earth sciences and information technology, to create a digital library environment for Earth science education. We report here on an ongoing (NSF-NSDL) project involving teachers' professional development in the pedagogy of plate tectonics in middle and high schools. This work included efforts in scientific database development in terms of contents and search tools, the development of an inquiry based learning approach, a two week professional development workshop attended by 15 teachers from across the nation, a classroom implementation of lesson plans developed by the teachers at the workshop and an evaluation/validation process for the success of their pedagogic approaches. This ERESE project offers a novel path for both science teaching and professional outreach for scientists, and includes four key components: (1) A true, long-term research partnership between educators and scientists, guiding each other with respect to the authenticity of the science taught and the educational soundness of a scientists' elaborations on science concepts. (2) Expansion of existing scientific databases through the use of metadata that tie scientific materials to a particular expert level and teaching goal. (3) The design of interfaces that make data accessible to the educational community. (4) The use of an inquiry based teaching approach that integrates the scientist-educator collaboration and the data base developments. Our pedagogic approach includes the development of a central hypotheses by the student in response to an initial general orientation and presentation of a well chosen central provocative phenomenon by the teacher. Then, the student develops a research plan that is devoted to address this hypothesis through the use of the materials provided by a scientific database allowing a students prove or disprove their hypothesis and to explore the limits of the (current) understanding of a particular science question. Our first experience with this ERESE project involved a steep learning curve, but the initial results are very promising, providing true professional development for educators as well as for the scientists, whereby the former learn about new ways of teaching science and the latter learn to communicate with teachers.

Measuring the evolution and output of cross-disciplinary collaborations within the NCI Physical Sciences–Oncology Centers Network

PubMed Central

Basner, Jodi E.; Theisz, Katrina I.; Jensen, Unni S.; Jones, C. David; Ponomarev, Ilya; Sulima, Pawel; Jo, Karen; Eljanne, Mariam; Espey, Michael G.; Franca-Koh, Jonathan; Hanlon, Sean E.; Kuhn, Nastaran Z.; Nagahara, Larry A.; Schnell, Joshua D.; Moore, Nicole M.

2013-01-01

Development of effective quantitative indicators and methodologies to assess the outcomes of cross-disciplinary collaborative initiatives has the potential to improve scientific program management and scientific output. This article highlights an example of a prospective evaluation that has been developed to monitor and improve progress of the National Cancer Institute Physical Sciences—Oncology Centers (PS-OC) program. Study data, including collaboration information, was captured through progress reports and compiled using the web-based analytic database: Interdisciplinary Team Reporting, Analysis, and Query Resource. Analysis of collaborations was further supported by data from the Thomson Reuters Web of Science database, MEDLINE database, and a web-based survey. Integration of novel and standard data sources was augmented by the development of automated methods to mine investigator pre-award publications, assign investigator disciplines, and distinguish cross-disciplinary publication content. The results highlight increases in cross-disciplinary authorship collaborations from pre- to post-award years among the primary investigators and confirm that a majority of cross-disciplinary collaborations have resulted in publications with cross-disciplinary content that rank in the top third of their field. With these evaluation data, PS-OC Program officials have provided ongoing feedback to participating investigators to improve center productivity and thereby facilitate a more successful initiative. Future analysis will continue to expand these methods and metrics to adapt to new advances in research evaluation and changes in the program. PMID:24808632

Creating a Library of Climate Change Education Resources for Audiences in the Southeast United States

NASA Astrophysics Data System (ADS)

Carroll, J.; McNeal, K. S.; Williams, C. C.; Paz, J. O.; Cho, H. "; Nair, U. S.; Geroux, J.; Guthrie, C.; Wright, K.; Hill, J.

2011-12-01

The Climate Literacy Partnership in the Southeast (CLiPSE) is a part of the Climate Change Education Program supported by the National Science Foundation (http://CLiPSE-project.org). The established CLiPSE partnership is dedicated to improving climate literacy in the southeast and promoting scientifically accurate, formal educational resources for the K-12 classroom audience, as well as informal educational resources for audiences such as agriculture, education, leisure, and religious organizations, to name a few. The CLiPSE project has been successful in creating partnerships with the National Geographic Alliances, Departments of Education, and Mississippi Environmental Education Alliance, among others, to determine an effective strategic plan for reaching K-12 audiences. One goal in the strategic plan is to create a catalog of climate change education resources that are aligned to state standards in the SE. Eighty-seven resources from the Climate Literacy and Energy Awareness Network (http://cleanet.org) have been aligned with the state education standards for grades six through twelve in the southeast, beginning with science in Mississippi and expanding to include science and math in the remaining SE states. The criteria for aligning the existing resources includes: matching key terms, topics, and lesson activities with the content strands and essential skills included in the state science framework. By developing a searchable database containing climate resources already aligned with state standards, CLiPSE will have made these resources more appealing to educators in the SE, increasing the likelihood of resources being implemented in the classroom. The CLiPSE Climate Science Team has also created an inventory of scientifically sound, informal resources, which will be available for dispersion to appropriate audiences and communities. Cataloged resources, both formal and informal, grouped by a variety of means, to include audience, grade level, and resource origin (e.g. government agency, organization, museum, climate-related websites, etc.), will be made available to the public through the CLiPSE website, promoting accessibility of these resources to the various CLiPSE publics. The process of alignment and vetting will be discussed in this paper, along with the information and education "gaps" that exist for the specific CLiPSE audiences in the SE US.

The quantitative measurement of organizational culture in health care: a review of the available instruments.

PubMed

Scott, Tim; Mannion, Russell; Davies, Huw; Marshall, Martin

2003-06-01

To review the quantitative instruments available to health service researchers who want to measure culture and cultural change. A literature search was conducted using Medline, Cinahl, Helmis, Psychlit, Dhdata, and the database of the King's Fund in London for articles published up to June 2001, using the phrase "organizational culture." In addition, all citations and the gray literature were reviewed and advice was sought from experts in the field to identify instruments not found on the electronic databases. The search focused on instruments used to quantify culture with a track record, or potential for use, in health care settings. For each instrument we examined the cultural dimensions addressed, the number of items for each questionnaire, the measurement scale adopted, examples of studies that had used the tool, the scientific properties of the instrument, and its strengths and limitations. Thirteen instruments were found that satisfied our inclusion criteria, of which nine have a track record in studies involving health care organizations. The instruments varied considerably in terms of their grounding in theory, format, length, scope, and scientific properties. A range of instruments with differing characteristics are available to researchers interested in organizational culture, all of which have limitations in terms of their scope, ease of use, or scientific properties. The choice of instrument should be determined by how organizational culture is conceptualized by the research team, the purpose of the investigation, intended use of the results, and availability of resources.

A 1.4-Billion Pixel Map of the Seafloor: BOEM's Mission to Visualize Dynamic Geology and Identify Natural Seep Sites in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Kramer, K.; Shedd, W. W.

2017-12-01

In May, 2017, the U.S. Department of the Interior's Bureau of Ocean Energy Management (BOEM) published a high-resolution seafloor map of the northern Gulf of Mexico region. The new map, derived from 3-D seismic surveys, provides the scientific community with enhanced resolution and reveals previously undiscovered and poorly resolved geologic features of the continental slope, salt minibasin province, abyssal plain, Mississippi Fan, and the Florida Shelf and Escarpment. It becomes an even more powerful scientific tool when paired with BOEM's public database of 35,000 seafloor features, identifying natural hydrocarbon seeps, hard grounds, mud volcanoes, sediment flows, pockmarks, slumps, and many others. BOEM has mapped the Gulf of Mexico seafloor since 1998 in a regulatory mission to identify natural oil and gas seeps and protect the coral and chemosynthetic communities growing at those sites. The nineteen-year mapping effort, still ongoing, resulted in the creation of the 1.4-billion pixel map and the seafloor features database. With these tools and continual collaboration with academia, professional scientific institutions, and the offshore energy industry, BOEM will continue to incorporate new data to update and expand these two resources on a regular basis. They can be downloaded for free from BOEM's website at https://www.boem.gov/Gulf-of-Mexico-Deepwater-Bathymetry/ and https://www.boem.gov/Seismic-Water-Bottom-Anomalies-Map-Gallery/.

International Space Station Utilization: Tracking Investigations from Objectives to Results

NASA Technical Reports Server (NTRS)

Ruttley, T. M.; Mayo, Susan; Robinson, J. A.

2011-01-01

Since the first module was assembled on the International Space Station (ISS), on-orbit investigations have been underway across all scientific disciplines. The facilities dedicated to research on ISS have supported over 1100 investigations from over 900 scientists representing over 60 countries. Relatively few of these investigations are tracked through the traditional NASA grants monitoring process and with ISS National Laboratory use growing, the ISS Program Scientist s Office has been tasked with tracking all ISS investigations from objectives to results. Detailed information regarding each investigation is now collected once, at the first point it is proposed for flight, and is kept in an online database that serves as a single source of information on the core objectives of each investigation. Different fields are used to provide the appropriate level of detail for research planning, astronaut training, and public communications. http://www.nasa.gov/iss-science/. With each successive year, publications of ISS scientific results, which are used to measure success of the research program, have shown steady increases in all scientific research areas on the ISS. Accurately identifying, collecting, and assessing the research results publications is a challenge and a priority for the ISS research program, and we will discuss the approaches that the ISS Program Science Office employs to meet this challenge. We will also address the online resources available to support outreach and communication of ISS research to the public. Keywords: International Space Station, Database, Tracking, Methods

Continual improvement: A bibliography with indexes, 1992-1993

NASA Technical Reports Server (NTRS)

1994-01-01

This bibliography lists 606 references to reports and journal articles entered into the NASA Scientific and Technical Information Database during 1992 to 1993. Topics cover the philosophy and history of Continual Improvement (CI), basic approaches and strategies for implementation, and lessons learned from public and private sector models. Entries are arranged according to the following categories: Leadership for Quality, Information and Analysis, Strategic Planning for CI, Human Resources Utilization, Management of Process Quality, Supplier Quality, Assessing Results, Customer Focus and Satisfaction, TQM Tools and Philosophies, and Applications. Indexes include subject, personal author, corporate source, contract number, report number, and accession number.

Workflow based framework for life science informatics.

PubMed

Tiwari, Abhishek; Sekhar, Arvind K T

2007-10-01

Workflow technology is a generic mechanism to integrate diverse types of available resources (databases, servers, software applications and different services) which facilitate knowledge exchange within traditionally divergent fields such as molecular biology, clinical research, computational science, physics, chemistry and statistics. Researchers can easily incorporate and access diverse, distributed tools and data to develop their own research protocols for scientific analysis. Application of workflow technology has been reported in areas like drug discovery, genomics, large-scale gene expression analysis, proteomics, and system biology. In this article, we have discussed the existing workflow systems and the trends in applications of workflow based systems.

Recent Advances in the GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, Bruce; Cogley, Graham; Zemp, Michael; Glaus, Ladina

2017-04-01

Glaciers are shrinking almost without exception. Glacier losses have impacts on local water availability and hazards, and contribute to sea level rise. To understand these impacts and the processes behind them, it is crucial to monitor glaciers through time by mapping their areal extent, changes in volume, elevation distribution, snow lines, ice flow velocities, and changes to associated water bodies. The glacier database of the Global Land Ice Measurements from Space (GLIMS) initiative is the only multi-temporal glacier database capable of tracking all these glacier measurements and providing them to the scientific community and broader public. Here we present recent results in 1) expansion of the geographic and temporal coverage of the GLIMS Glacier Database by drawing on the Randolph Glacier Inventory (RGI) and other new data sets; 2) improved tools for visualizing and downloading GLIMS data in a choice of formats and data models; and 3) a new data model for handling multiple glacier records through time while avoiding double-counting of glacier number or area. The result of this work is a more complete glacier data repository that shows not only the current state of glaciers on Earth, but how they have changed in recent decades. The database is useful for tracking changes in water resources, hazards, and mass budgets of the world's glaciers.

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

PubMed Central

Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang

2018-01-01

Abstract SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements. PMID:29092055

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases.

PubMed

Wang, Yongbo; Liu, Zexian; Cheng, Han; Gao, Tianshun; Pan, Zhicheng; Yang, Qing; Guo, Anyuan; Xue, Yu

2014-01-01

We present here EKPD (http://ekpd.biocuckoo.org), a hierarchical database of eukaryotic protein kinases (PKs) and protein phosphatases (PPs), the key molecules responsible for the reversible phosphorylation of proteins that are involved in almost all aspects of biological processes. As extensive experimental and computational efforts have been carried out to identify PKs and PPs, an integrative resource with detailed classification and annotation information would be of great value for both experimentalists and computational biologists. In this work, we first collected 1855 PKs and 347 PPs from the scientific literature and various public databases. Based on previously established rationales, we classified all of the known PKs and PPs into a hierarchical structure with three levels, i.e. group, family and individual PK/PP. There are 10 groups with 149 families for the PKs and 10 groups with 33 families for the PPs. We constructed 139 and 27 Hidden Markov Model profiles for PK and PP families, respectively. Then we systematically characterized ∼50,000 PKs and >10,000 PPs in eukaryotes. In addition, >500 PKs and >400 PPs were computationally identified by ortholog search. Finally, the online service of the EKPD database was implemented in PHP + MySQL + JavaScript.

NREL: Renewable Resource Data Center - Biomass Resource Publications

Science.gov Websites

Marginal Lands in APEC Economies NREL Publications Database For a comprehensive list of other NREL biomass resource publications, explore NREL's Publications Database. When searching the database, search on "

Securely and Flexibly Sharing a Biomedical Data Management System

PubMed Central

Wang, Fusheng; Hussels, Phillip; Liu, Peiya

2011-01-01

Biomedical database systems need not only to address the issues of managing complex data, but also to provide data security and access control to the system. These include not only system level security, but also instance level access control such as access of documents, schemas, or aggregation of information. The latter is becoming more important as multiple users can share a single scientific data management system to conduct their research, while data have to be protected before they are published or IP-protected. This problem is challenging as users’ needs for data security vary dramatically from one application to another, in terms of who to share with, what resources to be shared, and at what access level. We develop a comprehensive data access framework for a biomedical data management system SciPort. SciPort provides fine-grained multi-level space based access control of resources at not only object level (documents and schemas), but also space level (resources set aggregated in a hierarchy way). Furthermore, to simplify the management of users and privileges, customizable role-based user model is developed. The access control is implemented efficiently by integrating access privileges into the backend XML database, thus efficient queries are supported. The secure access approach we take makes it possible for multiple users to share the same biomedical data management system with flexible access management and high data security. PMID:21625285

Spatial database for a global assessment of undiscovered copper resources: Chapter Z in Global mineral resource assessment

USGS Publications Warehouse

Dicken, Connie L.; Dunlap, Pamela; Parks, Heather L.; Hammarstrom, Jane M.; Zientek, Michael L.; Zientek, Michael L.; Hammarstrom, Jane M.; Johnson, Kathleen M.

2016-07-13

As part of the first-ever U.S. Geological Survey global assessment of undiscovered copper resources, data common to several regional spatial databases published by the U.S. Geological Survey, including one report from Finland and one from Greenland, were standardized, updated, and compiled into a global copper resource database. This integrated collection of spatial databases provides location, geologic and mineral resource data, and source references for deposits, significant prospects, and areas permissive for undiscovered deposits of both porphyry copper and sediment-hosted copper. The copper resource database allows for efficient modeling on a global scale in a geographic information system (GIS) and is provided in an Esri ArcGIS file geodatabase format.

Modernization and new technologies: Coping with the information explosion

NASA Technical Reports Server (NTRS)

Blados, Walter R.; Cotter, Gladys A.

1993-01-01

Information has become a valuable and strategic resource in all societies and economies. Scientific and technical information is especially important in developing and maintaining a strong national science and technology base. The expanding use of information technology, the growth of interdisciplinary research, and an increase in international collaboration are changing characteristics of information. This modernization effort applies new technology to current processes to provide near-term benefits to the user. At the same time, we are developing a long-term modernization strategy designed to transition the program to a multimedia, global 'library without walls'. Notwithstanding this modernization program, it is recogized that no one information center can hope to collect all the relevant data. We see information and information systems changing and becoming more international in scope. We are finding that many nations are expending resources on national systems which duplicate each other. At the same time that this duplication exists, many useful sources of aerospace information are not being collected to cover expanded sources of information. This paper reviews the NASA modernization program and raises for consideration new possibilities for unification of the various aerospace database efforts toward a cooperative international aerospace database initiative, one that can optimize the cost/benefit equation for all participants.

Case Studies in Describing Scientific Research Efforts as Linked Data

NASA Astrophysics Data System (ADS)

Gandara, A.; Villanueva-Rosales, N.; Gates, A.

2013-12-01

The Web is growing with numerous scientific resources, prompting increased efforts in information management to consider integration and exchange of scientific resources. Scientists have many options to share scientific resources on the Web; however, existing options provide limited support to scientists in annotating and relating research resources resulting from a scientific research effort. Moreover, there is no systematic approach to documenting scientific research and sharing it on the Web. This research proposes the Collect-Annotate-Refine-Publish (CARP) Methodology as an approach for guiding documentation of scientific research on the Semantic Web as scientific collections. Scientific collections are structured descriptions about scientific research that make scientific results accessible based on context. In addition, scientific collections enhance the Linked Data data space and can be queried by machines. Three case studies were conducted on research efforts at the Cyber-ShARE Research Center of Excellence in order to assess the effectiveness of the methodology to create scientific collections. The case studies exposed the challenges and benefits of leveraging the Semantic Web and Linked Data data space to facilitate access, integration and processing of Web-accessible scientific resources and research documentation. As such, we present the case study findings and lessons learned in documenting scientific research using CARP.

Axiope tools for data management and data sharing.

PubMed

Goddard, Nigel H; Cannon, Robert C; Howell, Fred W

2003-01-01

Many areas of biological research generate large volumes of very diverse data. Managing this data can be a difficult and time-consuming process, particularly in an academic environment where there are very limited resources for IT support staff such as database administrators. The most economical and efficient solutions are those that enable scientists with minimal IT expertise to control and operate their own desktop systems. Axiope provides one such solution, Catalyzer, which acts as flexible cataloging system for creating structured records describing digital resources. The user is able specify both the content and structure of the information included in the catalog. Information and resources can be shared by a variety of means, including automatically generated sets of web pages. Federation and integration of this information, where needed, is handled by Axiope's Mercat server. Where there is a need for standardization or compatibility of the structures usedby different researchers this canbe achieved later by applying user-defined mappings in Mercat. In this way, large-scale data sharing can be achieved without imposing unnecessary constraints or interfering with the way in which individual scientists choose to record and catalog their work. We summarize the key technical issues involved in scientific data management and data sharing, describe the main features and functionality of Axiope Catalyzer and Axiope Mercat, and discuss future directions and requirements for an information infrastructure to support large-scale data sharing and scientific collaboration.

Social inequality, health policies and the training of physicians, nurses and dentists in Brazil and in Portugal.

PubMed

Craveiro, Isabel Maria Rodrigues; Hortale, Virginia Alonso; de Oliveira, Ana Paula Cavalcante; Dussault, Gilles

2015-10-01

This study analyzes the production of scientific knowledge on Health Inequalities (HI) and its use in policies of education of dentists, nurses and physicians in Brazil and Portugal. Documents published between January 2000 and December 2001, in Portuguese, French, English and Spanish, were identified by means of a combination of a manual and intentional electronic database survey of the grey literature. Fifty-three documents were selected from a total of 1,652. The findings revealed that there is still little knowledge available to enable an assessment of policies for human resource training in healthcare in general and for those related to physicians, nurses and dentists in particular. In Brazil, few studies have thus far been made to understand how such training can contribute towards reducing these inequalities and, in the case of Portugal, no studies were found that established a direct relationship between human resource training and the future role that these could play in combating inequality. Despite a vast increase in scientific production, many lacunae still exist in this field. Knowledge production and its relationship with decision-making still seem to be separate processes in these two countries.

EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom

PubMed Central

Kumari, Sangita; Pundhir, Sachin; Priya, Piyush; Jeena, Ganga; Punetha, Ankita; Chawla, Konika; Firdos Jafaree, Zohra; Mondal, Subhasish; Yadav, Gitanjali

2014-01-01

Plant essential oils are complex mixtures of volatile organic compounds, which play indispensable roles in the environment, for the plant itself, as well as for humans. The potential biological information stored in essential oil composition data can provide an insight into the silent language of plants, and the roles of these chemical emissions in defense, communication and pollinator attraction. In order to decipher volatile profile patterns from a global perspective, we have developed the ESSential OIL DataBase (EssOilDB), a continually updated, freely available electronic database designed to provide knowledge resource for plant essential oils, that enables one to address a multitude of queries on volatile profiles of native, invasive, normal or stressed plants, across taxonomic clades, geographical locations and several other biotic and abiotic influences. To our knowledge, EssOilDB is the only database in the public domain providing an opportunity for context based scientific research on volatile patterns in plants. EssOilDB presently contains 123 041 essential oil records spanning a century of published reports on volatile profiles, with data from 92 plant taxonomic families, spread across diverse geographical locations all over the globe. We hope that this huge repository of VOCs will facilitate unraveling of the true significance of volatiles in plants, along with creating potential avenues for industrial applications of essential oils. We also illustrate the use of this database in terpene biology and show how EssOilDB can be used to complement data from computational genomics to gain insights into the diversity and variability of terpenoids in the plant kingdom. EssOilDB would serve as a valuable information resource, for students and researchers in plant biology, in the design and discovery of new odor profiles, as well as for entrepreneurs—the potential for generating consumer specific scents being one of the most attractive and interesting topics in the cosmetic industry. Database URL: http://nipgr.res.in/Essoildb/ PMID:25534749

An Integrated Molecular Database on Indian Insects.

PubMed

Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

2018-01-01

MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents.

PubMed

Naderi, Nona; Kappler, Thomas; Baker, Christopher J O; Witte, René

2011-10-01

Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. witte@semanticsoftware.info.

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.

Open Core Data: Connecting scientific drilling data to scientists and community data resources

NASA Astrophysics Data System (ADS)

Fils, D.; Noren, A. J.; Lehnert, K.; Diver, P.

2016-12-01

Open Core Data (OCD) is an innovative, efficient, and scalable infrastructure for data generated by scientific drilling and coring to improve discoverability, accessibility, citability, and preservation of data from the oceans and continents. OCD is building on existing community data resources that manage, store, publish, and preserve scientific drilling data, filling a critical void that currently prevents linkages between these and other data systems and tools to realize the full potential of data generated through drilling and coring. We are developing this functionality through Linked Open Data (LOD) and semantic patterns that enable data access through the use of community ontologies such as GeoLink (geolink.org, an EarthCube Building Block), a collection of protocols, formats and vocabularies from a set of participating geoscience repositories. Common shared concepts of classes such as cruise, dataset, person and others allow easier resolution of common references through shared resource IDs. These graphs are then made available via SPARQL as well as incorporated into web pages following schema.org approaches. Additionally the W3C PROV vocabulary is under evaluation for use for documentation of provenance. Further, the application of persistent identifiers for samples (IGSNs); datasets, expeditions, and projects (DOIs); and people (ORCIDs), combined with LOD approaches, provides methods to resolve and incorporate metadata and datasets. Application Program Interfaces (APIs) complement these semantic approaches to the OCD data holdings. APIs are exposed following the Swagger guidelines (swagger.io) and will be evolved into the OpenAPI (openapis.org) approach. Currently APIs are in development for the NSF funded Flyover Country mobile geoscience app (fc.umn.edu), the Neotoma Paleoecology Database (neotomadb.org), Magnetics Information Consortium (MagIC; earthref.org/MagIC), and other community tools and data systems, as well as for internal OCD use.

THPdb: Database of FDA-approved peptide and protein therapeutics.

PubMed

Usmani, Salman Sadullah; Bedi, Gursimran; Samuel, Jesse S; Singh, Sandeep; Kalra, Sourav; Kumar, Pawan; Ahuja, Anjuman Arora; Sharma, Meenu; Gautam, Ankur; Raghava, Gajendra P S

2017-01-01

THPdb (http://crdd.osdd.net/raghava/thpdb/) is a manually curated repository of Food and Drug Administration (FDA) approved therapeutic peptides and proteins. The information in THPdb has been compiled from 985 research publications, 70 patents and other resources like DrugBank. The current version of the database holds a total of 852 entries, providing comprehensive information on 239 US-FDA approved therapeutic peptides and proteins and their 380 drug variants. The information on each peptide and protein includes their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, target of activity, etc. In addition, we have annotated the structure of most of the protein and peptides. A number of user-friendly tools have been integrated to facilitate easy browsing and data analysis. To assist scientific community, a web interface and mobile App have also been developed.

Web based aphasia test using service oriented architecture (SOA)

NASA Astrophysics Data System (ADS)

Voos, J. A.; Vigliecca, N. S.; Gonzalez, E. A.

2007-11-01

Based on an aphasia test for Spanish speakers which analyze the patient's basic resources of verbal communication, a web-enabled software was developed to automate its execution. A clinical database was designed as a complement, in order to evaluate the antecedents (risk factors, pharmacological and medical backgrounds, neurological or psychiatric symptoms, brain injury -anatomical and physiological characteristics, etc) which are necessary to carry out a multi-factor statistical analysis in different samples of patients. The automated test was developed following service oriented architecture and implemented in a web site which contains a tests suite, which would allow both integrating the aphasia test with other neuropsychological instruments and increasing the available site information for scientific research. The test design, the database and the study of its psychometric properties (validity, reliability and objectivity) were made in conjunction with neuropsychological researchers, who participate actively in the software design, based on the patients or other subjects of investigation feedback.

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

PubMed Central

Bluhm, Wolfgang F.; Beran, Bojan; Bi, Chunxiao; Dimitropoulos, Dimitris; Prlić, Andreas; Quinn, Gregory B.; Rose, Peter W.; Shah, Chaitali; Young, Jasmine; Yukich, Benjamin; Berman, Helen M.; Bourne, Philip E.

2011-01-01

The RCSB Protein Data Bank (RCSB PDB, www.pdb.org) is a key online resource for structural biology and related scientific disciplines. The website is used on average by 165 000 unique visitors per month, and more than 2000 other websites link to it. The amount and complexity of PDB data as well as the expectations on its usage are growing rapidly. Therefore, ensuring the reliability and robustness of the RCSB PDB query and distribution systems are crucially important and increasingly challenging. This article describes quality assurance for the RCSB PDB website at several distinct levels, including: (i) hardware redundancy and failover, (ii) testing protocols for weekly database updates, (iii) testing and release procedures for major software updates and (iv) miscellaneous monitoring and troubleshooting tools and practices. As such it provides suggestions for how other websites might be operated. Database URL: www.pdb.org PMID:21382834

The NBER-Rensselaer Scientific Papers Database: Form, Nature, and Function. NBER Working Paper No. 14575

ERIC Educational Resources Information Center

Adams, James D.; Clemmons, J. Roger

2008-01-01

This article is a guide to the NBER-Rensselaer Scientific Papers Database, which includes more than 2.5 million scientific publications and over 21 million citations to those papers. The data cover an important sample of 110 top U.S. universities and 200 top U.S.-based R&D-performing firms during the period 1981-1999. This article describes the…

Experiences with the Application of Services Oriented Approaches to the Federation of Heterogeneous Geologic Data Resources

NASA Astrophysics Data System (ADS)

Cervato, C.; Fils, D.; Bohling, G.; Diver, P.; Greer, D.; Reed, J.; Tang, X.

2006-12-01

The federation of databases is not a new endeavor. Great strides have been made e.g. in the health and astrophysics communities. Reviews of those successes indicate that they have been able to leverage off key cross-community core concepts. In its simplest implementation, a federation of databases with identical base schemas that can be extended to address individual efforts, is relatively easy to accomplish. Efforts of groups like the Open Geospatial Consortium have shown methods to geospatially relate data between different sources. We present here a summary of CHRONOS's (http://www.chronos.org) experience with highly heterogeneous data. Our experience with the federation of very diverse databases shows that the wide variety of encoding options for items like locality, time scale, taxon ID, and other key parameters makes it difficult to effectively join data across them. However, the response to this is not to develop one large, monolithic database, which will suffer growth pains due to social, national, and operational issues, but rather to systematically develop the architecture that will enable cross-resource (database, repository, tool, interface) interaction. CHRONOS has accomplished the major hurdle of federating small IT database efforts with service-oriented and XML-based approaches. The application of easy-to-use procedures that allow groups of all sizes to implement and experiment with searches across various databases and to use externally created tools is vital. We are sharing with the geoinformatics community the difficulties with application frameworks, user authentication, standards compliance, and data storage encountered in setting up web sites and portals for various science initiatives (e.g., ANDRILL, EARTHTIME). The ability to incorporate CHRONOS data, services, and tools into the existing framework of a group is crucial to the development of a model that supports and extends the vitality of the small- to medium-sized research effort that is essential for a vibrant scientific community. This presentation will directly address issues of portal development related to JSR-168 and other portal API's as well as issues related to both federated and local directory-based authentication. The application of service-oriented architecture in connection with ReST-based approaches is vital to facilitate service use by experienced and less experienced information technology groups. Application of these services with XML- based schemas allows for the connection to third party tools such a GIS-based tools and software designed to perform a specific scientific analysis. The connection of all these capabilities into a combined framework based on the standard XHTML Document object model and CSS 2.0 standards used in traditional web development will be demonstrated. CHRONOS also utilizes newer client techniques such as AJAX and cross- domain scripting along with traditional server-side database, application, and web servers. The combination of the various components of this architecture creates an environment based on open and free standards that allows for the discovery, retrieval, and integration of tools and data.

Workshop Report on a Future Information Infrastructure for the Physical Sciences. The Facts of the Matter: Finding, Understanding, and Using Information about out Physical World Held at the National Academy of Sciences on May 30-31, 2000

DTIC Science & Technology

2000-05-31

Grey Literature Network Service ( Farace , Dominic,1997) as, “that which is produced on all levels of government, academics, business and industry in... literature is available, on-line, to scientific workers throughout the world, for a world scientific database.” These reports served as the base to begin...all the world’s formal scientific literature is available, on-line, to scientific workers throughout the world, for a world scientific database

Study of water-table behaviour for the Indian Punjab using GIS.

PubMed

Kaur, Samanpreet; Aggarwal, Rajan; Soni, Ashwani

2011-01-01

The state of Punjab (India) has witnessed a spectacular increase in agricultural production in the last few decades. This has been possible due to high use of fertilizers, good quality seeds and increased use of water resources. This increased demand of water resources has resulted in extensive use of groundwater in the central districts of the state and surface water (canals) in South-West Punjab, where groundwater is of poor quality in general. The state has been facing the twin problem of water table decline/rise in different parts. Efficient management relies on comprehensive database and regular monitoring of the resources. GIS is one of the important tools for integrating and analyzing spatial information from different sources or disciplines. It helps to integrate, analyze and represent spatial information and database of any resource, which could be easily used for planning of resource development, environmental protection and scientific researches and investigations. Geographical Information Systems (GIS) have been used for a variety of groundwater studies. Groundwater level change maps are useful in determining areas of greatest changes in storage in the regional systems. In this study, an attempt has been made to assess the long term groundwater behaviour of the state using GIS to visually and spatially analyze water level data obtained from the state and central agencies. The data was analysed for 0-3 m, 3-10 m, 10-20 m and beyond 20 m. The study revealed that per cent area with water table depth > 10 m was 20% in 1998 and has increased to 58% by 2006 which is critical limit for shifting from centrifugal pump to submersible pump.

International Polar Year Information Resources: Science Librarians Behind the Scenes and in the Field

NASA Astrophysics Data System (ADS)

Hicks, G. J.; Sommer, S.

2006-12-01

As the International Polar Year approaches, research institutes, scientists, and students are preparing for the challenges of field research and the resulting reports and papers. In support of these researchers, libraries and information centers are developing programs and special projects to provide the information and repositories vital to dissemination of the resulting data and reports. From the National Snow and Ice Data Center's DAHLI project to Scott Polar Research Institute's Discovering the Poles, polar science librarians around the world are gearing up to provide service and information to researchers at home and in the field. Not only will these information specialists and librarians provide resources or answer questions for the scientist in the office, they will also provide much of those same services to the researcher in the field. IPY resources are a special case of the on-demand services science librarians typically provide. They help scientists formulate search strategies and take advantage of new developments in scientific databases at their home institutes. They provide many of the same services to researchers in the field. Whether sitting on an ice breaker in the Southern Ocean or in a tent on a glacier in Spitsbergen, field scientists can email or IM a question to a librarian for digital copies of papers, answers to reference questions, or information from a source in the office. IPY data and publications will be distributed among many existing and a few new clearinghouses and article databases. Science librarians will ensure that their researchers can locate and use these resources, providing a vital service and many important resources for this global effort to understand the current status of climate change and its effect around the globe.

Astronomy Education Research Observations from the iSTAR international Study of Astronomical Reasoning Database

NASA Astrophysics Data System (ADS)

Tatge, C. B.; Slater, S. J.; Slater, T. F.; Schleigh, S.; McKinnon, D.

2016-12-01

Historically, an important part of the scientific research cycle is to situate any research project within the landscape of the existing scientific literature. In the field of discipline-based astronomy education research, grappling with the existing literature base has proven difficult because of the difficulty in obtaining research reports from around the world, particularly early ones. In order to better survey and efficiently utilize the wide and fractured range and domain of astronomy education research methods and results, the iSTAR international Study of Astronomical Reasoning database project was initiated. The project aims to host a living, online repository of dissertations, theses, journal articles, and grey literature resources to serve the world's discipline-based astronomy education research community. The first domain of research artifacts ingested into the iSTAR database were doctoral dissertations. To the authors' great surprise, nearly 300 astronomy education research dissertations were found from the last 100-years. Few, if any, of the literature reviews from recent astronomy education dissertations surveyed even come close to summarizing this many dissertations, most of which have not been published in traditional journals, as re-publishing one's dissertation research as a journal article was not a widespread custom in the education research community until recently. A survey of the iSTAR database dissertations reveals that the vast majority of work has been largely quantitative in nature until the last decade. We also observe that modern-era astronomy education research writings reaches as far back as 1923 and that the majority of dissertations come from the same eight institutions. Moreover, most of the astronomy education research work has been done covering learners' grasp of broad knowledge of astronomy rather than delving into specific learning targets, which has been more in vogue during the last two decades. The surprisingly wide breadth of largely unknown research revealed in the iSTAR database motivates us to begin to synthesize the research and look for broader themes using widely accepted meta analysis techniques.

The Computing and Data Grid Approach: Infrastructure for Distributed Science Applications

NASA Technical Reports Server (NTRS)

Johnston, William E.

2002-01-01

With the advent of Grids - infrastructure for using and managing widely distributed computing and data resources in the science environment - there is now an opportunity to provide a standard, large-scale, computing, data, instrument, and collaboration environment for science that spans many different projects and provides the required infrastructure and services in a relatively uniform and supportable way. Grid technology has evolved over the past several years to provide the services and infrastructure needed for building 'virtual' systems and organizations. We argue that Grid technology provides an excellent basis for the creation of the integrated environments that can combine the resources needed to support the large- scale science projects located at multiple laboratories and universities. We present some science case studies that indicate that a paradigm shift in the process of science will come about as a result of Grids providing transparent and secure access to advanced and integrated information and technologies infrastructure: powerful computing systems, large-scale data archives, scientific instruments, and collaboration tools. These changes will be in the form of services that can be integrated with the user's work environment, and that enable uniform and highly capable access to these computers, data, and instruments, regardless of the location or exact nature of these resources. These services will integrate transient-use resources like computing systems, scientific instruments, and data caches (e.g., as they are needed to perform a simulation or analyze data from a single experiment); persistent-use resources. such as databases, data catalogues, and archives, and; collaborators, whose involvement will continue for the lifetime of a project or longer. While we largely address large-scale science in this paper, Grids, particularly when combined with Web Services, will address a broad spectrum of science scenarios. both large and small scale.

Text mining in livestock animal science: introducing the potential of text mining to animal sciences.

PubMed

Sahadevan, S; Hofmann-Apitius, M; Schellander, K; Tesfaye, D; Fluck, J; Friedrich, C M

2012-10-01

In biological research, establishing the prior art by searching and collecting information already present in the domain has equal importance as the experiments done. To obtain a complete overview about the relevant knowledge, researchers mainly rely on 2 major information sources: i) various biological databases and ii) scientific publications in the field. The major difference between the 2 information sources is that information from databases is available, typically well structured and condensed. The information content in scientific literature is vastly unstructured; that is, dispersed among the many different sections of scientific text. The traditional method of information extraction from scientific literature occurs by generating a list of relevant publications in the field of interest and manually scanning these texts for relevant information, which is very time consuming. It is more than likely that in using this "classical" approach the researcher misses some relevant information mentioned in the literature or has to go through biological databases to extract further information. Text mining and named entity recognition methods have already been used in human genomics and related fields as a solution to this problem. These methods can process and extract information from large volumes of scientific text. Text mining is defined as the automatic extraction of previously unknown and potentially useful information from text. Named entity recognition (NER) is defined as the method of identifying named entities (names of real world objects; for example, gene/protein names, drugs, enzymes) in text. In animal sciences, text mining and related methods have been briefly used in murine genomics and associated fields, leaving behind other fields of animal sciences, such as livestock genomics. The aim of this work was to develop an information retrieval platform in the livestock domain focusing on livestock publications and the recognition of relevant data from cattle and pigs. For this purpose, the rather noncomprehensive resources of pig and cattle gene and protein terminologies were enriched with orthologue synonyms, integrated in the NER platform, ProMiner, which is successfully used in human genomics domain. Based on the performance tests done, the present system achieved a fair performance with precision 0.64, recall 0.74, and F(1) measure of 0.69 in a test scenario based on cattle literature.

Using distant supervised learning to identify protein subcellular localizations from full-text scientific articles.

PubMed

Zheng, Wu; Blake, Catherine

2015-10-01

Databases of curated biomedical knowledge, such as the protein-locations reflected in the UniProtKB database, provide an accurate and useful resource to researchers and decision makers. Our goal is to augment the manual efforts currently used to curate knowledge bases with automated approaches that leverage the increased availability of full-text scientific articles. This paper describes experiments that use distant supervised learning to identify protein subcellular localizations, which are important to understand protein function and to identify candidate drug targets. Experiments consider Swiss-Prot, the manually annotated subset of the UniProtKB protein knowledge base, and 43,000 full-text articles from the Journal of Biological Chemistry that contain just under 11.5 million sentences. The system achieves 0.81 precision and 0.49 recall at sentence level and an accuracy of 57% on held-out instances in a test set. Moreover, the approach identifies 8210 instances that are not in the UniProtKB knowledge base. Manual inspection of the 50 most likely relations showed that 41 (82%) were valid. These results have immediate benefit to researchers interested in protein function, and suggest that distant supervision should be explored to complement other manual data curation efforts. Copyright © 2015 Elsevier Inc. All rights reserved.

Governance and oversight of researcher access to electronic health data: the role of the Independent Scientific Advisory Committee for MHRA database research, 2006-2015.

PubMed

Waller, P; Cassell, J A; Saunders, M H; Stevens, R

2017-03-01

In order to promote understanding of UK governance and assurance relating to electronic health records research, we present and discuss the role of the Independent Scientific Advisory Committee (ISAC) for MHRA database research in evaluating protocols proposing the use of the Clinical Practice Research Datalink. We describe the development of the Committee's activities between 2006 and 2015, alongside growth in data linkage and wider national electronic health records programmes, including the application and assessment processes, and our approach to undertaking this work. Our model can provide independence, challenge and support to data providers such as the Clinical Practice Research Datalink database which has been used for well over 1,000 medical research projects. ISAC's role in scientific oversight ensures feasible and scientifically acceptable plans are in place, while having both lay and professional membership addresses governance issues in order to protect the integrity of the database and ensure that public confidence is maintained.

Towards Semantic e-Science for Traditional Chinese Medicine

PubMed Central

Chen, Huajun; Mao, Yuxin; Zheng, Xiaoqing; Cui, Meng; Feng, Yi; Deng, Shuiguang; Yin, Aining; Zhou, Chunying; Tang, Jinming; Jiang, Xiaohong; Wu, Zhaohui

2007-01-01

Background Recent advances in Web and information technologies with the increasing decentralization of organizational structures have resulted in massive amounts of information resources and domain-specific services in Traditional Chinese Medicine. The massive volume and diversity of information and services available have made it difficult to achieve seamless and interoperable e-Science for knowledge-intensive disciplines like TCM. Therefore, information integration and service coordination are two major challenges in e-Science for TCM. We still lack sophisticated approaches to integrate scientific data and services for TCM e-Science. Results We present a comprehensive approach to build dynamic and extendable e-Science applications for knowledge-intensive disciplines like TCM based on semantic and knowledge-based techniques. The semantic e-Science infrastructure for TCM supports large-scale database integration and service coordination in a virtual organization. We use domain ontologies to integrate TCM database resources and services in a semantic cyberspace and deliver a semantically superior experience including browsing, searching, querying and knowledge discovering to users. We have developed a collection of semantic-based toolkits to facilitate TCM scientists and researchers in information sharing and collaborative research. Conclusion Semantic and knowledge-based techniques are suitable to knowledge-intensive disciplines like TCM. It's possible to build on-demand e-Science system for TCM based on existing semantic and knowledge-based techniques. The presented approach in the paper integrates heterogeneous distributed TCM databases and services, and provides scientists with semantically superior experience to support collaborative research in TCM discipline. PMID:17493289

Improved oilfield GHG accounting using a global oilfield database

NASA Astrophysics Data System (ADS)

Roberts, S.; Brandt, A. R.; Masnadi, M.

2016-12-01

The definition of oil is shifting in considerable ways. Conventional oil resources are declining as oil sands, heavy oils, and others emerge. Technological advances mean that these unconventional hydrocarbons are now viable resources. Meanwhile, scientific evidence is mounting that climate change is occurring. The oil sector is responsible for 35% of global greenhouse gas (GHG) emissions, but the climate impacts of these new unconventional oils are not well understood. As such, the Oil Climate Index (OCI) project has been an international effort to evaluate the total life-cycle environmental GHG emissions of different oil fields globally. Over the course of the first and second phases of the project, 30 and 75 global oil fields have been investigated, respectively. The 75 fields account for about 25% of global oil production. For the third phase of the project, it is aimed to expand the OCI to contain closing to 100% of global oil production; leading to the analysis of 8000 fields. To accomplish this, a robust database system is required to handle and manipulate the data. Therefore, the integration of the data into the computer science language SQL (Structured Query Language) was performed. The implementation of SQL allows users to process the data more efficiently than would be possible by using the previously established program (Microsoft Excel). Next, a graphic user interface (gui) was implemented, in the computer science language of C#, in order to make the data interactive; enabling people to update the database without prior knowledge of SQL being necessary.

ProCarDB: a database of bacterial carotenoids.

PubMed

Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

2016-05-26

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

Patent Documents as a Resource for Studies and Education in Geophysics - An Approach.

NASA Astrophysics Data System (ADS)

Wollny, K. G.

2016-12-01

Patents are a highly neglected source of information in geophysics, although they supply a wealth of technical and historically relevant data and might be an important asset for researchers and students. The technical drawings and descriptions in patent documents provide insight into the personal work of a researcher or a scientific group and give detailed technical background information, show interdisciplinary solutions for similar problems, help to learn about inventions too advanced for their time but maybe useful now, and to explore the historical background and timelines of inventions and their inventors. It will be shown how to get access to patent documents and how to use them for research and education purposes. Exemplary inventions by well-known geoscientists or scientists in related fields will be presented to illustrate the usefulness of patent documents. The data pool used is the International Patent Classification (IPC) class G01V that the United Nations' World Intellectual Property Organisation (WIPO) has set up mainly for inventions with key aspects in geophysics. This class contains approximately 235,000 patent documents (July 2016) for methods, apparatuses or scientific instruments developed during scientific projects or by geophysical companies. The patent documents can be accessed via patent databases. The most important patent databases are for free, search functionality is self-explanatory and the amount of information to be extracted is enormous. For example, more than 90 million multilingual patent documents are currently available online (July 2016) in DEPATIS database of the German Patent and Trade Mark Office or ESPACENET of the European Patent Office. To summarize, patent documents are a highly useful tool for educational and research purposes to strengthen students' and scientists' knowledge in a practically orientated geophysical field and to widen the horizon to adjacent technical areas. Last but not least, they also provide insight into historical aspects of geophysics and the persons working in that area.

Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research.

PubMed

Malin, Bradley; Karp, David; Scheuermann, Richard H

2010-01-01

Clinical researchers need to share data to support scientific validation and information reuse and to comply with a host of regulations and directives from funders. Various organizations are constructing informatics resources in the form of centralized databases to ensure reuse of data derived from sponsored research. The widespread use of such open databases is contingent on the protection of patient privacy. We review privacy-related problems associated with data sharing for clinical research from technical and policy perspectives. We investigate existing policies for secondary data sharing and privacy requirements in the context of data derived from research and clinical settings. In particular, we focus on policies specified by the US National Institutes of Health and the Health Insurance Portability and Accountability Act and touch on how these policies are related to current and future use of data stored in public database archives. We address aspects of data privacy and identifiability from a technical, although approachable, perspective and summarize how biomedical databanks can be exploited and seemingly anonymous records can be reidentified using various resources without hacking into secure computer systems. We highlight which clinical and translational data features, specified in emerging research models, are potentially vulnerable or exploitable. In the process, we recount a recent privacy-related concern associated with the publication of aggregate statistics from pooled genome-wide association studies that have had a significant impact on the data sharing policies of National Institutes of Health-sponsored databanks. Based on our analysis and observations we provide a list of recommendations that cover various technical, legal, and policy mechanisms that open clinical databases can adopt to strengthen data privacy protection as they move toward wider deployment and adoption.

Technical and Policy Approaches to Balancing Patient Privacy and Data Sharing in Clinical and Translational Research

PubMed Central

Malin, Bradley; Karp, David; Scheuermann, Richard H.

2010-01-01

Clinical researchers need to share data to support scientific validation and information reuse, and to comply with a host of regulations and directives from funders. Various organizations are constructing informatics resources in the form of centralized databases to ensure widespread availability of data derived from sponsored research. The widespread use of such open databases is contingent on the protection of patient privacy. In this paper, we review several aspects of the privacy-related problems associated with data sharing for clinical research from technical and policy perspectives. We begin with a review of existing policies for secondary data sharing and privacy requirements in the context of data derived from research and clinical settings. In particular, we focus on policies specified by the U.S. National Institutes of Health and the Health Insurance Portability and Accountability Act and touch upon how these policies are related to current, as well as future, use of data stored in public database archives. Next, we address aspects of data privacy and “identifiability” from a more technical perspective, and review how biomedical databanks can be exploited and seemingly anonymous records can be “re-identified” using various resources without compromising or hacking into secure computer systems. We highlight which data features specified in clinical research data models are potentially vulnerable or exploitable. In the process, we recount a recent privacy-related concern associated with the publication of aggregate statistics from pooled genome-wide association studies that has had a significant impact on the data sharing policies of NIH-sponsored databanks. Finally, we conclude with a list of recommendations that cover various technical, legal, and policy mechanisms that open clinical databases can adopt to strengthen data privacy protections as they move toward wider deployment and adoption. PMID:20051768

A DBMS architecture for global change research

NASA Astrophysics Data System (ADS)

Hachem, Nabil I.; Gennert, Michael A.; Ward, Matthew O.

1993-08-01

The goal of this research is the design and development of an integrated system for the management of very large scientific databases, cartographic/geographic information processing, and exploratory scientific data analysis for global change research. The system will represent both spatial and temporal knowledge about natural and man-made entities on the eath's surface, following an object-oriented paradigm. A user will be able to derive, modify, and apply, procedures to perform operations on the data, including comparison, derivation, prediction, validation, and visualization. This work represents an effort to extend the database technology with an intrinsic class of operators, which is extensible and responds to the growing needs of scientific research. Of significance is the integration of many diverse forms of data into the database, including cartography, geography, hydrography, hypsography, images, and urban planning data. Equally important is the maintenance of metadata, that is, data about the data, such as coordinate transformation parameters, map scales, and audit trails of previous processing operations. This project will impact the fields of geographical information systems and global change research as well as the database community. It will provide an integrated database management testbed for scientific research, and a testbed for the development of analysis tools to understand and predict global change.

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

Troyer Syndrome

MedlinePlus

... Coordinating Committees CounterACT Rigor & Transparency Scientific Resources Animal Models Cell/Tissue/DNA Clinical and Translational Resources Gene ... Coordinating Committees CounterACT Rigor & Transparency Scientific Resources Animal Models Cell/Tissue/DNA Clinical and Translational Resources Gene ...

Water resources scientific information center

USGS Publications Warehouse

Cardin, C. William; Campbell, J.T.

1986-01-01

The Water Resources Scientific Information Center (WRSIC) acquires, abstracts and indexes the major water resources related literature of the world, and makes information available to the water resources community and the public. A component of the Water Resources Division of the US Geological Survey, the Center maintains a searchable computerized bibliographic data base, and publishers a monthly journal of abstracts. Through its services, the Center is able to provide reliable scientific and technical information about the most recent water resources developments, as well as long-term trends and changes. WRSIC was established in 1966 by the Secretary of the Interior to further the objectives of the Water Resources Research Act of 1964--legislation that encouraged research in water resources and the prevention of needless duplication of research efforts. It was determined the WRSIC should be the national center for information on water resources, covering research reports, scientific journals, and other water resources literature of the world. WRSIC would evaluate all water resources literature, catalog selected articles, and make the information available in publications or by computer access. In this way WRSIC would increase the availability and awareness of water related scientific and technical information. (Lantz-PTT)

Community Level Stressors and Their Impacts on Food ...

EPA Pesticide Factsheets

Research is needed to understand a community’s food resources, utilization of those resources, and how the built and natural environment impact access to resources and potential chemical exposures. This research will identify stressors, relationships between those stressors, and explore potential interactions between food resources and chemical and non-chemical stressors. By evaluating various chemical and non-chemical stressors, an understanding of a community’s food resources and utilization with potential exposures can be obtained. With this understanding about the community’s potential dietary exposures and contributing factors, it will be possible to evaluate ways to mitigate and alleviate issues that could impact public health. The objectives of this research are 1) to obtain information on a community’s environmental exposures (chemical and non-chemical stressors) from various available databases and data and 2) to evaluate impacts on dietary exposure which may lead to adverse public health outcomes. This research will enhance public tools, in particular, the Community-Focused Exposure and Risk Screening Tool (CFERST), which can be utilized by community leaders in decision making by bridging all pertinent information to inform policy. Community level health analyses can support protective actions, be used by communities to identify and prioritize their risks based on scientific data and ensure that resources are directed where they will provi

Characteristics of Resources Represented in the OCLC CORC Database.

ERIC Educational Resources Information Center

Connell, Tschera Harkness; Prabha, Chandra

2002-01-01

Examines the characteristics of Web resources in Online Computer Library Center's (OCLC) Cooperative Online Resource Catalog (CORC) in terms of subject matter, source of content, publication patterns, and units of information chosen for representation in the database. Suggests that the ability to successfully use a database depends on…

Promoting Access, Retention, and Interest in Astronomy Higher Education: Developing the STEM Professionals of Tomorrow in New Mexico

NASA Astrophysics Data System (ADS)

Vogt, N. P.; Muise, A. S.; Cook, S.; Voges, E.

2011-09-01

Economic stability and success are becoming increasingly tied to the successful acquisition of basic academic skills, with the emergence of a computer- and data-oriented society. The recent doubling of the statewide requirement for laboratory science courses at the college level in New Mexico thus represents both an opportunity to further aid in the development of math and science skills in our general population and an added barrier to degree completion. Couple this to a geographically dispersed population of non-traditional students, with workforce and family responsibilities that compete directly for time with academics, and we have a compelling need for alternate methods of teaching science in New Mexico. We present a set of NASA- and NSF-sponsored resources under development to aid in teaching astronomy as a laboratory science at the college level, with usage results for a pilot group of students. Primary components include a self-review database of 10,000+ questions, an instructor review interface, a set of laboratory exercises suitable for students working alone at a distance, and interviews with diverse science, technology, engineering, and mathematics (STEM) individuals to help combat stereotype threat. We discuss learning strategies often employed by students without substantial scientific training and ways to incorporate these strategies into a conceptual framework based on the scientific method and basic techniques for data analysis. Interested science educators may request guest user status to access our self-review database and explore the possibility of using the database for a class or cohort of students at their own institutions.

[25 Years in nutrition and food research in the Iberoamerican knowledge area].

PubMed

Wanden-Berghe, C; Martín-Rodero, H

2012-11-01

Research is usually considered a reliable indicator of the degree of development. Research in a problematic area such as food and nutrition for a given region, should have an impact on scientific production in agreement with the importance of the problem, the research capacity and the available resources for generating such a research. To identify some indicators of Iberoamerican research in nutrition and food. Retrospective study of Iberoamerican scientific production in nutrition and food in the last 25 years. The data were obtained from the bibliographic database Science Citation Index Expanded, Journal Citation Reports Science Edition Database 2011, both included in the Web of Knowledge (Thomson Reuters), and the database of the World Bank. 49,808 papers were registered, the 3.20% of the Health Sciences collection in SCI. The evolution was fitted to an exponential model, N&D (R² 0.962) and FS&T (R² 0.995). The average production in N&D per average population was higher in Spain with 0.659 papers/million. The highest rates of productivity and profitability were found in Guatemala with 12.963 papers/1000 researchers and 1.486 papers/million $ respectively. The average production in FS&T of the different countries per average population was higher in Cuba with 21.624 papers/million. The productivity index was higher in Uruguay with 25.999 papers/thousand researchers. The profitability index was higher in Guatemala with 0.271 papers/million $. There is exponential growth in the two categories studied N&D and FS&T. Productivity and profitability was higher in countries with low R&D (Research & Development) budget.

Transient Ischemic Attack

MedlinePlus

... Coordinating Committees CounterACT Rigor & Transparency Scientific Resources Animal Models Cell/Tissue/DNA Clinical and Translational Resources Gene ... Coordinating Committees CounterACT Rigor & Transparency Scientific Resources Animal Models Cell/Tissue/DNA Clinical and Translational Resources Gene ...

NASA scientific and technical information for the 1990s

NASA Technical Reports Server (NTRS)

Cotter, Gladys A.

1990-01-01

Projections for NASA scientific and technical information (STI) in the 1990s are outlined. NASA STI for the 1990s will maintain a quality bibliographic and full-text database, emphasizing electronic input and products supplemented by networked access to a wide variety of sources, particularly numeric databases.

The Quantitative Measurement of Organizational Culture in Health Care: A Review of the Available Instruments

PubMed Central

Scott, Tim; Mannion, Russell; Davies, Huw; Marshall, Martin

2003-01-01

Objective To review the quantitative instruments available to health service researchers who want to measure culture and cultural change. Data Sources A literature search was conducted using Medline, Cinahl, Helmis, Psychlit, Dhdata, and the database of the King's Fund in London for articles published up to June 2001, using the phrase “organizational culture.” In addition, all citations and the gray literature were reviewed and advice was sought from experts in the field to identify instruments not found on the electronic databases. The search focused on instruments used to quantify culture with a track record, or potential for use, in health care settings. Data Extraction For each instrument we examined the cultural dimensions addressed, the number of items for each questionnaire, the measurement scale adopted, examples of studies that had used the tool, the scientific properties of the instrument, and its strengths and limitations. Principal Findings Thirteen instruments were found that satisfied our inclusion criteria, of which nine have a track record in studies involving health care organizations. The instruments varied considerably in terms of their grounding in theory, format, length, scope, and scientific properties. Conclusions A range of instruments with differing characteristics are available to researchers interested in organizational culture, all of which have limitations in terms of their scope, ease of use, or scientific properties. The choice of instrument should be determined by how organizational culture is conceptualized by the research team, the purpose of the investigation, intended use of the results, and availability of resources. PMID:12822919

A scoping review of competencies for scientific editors of biomedical journals.

PubMed

Galipeau, James; Barbour, Virginia; Baskin, Patricia; Bell-Syer, Sally; Cobey, Kelly; Cumpston, Miranda; Deeks, Jon; Garner, Paul; MacLehose, Harriet; Shamseer, Larissa; Straus, Sharon; Tugwell, Peter; Wager, Elizabeth; Winker, Margaret; Moher, David

2016-02-02

Biomedical journals are the main route for disseminating the results of health-related research. Despite this, their editors operate largely without formal training or certification. To our knowledge, no body of literature systematically identifying core competencies for scientific editors of biomedical journals exists. Therefore, we aimed to conduct a scoping review to determine what is known on the competency requirements for scientific editors of biomedical journals. We searched the MEDLINE®, Cochrane Library, Embase®, CINAHL, PsycINFO, and ERIC databases (from inception to November 2014) and conducted a grey literature search for research and non-research articles with competency-related statements (i.e. competencies, knowledge, skills, behaviors, and tasks) pertaining to the role of scientific editors of peer-reviewed health-related journals. We also conducted an environmental scan, searched the results of a previous environmental scan, and searched the websites of existing networks, major biomedical journal publishers, and organizations that offer resources for editors. A total of 225 full-text publications were included, 25 of which were research articles. We extracted a total of 1,566 statements possibly related to core competencies for scientific editors of biomedical journals from these publications. We then collated overlapping or duplicate statements which produced a list of 203 unique statements. Finally, we grouped these statements into seven emergent themes: (1) dealing with authors, (2) dealing with peer reviewers, (3) journal publishing, (4) journal promotion, (5) editing, (6) ethics and integrity, and (7) qualities and characteristics of editors. To our knowledge, this scoping review is the first attempt to systematically identify possible competencies of editors. Limitations are that (1) we may not have captured all aspects of a biomedical editor's work in our searches, (2) removing redundant and overlapping items may have led to the elimination of some nuances between items, (3) restricting to certain databases, and only French and English publications, may have excluded relevant publications, and (4) some statements may not necessarily be competencies. This scoping review is the first step of a program to develop a minimum set of core competencies for scientific editors of biomedical journals which will be followed by a training needs assessment, a Delphi exercise, and a consensus meeting.

HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma

PubMed Central

Henrique, Tiago; José Freitas da Silveira, Nelson; Henrique Cunha Volpato, Arthur; Mioto, Mayra Mataruco; Carolina Buzzo Stefanini, Ana; Bachir Fares, Adil; Gustavo da Silva Castro Andrade, João; Masson, Carolina; Verónica Mendoza López, Rossana; Daumas Nunes, Fabio; Paulo Kowalski, Luis; Severino, Patricia; Tajara, Eloiza Helena

2016-01-01

The total amount of scientific literature has grown rapidly in recent years. Specifically, there are several million citations in the field of cancer. This makes it difficult, if not impossible, to manually retrieve relevant information on the mechanisms that govern tumor behavior or the neoplastic process. Furthermore, cancer is a complex disease or, more accurately, a set of diseases. The heterogeneity that permeates many tumors is particularly evident in head and neck (HN) cancer, one of the most common types of cancer worldwide. In this study, we present HNdb, a free database that aims to provide a unified and comprehensive resource of information on genes and proteins involved in HN squamous cell carcinoma, covering data on genomics, transcriptomics, proteomics, literature citations and also cross-references of external databases. Different literature searches of MEDLINE abstracts were performed using specific Medical Subject Headings (MeSH terms) for oral, oropharyngeal, hypopharyngeal and laryngeal squamous cell carcinomas. A curated gene-to-publication assignment yielded a total of 1370 genes related to HN cancer. The diversity of results allowed identifying novel and mostly unexplored gene associations, revealing, for example, that processes linked to response to steroid hormone stimulus are significantly enriched in genes related to HN carcinomas. Thus, our database expands the possibilities for gene networks investigation, providing potential hypothesis to be tested. Database URL: http://www.gencapo.famerp.br/hndb PMID:27013077

RaftProt: mammalian lipid raft proteome database.

PubMed

Shah, Anup; Chen, David; Boda, Akash R; Foster, Leonard J; Davis, Melissa J; Hill, Michelle M

2015-01-01

RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

GBIS: the information system of the German Genebank

PubMed Central

Oppermann, Markus; Weise, Stephan; Dittmann, Claudia; Knüpffer, Helmut

2015-01-01

The German Federal ex situ Genebank of Agricultural and Horticultural Crop Species is the largest collection of its kind in the countries of the European Union and amongst the 10 largest collections worldwide. Beside its enormous scientific value as a safeguard of plant biodiversity, the plant genetic resources maintained are also of high importance for breeders to provide new impulses. The complex processes of managing such a collection are supported by the Genebank Information System (GBIS). GBIS is an important source of information for researchers and plant breeders, e.g. for identifying appropriate germplasm for breeding purposes. In addition, the access to genebank material as a sovereign task is also of high interest to the general public. Moreover, GBIS acts as a data source for global information systems, such as the Global Biodiversity Information Facility (GBIF) or the European Search Catalogue for Plant Genetic Resources (EURISCO). Database URL: http://gbis.ipk-gatersleben.de/ PMID:25953079

An object-oriented programming system for the integration of internet-based bioinformatics resources.

PubMed

Beveridge, Allan

2006-01-01

The Internet consists of a vast inhomogeneous reservoir of data. Developing software that can integrate a wide variety of different data sources is a major challenge that must be addressed for the realisation of the full potential of the Internet as a scientific research tool. This article presents a semi-automated object-oriented programming system for integrating web-based resources. We demonstrate that the current Internet standards (HTML, CGI [common gateway interface], Java, etc.) can be exploited to develop a data retrieval system that scans existing web interfaces and then uses a set of rules to generate new Java code that can automatically retrieve data from the Web. The validity of the software has been demonstrated by testing it on several biological databases. We also examine the current limitations of the Internet and discuss the need for the development of universal standards for web-based data.

The National Landslide Database and GIS for Great Britain: construction, development, data acquisition, application and communication

NASA Astrophysics Data System (ADS)

Pennington, Catherine; Dashwood, Claire; Freeborough, Katy

2014-05-01

The National Landslide Database has been developed by the British Geological Survey (BGS) and is the focus for national geohazard research for landslides in Great Britain. The history and structure of the geospatial database and associated Geographical Information System (GIS) are explained, along with the future developments of the database and its applications. The database is the most extensive source of information on landslides in Great Britain with over 16,500 records of landslide events, each documented as fully as possible. Data are gathered through a range of procedures, including: incorporation of other databases; automated trawling of current and historical scientific literature and media reports; new field- and desk-based mapping technologies with digital data capture, and crowd-sourcing information through social media and other online resources. This information is invaluable for the investigation, prevention and mitigation of areas of unstable ground in accordance with Government planning policy guidelines. The national landslide susceptibility map (GeoSure) and a national landslide domain map currently under development rely heavily on the information contained within the landslide database. Assessing susceptibility to landsliding requires knowledge of the distribution of failures and an understanding of causative factors and their spatial distribution, whilst understanding the frequency and types of landsliding present is integral to modelling how rainfall will influence the stability of a region. Communication of landslide data through the Natural Hazard Partnership (NHP) contributes to national hazard mitigation and disaster risk reduction with respect to weather and climate. Daily reports of landslide potential are published by BGS through the NHP and data collected for the National Landslide Database is used widely for the creation of these assessments. The National Landslide Database is freely available via an online GIS and is used by a variety of stakeholders for research purposes.

McMaster Optimal Aging Portal: an evidence-based database for geriatrics-focused health professionals.

PubMed

Barbara, Angela M; Dobbins, Maureen; Brian Haynes, R; Iorio, Alfonso; Lavis, John N; Raina, Parminder; Levinson, Anthony J

2017-07-11

The objective of this work was to provide easy access to reliable health information based on good quality research that will help health care professionals to learn what works best for seniors to stay as healthy as possible, manage health conditions and build supportive health systems. This will help meet the demands of our aging population that clinicians provide high quality care for older adults, that public health professionals deliver disease prevention and health promotion strategies across the life span, and that policymakers address the economic and social need to create a robust health system and a healthy society for all ages. The McMaster Optimal Aging Portal's (Portal) professional bibliographic database contains high quality scientific evidence about optimal aging specifically targeted to clinicians, public health professionals and policymakers. The database content comes from three information services: McMaster Premium LiteratUre Service (MacPLUS™), Health Evidence™ and Health Systems Evidence. The Portal is continually updated, freely accessible online, easily searchable, and provides email-based alerts when new records are added. The database is being continually assessed for value, usability and use. A number of improvements are planned, including French language translation of content, increased linkages between related records within the Portal database, and inclusion of additional types of content. While this article focuses on the professional database, the Portal also houses resources for patients, caregivers and the general public, which may also be of interest to geriatric practitioners and researchers.

LiMPETS: Scientists Contributions to Coastal Protection Program for Youth

NASA Astrophysics Data System (ADS)

Saltzman, J.; Osborn, D. A.

2004-12-01

In the West Coast National Marine Sanctuaries' LiMPETS (Long-term Monitoring Experiential Training for Students), scientists have partnered with local sanctuaries to develop an educational and scientifically-based monitoring program. With different levels of commitment and interest, scientists have contributed to developing protocols that youth can successfully use to monitor coastal habitats. LiMPETS was developed to address the gap in marine science education for high school students. The team of sanctuary educators together with local scientists collaborate and compromise to develop scientifically accurate and meaningful monitoring projects. By crossing the border between scientists and educators, LiMPETS has become a rich program which provides to teachers professional development, monitoring equipment, an online database, and field support. In the Sandy Beach Monitoring Project, we called on an expert on the sand crab Emerita analoga to help us modify the protocols that she uses to monitor crabs regularly. This scientist brings inspiration to teachers at teacher workshops by explaining how the student monitoring compliments her research. The Rocky Intertidal Monitoring Project was developed by scientists at University of California at Santa Cruz with the intention of passing on this project to an informal learning center. After receiving California Sea Grant funding, the protocols used for over 30 years with undergraduates were modified for middle and high school students. With the help of teachers, classroom activities were developed to train students for fieldwork. The online database was envisioned by the scientists to house the historical data from undergraduate students while growing with new data collected middle and high school students. The support of scientists in this program has been crucial to develop a meaningful program for both youth and resource managers. The hours that a scientist contributes to this program may be minimal, a weeklong workshop or even a part-time job. The framework of resource protection agencies partnering with scientists can be replicated to monitor other natural habitats. Through LiMPETS, scientists are helping to develop scientifically literate youth who are engaged in environmental monitoring.

A bibliometric analysis of systematic reviews on vaccines and immunisation.

PubMed

Fernandes, Silke; Jit, Mark; Bozzani, Fiammetta; Griffiths, Ulla K; Scott, J Anthony G; Burchett, Helen E D

2018-04-19

SYSVAC is an online bibliographic database of systematic reviews and systematic review protocols on vaccines and immunisation compiled by the London School of Hygiene & Tropical Medicine and hosted by the World Health Organization (WHO) through their National Immunization Technical Advisory Groups (NITAG) resource centre (www.nitag-resource.org). Here the development of the database and a bibliometric review of its content is presented, describing trends in the publication of policy-relevant systematic reviews on vaccines and immunisation from 2008 to 2016. Searches were conducted in seven scientific databases according to a standardized search protocol, initially in 2014 with the most recent update in January 2017. Abstracts and titles were screened according to specific inclusion criteria. All included publications were coded into relevant categories based on a standardized protocol and subsequently analysed to look at trends in time, topic, area of focus, population and geographic location. After screening for inclusion criteria, 1285 systematic reviews were included in the database. While in 2008 there were only 34 systematic reviews on a vaccine-related topic, this increased to 322 in 2016. The most frequent pathogens/diseases studied were influenza, human papillomavirus and pneumococcus. There were several areas of duplication and overlap. As more systematic reviews are published it becomes increasingly time-consuming for decision-makers to identify relevant information among the ever-increasing volume available. The risk of duplication also increases, particularly given the current lack of coordination of systematic reviews on vaccine-related questions, both in terms of their commissioning and their execution. The SYSVAC database offers an accessible catalogue of vaccine-relevant systematic reviews with, where possible access or a link to the full-text. SYSVAC provides a freely searchable platform to identify existing vaccine-policy-relevant systematic reviews. Systematic reviews will need to be assessed adequately for each specific question and quality. Copyright © 2018. Published by Elsevier Ltd.

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.

CPLA 1.0: an integrated database of protein lysine acetylation.

PubMed

Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

2011-01-01

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein-protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org.

MRPrimerV: a database of PCR primers for RNA virus detection

PubMed Central

Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Kim, Doyun; Koo, JaeHyung; Kim, Min-Soo

2017-01-01

Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks. PMID:27899620

Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas.

PubMed

Chu, Philip; Peck, Joshua; Brumberg, Joshua C

2015-01-01

Laboratory instruction of neuroscience is often limited by the lack of physical resources and supplies (e.g., brains specimens, dissection kits, physiological equipment). Online databases can serve as supplements to material labs by providing professionally collected images of brain specimens and their underlying cellular populations with resolution and quality that is extremely difficult to access for strictly pedagogical purposes. We describe a method using two online databases, the Neuromorpho.org and the Allen Brain Atlas (ABA), that freely provide access to data from working brain scientists that can be modified for laboratory instruction/exercises. Neuromorpho.org is the first neuronal morphology database that provides qualitative and quantitative data from reconstructed cells analyzed in published scientific reports. The Neuromorpho.org database contains cross species and multiple neuronal phenotype datasets which allows for comparative examinations. The ABA provides modules that allow students to study the anatomy of the rodent brain, as well as observe the different cellular phenotypes that exist using histochemical labeling. Using these tools in conjunction, advanced students can ask questions about qualitative and quantitative neuronal morphology, then examine the distribution of the same cell types across the entire brain to gain a full appreciation of the magnitude of the brain's complexity.

CPLA 1.0: an integrated database of protein lysine acetylation

PubMed Central

Liu, Zexian; Cao, Jun; Gao, Xinjiao; Zhou, Yanhong; Wen, Longping; Yang, Xiangjiao; Yao, Xuebiao; Ren, Jian; Xue, Yu

2011-01-01

As a reversible post-translational modification (PTM) discovered decades ago, protein lysine acetylation was known for its regulation of transcription through the modification of histones. Recent studies discovered that lysine acetylation targets broad substrates and especially plays an essential role in cellular metabolic regulation. Although acetylation is comparable with other major PTMs such as phosphorylation, an integrated resource still remains to be developed. In this work, we presented the compendium of protein lysine acetylation (CPLA) database for lysine acetylated substrates with their sites. From the scientific literature, we manually collected 7151 experimentally identified acetylation sites in 3311 targets. We statistically studied the regulatory roles of lysine acetylation by analyzing the Gene Ontology (GO) and InterPro annotations. Combined with protein–protein interaction information, we systematically discovered a potential human lysine acetylation network (HLAN) among histone acetyltransferases (HATs), substrates and histone deacetylases (HDACs). In particular, there are 1862 triplet relationships of HAT-substrate-HDAC retrieved from the HLAN, at least 13 of which were previously experimentally verified. The online services of CPLA database was implemented in PHP + MySQL + JavaScript, while the local packages were developed in JAVA 1.5 (J2SE 5.0). The CPLA database is freely available for all users at: http://cpla.biocuckoo.org. PMID:21059677

Biological network extraction from scientific literature: state of the art and challenges.

PubMed

Li, Chen; Liakata, Maria; Rebholz-Schuhmann, Dietrich

2014-09-01

Networks of molecular interactions explain complex biological processes, and all known information on molecular events is contained in a number of public repositories including the scientific literature. Metabolic and signalling pathways are often viewed separately, even though both types are composed of interactions involving proteins and other chemical entities. It is necessary to be able to combine data from all available resources to judge the functionality, complexity and completeness of any given network overall, but especially the full integration of relevant information from the scientific literature is still an ongoing and complex task. Currently, the text-mining research community is steadily moving towards processing the full body of the scientific literature by making use of rich linguistic features such as full text parsing, to extract biological interactions. The next step will be to combine these with information from scientific databases to support hypothesis generation for the discovery of new knowledge and the extension of biological networks. The generation of comprehensive networks requires technologies such as entity grounding, coordination resolution and co-reference resolution, which are not fully solved and are required to further improve the quality of results. Here, we analyse the state of the art for the extraction of network information from the scientific literature and the evaluation of extraction methods against reference corpora, discuss challenges involved and identify directions for future research. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Family care of people with severe mental disorders: an integrative review

PubMed Central

Juan-Porcar, Maria; Guillamón-Gimeno, Lledó; Pedraz-Marcos, Azucena; Palmar-Santos, Ana María

2015-01-01

OBJECTIVE: to analyze the scientific literature on home-based family care of people with severe mental illness. METHOD: integrative review of 14 databases (CINALH, Cochrane Plus, Cuidatge, CUIDEN, Eric, IBECS, EMI, ISOC, JBI COnNECT, LILACS, PsycINFO, PubMed, SciELO, and Scopus) searched with the key words "family caregivers", "severe mental illness", and "home" between 2003 and 2013. RESULTS: of 787 articles retrieved, only 85 met the inclusion criteria. The articles appeared in 61 journals from different areas and disciplines, mainly from nursing (36%). The countries producing the most scientific literature on nursing were Brazil, the UK, and the US, and authorship predominantly belonged to university centers. A total of 54.12% of the studies presented quantitative designs, with descriptive ones standing out. Work overload, subjective perspectives, and resources were the main topics of these papers. CONCLUSIONS: the international scientific literature on home-based, informal family care of people with severe mental disorder is limited. Nursing research stands out in this field. The prevalent topics coincide with the evolution of the mental health system. The expansion of the scientific approach to family care is promoted to create evidence-based guidelines for family caregivers and for the clinical practice of professional caregivers. PMID:26039308

Mass-storage management for distributed image/video archives

NASA Astrophysics Data System (ADS)

Franchi, Santina; Guarda, Roberto; Prampolini, Franco

1993-04-01

The realization of image/video database requires a specific design for both database structures and mass storage management. This issue has addressed the project of the digital image/video database system that has been designed at IBM SEMEA Scientific & Technical Solution Center. Proper database structures have been defined to catalog image/video coding technique with the related parameters, and the description of image/video contents. User workstations and servers are distributed along a local area network. Image/video files are not managed directly by the DBMS server. Because of their wide size, they are stored outside the database on network devices. The database contains the pointers to the image/video files and the description of the storage devices. The system can use different kinds of storage media, organized in a hierarchical structure. Three levels of functions are available to manage the storage resources. The functions of the lower level provide media management. They allow it to catalog devices and to modify device status and device network location. The medium level manages image/video files on a physical basis. It manages file migration between high capacity media and low access time media. The functions of the upper level work on image/video file on a logical basis, as they archive, move and copy image/video data selected by user defined queries. These functions are used to support the implementation of a storage management strategy. The database information about characteristics of both storage devices and coding techniques are used by the third level functions to fit delivery/visualization requirements and to reduce archiving costs.

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

Database resources of the National Center for Biotechnology Information: 2002 update

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2002-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:11752242

Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).

PubMed

Gilbert, Jack A; Dick, Gregory J; Jenkins, Bethany; Heidelberg, John; Allen, Eric; Mackey, Katherine R M; DeLong, Edward F

2014-06-15

The National Science Foundation's EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on 'omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, "big-data capable" analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean 'omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the 'omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.

Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013)

PubMed Central

Gilbert, Jack A; Dick, Gregory J.; Jenkins, Bethany; Heidelberg, John; Allen, Eric; Mackey, Katherine R. M.

2014-01-01

The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography. PMID:25197495

Enhancing the MeSH thesaurus to retrieve French online health resources in a quality-controlled gateway.

PubMed

Douyère, Magaly; Soualmia, Lina F; Névéol, Aurélie; Rogozan, Alexandrina; Dahamna, Badisse; Leroy, Jean-Philippe; Thirion, Benoît; Darmoni, Stefan J

2004-12-01

The amount of health information available on the Internet is considerable. In this context, several health gateways have been developed. Among them, CISMeF (Catalogue and Index of Health Resources in French) was designed to catalogue and index health resources in French. The goal of this article is to describe the various enhancements to the MeSH thesaurus developed by the CISMeF team to adapt this terminology to the broader field of health Internet resources instead of scientific articles for the medline bibliographic database. CISMeF uses two standard tools for organizing information: the MeSH thesaurus and several metadata element sets, in particular the Dublin Core metadata format. The heterogeneity of Internet health resources led the CISMeF team to enhance the MeSH thesaurus with the introduction of two new concepts, respectively, resource types and metaterms. CISMeF resource types are a generalization of the publication types of medline. A resource type describes the nature of the resource and MeSH keyword/qualifier pairs describe the subject of the resource. A metaterm is generally a medical specialty or a biological science, which has semantic links with one or more MeSH keywords, qualifiers and resource types. The CISMeF terminology is exploited for several tasks: resource indexing performed manually, resource categorization performed automatically, visualization and navigation through the concept hierarchies and information retrieval using the Doc'CISMeF search engine. The CISMeF health gateway uses several MeSH thesaurus enhancements to optimize information retrieval, hierarchy navigation and automatic indexing.

Analysis and interpretation of diffuse x-ray emission using data from the Einstein satellite

NASA Technical Reports Server (NTRS)

Helfand, David J.

1991-01-01

An ambitious program to create a powerful and accessible archive of the HEAO-2 Imaging Proportional Counter (IPC) database was outlined. The scientific utility of that database for studies of diffuse x ray emissions was explored. Technical and scientific accomplishments are reviewed. Three papers were presented which have major new scientific findings relevant to the global structure of the interstellar medium and the origin of the cosmic x ray background. An all-sky map of diffuse x ray emission was constructed.

How Do You Like Your Science, Wet or Dry? How Two Lab Experiences Influence Student Understanding of Science Concepts and Perceptions of Authentic Scientific Practice

PubMed Central

Munn, Maureen; Knuth, Randy; Van Horne, Katie; Shouse, Andrew W.; Levias, Sheldon

2017-01-01

This study examines how two kinds of authentic research experiences related to smoking behavior—genotyping human DNA (wet lab) and using a database to test hypotheses about factors that affect smoking behavior (dry lab)—influence students’ perceptions and understanding of scientific research and related science concepts. The study used pre and post surveys and a focus group protocol to compare students who conducted the research experiences in one of two sequences: genotyping before database and database before genotyping. Students rated the genotyping experiment to be more like real science than the database experiment, in spite of the fact that they associated more scientific tasks with the database experience than genotyping. Independent of the order of completing the labs, students showed gains in their understanding of science concepts after completion of the two experiences. There was little change in students’ attitudes toward science pre to post, as measured by the Scientific Attitude Inventory II. However, on the basis of their responses during focus groups, students developed more sophisticated views about the practices and nature of science after they had completed both research experiences, independent of the order in which they experienced them. PMID:28572181

[Bio-Resources and Database for Preemptive Medicine.

PubMed

Saito, Kuniaki

2016-05-01

Establishing a primary defense for the improvement of individual quality of life by epidemiology and various clinical studies applying bio-resources/database analysis is very important. Furthermore, recent studies on understanding the epigenetic regulatory mechanisms of developmental origins of health and diseases are attracting increasing interest. Therefore, the storing of not only bio-fluid (i.e., blood, urine) but also certain tissues (i.e., placenta, cord) is very important for research. The Resource Center for Health Science (RECHS) and Bio-databases Institute of Reproductive and Developmental Medicine (BIRD) have estab- lished Bio-bank and initiated a project based on the development and utilization of bio-resources/database, comprising personal health records (PHR), such as health/medical records including individual records of daily diet and exercise, physically consolidated with bio-resources, taken from the same individuals. These Bio-Resources/Database projects are very important for the establishment of preemptive medicine and un- derstanding the mechanisms of the developmental origins of health and diseases.

International Collaboration in Data Management for Scientific Ocean Drilling: Preserving Legacy Data While Implementing New Requirements.

NASA Astrophysics Data System (ADS)

Rack, F. R.

2005-12-01

The Integrated Ocean Drilling Program (IODP: 2003-2013 initial phase) is the successor to the Deep Sea Drilling Project (DSDP: 1968-1983) and the Ocean Drilling Program (ODP: 1985-2003). These earlier scientific drilling programs amassed collections of sediment and rock cores (over 300 kilometers stored in four repositories) and data organized in distributed databases and in print or electronic publications. International members of the IODP have established, through memoranda, the right to have access to: (1) all data, samples, scientific and technical results, all engineering plans, data or other information produced under contract to the program; and, (2) all data from geophysical and other site surveys performed in support of the program which are used for drilling planning. The challenge that faces the individual platform operators and management of IODP is to find the right balance and appropriate synergies among the needs, expectations and requirements of stakeholders. The evolving model for IODP database services consists of the management and integration of data collected onboard the various IODP platforms (including downhole logging and syn-cruise site survey information), legacy data from DSDP and ODP, data derived from post-cruise research and publications, and other IODP-relevant information types, to form a common, program-wide IODP information system (e.g., IODP Portal) which will be accessible to both researchers and the public. The JANUS relational database of ODP was introduced in 1997 and the bulk of ODP shipboard data has been migrated into this system, which is comprised of a relational data model consisting of over 450 tables. The JANUS database includes paleontological, lithostratigraphic, chemical, physical, sedimentological, and geophysical data from a global distribution of sites. For ODP Legs 100 through 210, and including IODP Expeditions 301 through 308, JANUS has been used to store data from 233,835 meters of core recovered, which are comprised of 38,039 cores, with 202,281 core sections stored in repositories, which have resulted in the taking of 2,299,180 samples for scientists and other users (http://iodp.tamu.edu/janusweb/general/dbtable.cgi). JANUS and other IODP databases are viewed as components of an evolving distributed network of databases, supported by metadata catalogs and middleware with XML workflows, that are intended to provide access to DSDP/ODP/IODP cores and sample-based data as well as other distributed geoscience data collections (e.g., CHRONOS, PetDB, SedDB). These data resources can be explored through the use of emerging data visualization environments, such as GeoWall, CoreWall (http://(www.evl.uic.edu/cavern/corewall), a multi-screen display for viewing cores and related data, GeoWall-2 and LambdaVision, a very-high resolution, networked environment for data exploration and visualization, and others. The U.S Implementing Organization (USIO) for the IODP, also known as the JOI Alliance, is a partnership between Joint Oceanographic Institutions (JOI), Texas A&M University, and Lamont-Doherty Earth Observatory of Columbia University. JOI is a consortium of 20 premier oceanographic research institutions that serves the U.S. scientific community by leading large-scale, global research programs in scientific ocean drilling and ocean observing. For more than 25 years, JOI has helped facilitate discovery and advance global understanding of the Earth and its oceans through excellence in program management.

RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

PubMed Central

Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

2014-01-01

Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA–RNA/RNA–protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA–RNA interactions and 1619 RNA–protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA–RNA/RNA–protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA–RNA/RNA–protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. PMID:24803509

Geospatial analysis identifies critical mineral-resource potential in Alaska

USGS Publications Warehouse

Karl, Susan M.; Labay, Keith A.; Jacques, Katherine; Landowski, Claire

2017-03-03

Alaska consists of more than 663,000 square miles (1,717,000 square kilometers) of land—more than a sixth of the total area of the United States—and large tracts of it have not been systematically studied or sampled for mineral-resource potential. Many regions of the State are known to have significant mineral-resource potential, and there are currently six operating mines in the State along with numerous active mineral exploration projects. The U.S. Geological Survey and the Alaska Division of Geological & Geophysical Surveys have developed a new geospatial tool that integrates and analyzes publicly available databases of geologic information and estimates the mineral-resource potential for critical minerals, which was recently used to evaluate Alaska. The results of the analyses highlight areas that have known mineral deposits and also reveal areas that were not previously considered to be prospective for these deposit types. These results will inform land management decisions by Federal, State, and private landholders, and will also help guide future exploration activities and scientific investigations in Alaska.

GGDonto ontology as a knowledge-base for genetic diseases and disorders of glycan metabolism and their causative genes.

PubMed

Solovieva, Elena; Shikanai, Toshihide; Fujita, Noriaki; Narimatsu, Hisashi

2018-04-18

Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes. Many biomedical resources provide information about genetic disorders and genes involved in their pathogenesis, but resources focused on genetic disorders known to be related to glycan metabolism are lacking. With the aim of providing more comprehensive knowledge on genetic diseases and disorders of glycan biosynthesis and degradation, we enriched the content of the GDGDB database and improved the methods for data representation. We developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto content using Semantic Web languages, such as RDF, RDFS, SKOS, and OWL, and created an interactive user interface based on SPARQL queries. This user interface provides features to browse the hierarchy of the ontology, view detailed information on diseases and related genes, and find relevant background information. Moreover, it provides the ability to filter and search information by faceted and keyword searches. Focused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.

Protein Bioinformatics Databases and Resources

PubMed Central

Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.

2017-01-01

Many publicly available data repositories and resources have been developed to support protein related information management, data-driven hypothesis generation and biological knowledge discovery. To help researchers quickly find the appropriate protein related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era. PMID:28150231

EOSCUBE: A Constraint Database System for High-Level Specification and Efficient Generation of EOSDIS Products. Phase 1; Proof-of-Concept

NASA Technical Reports Server (NTRS)

Brodsky, Alexander; Segal, Victor E.

1999-01-01

The EOSCUBE constraint database system is designed to be a software productivity tool for high-level specification and efficient generation of EOSDIS and other scientific products. These products are typically derived from large volumes of multidimensional data which are collected via a range of scientific instruments.

The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index.

PubMed

Larsen, Peder Olesen; von Ins, Markus

2010-09-01

The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source.

The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index

PubMed Central

von Ins, Markus

2010-01-01

The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source. PMID:20700371

Geographic analysis and monitoring at the United States Geological Survey

USGS Publications Warehouse

Findley, J.

2003-01-01

The Geographic Analysis and Monitoring (GAM) Program of the U.S. Geological Survey assesses the Nation's land surface at a variety of spatial and temporal scales to understand the rates, causes, and consequences of natural and human-induced processes and their interactions that affect the landscape over time. The program plays an important role in developing National Map tools and application. The GAM is a science and synthesis program that not only assesses the rates of changes to the Earth's land surface, but also provides reports on the status and trends of the Nation's land resources on a periodic basis, produces a land-use and land- cover database for the periodically updated map and data set-the Geographic Face of the Nation, and conducts research leading to improved understanding and knowledge about geographic processes. Scientific investigations provide comprehensive information needed to understand the environmental, resource, and economic consequences of landscape change. These analyses responds to the needs of resource managers and offers the American public baseline information to help them understand the dynamic nature of our national landscape and to anticipate the opportunities and consequences of our actions.

Quantitative evaluation of Iranian radiology papers and its comparison with selected countries.

PubMed

Ghafoori, Mahyar; Emami, Hasan; Sedaghat, Abdolrasoul; Ghiasi, Mohammad; Shakiba, Madjid; Alavi, Manijeh

2014-01-01

Recent technological developments in medicine, including modern radiology have promoted the impact of scientific researches on social life. The scientific outputs such as article and patents are products that show the scientists' attempt to access these achievements. In the current study, we evaluate the current situation of Iranian scientists in the field of radiology and compare it with the selected countries in terms of scientific papers. For this purpose, we used scientometric tools to quantitatively assess the scientific papers in the field of radiology. Radiology papers were evaluated in the context of medical field audit using retrospective model. We used the related databases of biomedical sciences for extraction of articles related to radiology. In the next step, the situation of radiology scientific products of the country were determined with respect to the under study regional countries. Results of the current study showed a ratio of 0.19% for Iranian papers in PubMed database published in 2009. In addition, in 2009, Iranian papers constituted 0.29% of the Scopus scientific database. The proportion of Iranian papers in the understudy region was 7.6%. To diminish the gap between Iranian scientific radiology papers and other competitor countries in the region and achievement of document 2025 goals, multifold effort of the society of radiology is necessary.

The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows.

PubMed

Bellec, Pierre; Lavoie-Courchesne, Sébastien; Dickinson, Phil; Lerch, Jason P; Zijdenbos, Alex P; Evans, Alan C

2012-01-01

The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources.

The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows

PubMed Central

Bellec, Pierre; Lavoie-Courchesne, Sébastien; Dickinson, Phil; Lerch, Jason P.; Zijdenbos, Alex P.; Evans, Alan C.

2012-01-01

The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources. PMID:22493575

A comparative study of six European databases of medically oriented Web resources.

PubMed

Abad García, Francisca; González Teruel, Aurora; Bayo Calduch, Patricia; de Ramón Frias, Rosa; Castillo Blasco, Lourdes

2005-10-01

The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

The BioMart community portal: an innovative alternative to large, centralized data repositories

PubMed Central

Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Andrew; Bonierbale, Merideth; Brookes, Anthony J.; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cédric; Carlson, Joseph W.; Chelala, Claude; Chrysostomou, Charalambos; Cittaro, Davide; Collin, Olivier; Cordova, Raul; Cutts, Rosalind J.; Dassi, Erik; Genova, Alex Di; Djari, Anis; Esposito, Anthony; Estrella, Heather; Eyras, Eduardo; Fernandez-Banet, Julio; Forbes, Simon; Free, Robert C.; Fujisawa, Takatomo; Gadaleta, Emanuela; Garcia-Manteiga, Jose M.; Goodstein, David; Gray, Kristian; Guerra-Assunção, José Afonso; Haggarty, Bernard; Han, Dong-Jin; Han, Byung Woo; Harris, Todd; Harshbarger, Jayson; Hastings, Robert K.; Hayes, Richard D.; Hoede, Claire; Hu, Shen; Hu, Zhi-Liang; Hutchins, Lucie; Kan, Zhengyan; Kawaji, Hideya; Keliet, Aminah; Kerhornou, Arnaud; Kim, Sunghoon; Kinsella, Rhoda; Klopp, Christophe; Kong, Lei; Lawson, Daniel; Lazarevic, Dejan; Lee, Ji-Hyun; Letellier, Thomas; Li, Chuan-Yun; Lio, Pietro; Liu, Chu-Jun; Luo, Jie; Maass, Alejandro; Mariette, Jerome; Maurel, Thomas; Merella, Stefania; Mohamed, Azza Mostafa; Moreews, Francois; Nabihoudine, Ibounyamine; Ndegwa, Nelson; Noirot, Céline; Perez-Llamas, Cristian; Primig, Michael; Quattrone, Alessandro; Quesneville, Hadi; Rambaldi, Davide; Reecy, James; Riba, Michela; Rosanoff, Steven; Saddiq, Amna Ali; Salas, Elisa; Sallou, Olivier; Shepherd, Rebecca; Simon, Reinhard; Sperling, Linda; Spooner, William; Staines, Daniel M.; Steinbach, Delphine; Stone, Kevin; Stupka, Elia; Teague, Jon W.; Dayem Ullah, Abu Z.; Wang, Jun; Ware, Doreen; Wong-Erasmus, Marie; Youens-Clark, Ken; Zadissa, Amonida; Zhang, Shi-Jian; Kasprzyk, Arek

2015-01-01

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations. PMID:25897122

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer.

PubMed

Krupke, Debra M; Begley, Dale A; Sundberg, John P; Richardson, Joel E; Neuhauser, Steven B; Bult, Carol J

2017-11-01

Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. The Mouse Tumor Biology (MTB) database is an expertly curated, comprehensive compendium of mouse models of human cancer. Through the enforcement of nomenclature and related annotation standards, MTB supports aggregation of data about a cancer model from diverse sources and assessment of how genetic background of a mouse strain influences the biological properties of a specific tumor type and model utility. Cancer Res; 77(21); e67-70. ©2017 AACR . ©2017 American Association for Cancer Research.

Expedition Memory: Towards Agent-based Web Services for Creating and Using Mars Exploration Data.

NASA Technical Reports Server (NTRS)

Clancey, William J.; Sierhuis, Maarten; Briggs, Geoff; Sims, Mike

2005-01-01

Explorers ranging over kilometers of rugged, sometimes "feature-less" terrain for over a year could be overwhelmed by tracking and sharing what they have done and learned. An automated system based on the existing Mobile Agents design [ I ] and Mars Exploration Rover experience [2], could serve as an "expedition memory" that would be indexed by voice as wel1 as a web interface, linking people, places, activities, records (voice notes, photographs, samples). and a descriptive scientific ontology. This database would be accessible during EVAs by astronauts, annotated by the remote science team, linked to EVA plans, and allow cross indexing between sites and expeditions. We consider the basic problem, our philosophical approach, technical methods, and uses of the expedition memory for facilitating long-term collaboration between Mars crews and Earth support teams. We emphasize that a "memory" does not mean a database per se, but an interactive service that combines different resources, and ultimately could be like a helpful librarian.

CORUM: the comprehensive resource of mammalian protein complexes

PubMed Central

Ruepp, Andreas; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Stransky, Michael; Waegele, Brigitte; Schmidt, Thorsten; Doudieu, Octave Noubibou; Stümpflen, Volker; Mewes, H. Werner

2008-01-01

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes. PMID:17965090

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

PubMed Central

Castagnetto, Jesus M.; Hennessy, Sean W.; Roberts, Victoria A.; Getzoff, Elizabeth D.; Tainer, John A.; Pique, Michael E.

2002-01-01

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB. PMID:11752342

Australian Twin Registry: a nationally funded resource for medical and scientific research, incorporating match and WATCH.

PubMed

Hopper, John L; Treloar, Susan A; de Klerk, Nicholas H; Morley, Ruth

2006-12-01

The Australian Twin Registry (ATR) has, since the late 1970s, enrolled more than 30,000 pairs of all zygosity types and ages willing to consider participation in approved research studies. Its core functions are the recruitment to, and maintenance of, an up-to-date database containing contact details and baseline information, and the management of fair and equitable access so as to enhance medical and scientific research. The ATR has facilitated more than 430 studies producing 525 peer-reviewed publications using a variety of designs including classic biometrical twin and twin family studies, co-twin control studies, intervention studies, longitudinal studies, and studies of issues relevant specifically to twins. The ATR is supported for 2004 to 2009 by an Australian National Health and Medical Research Council (NHMRC) Enabling Grant, a new form of funding which recognizes the importance of long-term support for shared national resources. New initiatives include: integration with the Western Australian Twin Child Health (WATCH) cohort and the new Western Australian Twin Registry (WATR); foundation of a cohort of mothers and their twin children recruited from the time of diagnosis of the multiple gestation (match); a national Twins Festival run in collaboration with the Australian Multiple Birth Association (AMBA); promotion of the ATR at medical conferences; and fostering an active network of researchers from a range of disciplines and providing financial support for new researchers to attend international twin research workshops. Consistent with its mission statement, the long-term goal of the ATR is to make twin studies a standard component of medical and scientific research.

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Johnson, Robin J.; Lennon-Hopkins, Kelley; Sciaky, Daniela; Rosenstein, Michael C.; Wiegers, Thomas C.; Mattingly, Carolyn J.

2012-01-01

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators read the scientific literature and manually curate a triad of chemical–gene, chemical–disease and gene–disease interactions. Typically, articles for CTD are selected using a chemical-centric approach by querying PubMed to retrieve a corpus containing the chemical of interest. Although this technique ensures adequate coverage of knowledge about the chemical (i.e. data completeness), it does not necessarily reflect the most current state of all toxicological research in the community at large (i.e. data currency). Keeping databases current with the most recent scientific results, as well as providing a rich historical background from legacy articles, is a challenging process. To address this issue of data currency, CTD designed and tested a journal-centric approach of curation to complement our chemical-centric method. We first identified priority journals based on defined criteria. Next, over 7 weeks, three biocurators reviewed 2425 articles from three consecutive years (2009–2011) of three targeted journals. From this corpus, 1252 articles contained relevant data for CTD and 52 752 interactions were manually curated. Here, we describe our journal selection process, two methods of document delivery for the biocurators and the analysis of the resulting curation metrics, including data currency, and both intra-journal and inter-journal comparisons of research topics. Based on our results, we expect that curation by select journals can (i) be easily incorporated into the curation pipeline to complement our chemical-centric approach; (ii) build content more evenly for chemicals, genes and diseases in CTD (rather than biasing data by chemicals-of-interest); (iii) reflect developing areas in environmental health and (iv) improve overall data currency for chemicals, genes and diseases. Database URL: http://ctdbase.org/ PMID:23221299

[TOPICS-MDS: a versatile resource for generating scientific and social knowledge for elderly care].

PubMed

van den Brink, Danielle; Lutomski, Jennifer E; Qin, Li; den Elzen, Wendy P J; Kempen, Gertrudis I J M; Krabbe, Paul F M; Steyerberg, Ewout W; Muntinga, Maaike; Moll van Charante, Eric P; Bleijenberg, Nienke; Olde Rikkert, Marcel G M; Melis, René J F

2015-04-01

Developed as part of the National Care for the Elderly Programme (NPO), TOPICS-MDS is a uniform, national database on the health and wellbeing of the older persons and caregivers who participated in NPO-funded projects. TOPICS-MDS Consortium has gained extensive experience in constructing a standardized questionnaire to collect relevant health care data on quality of life, health services utilization, and informal care use. A proactive approach has been undertaken not only to ensure the standardization and validation of instruments but also the infrastructure for external data requests. Efforts have been made to promote scientifically and socially responsible use of TOPICS-MDS; data has been available for secondary use since early 2014. Through this data sharing initiative, researchers can explore health issues in a broader framework which may have not been possible within individual NPO projects; this broader framework is highly relevant for influencing health policy. In this article, we provide an overview of the development and on-going progress of TOPICS-MDS. We further describe how information derived from TOPICS-MDS can be applied to facilitate future scientific innovations and public health initiatives to improve care for frail older persons and their caregivers.

Freely Accessible Chemical Database Resources of Compounds for in Silico Drug Discovery.

PubMed

Yang, JingFang; Wang, Di; Jia, Chenyang; Wang, Mengyao; Hao, GeFei; Yang, GuangFu

2018-05-07

In silico drug discovery has been proved to be a solidly established key component in early drug discovery. However, this task is hampered by the limitation of quantity and quality of compound databases for screening. In order to overcome these obstacles, freely accessible database resources of compounds have bloomed in recent years. Nevertheless, how to choose appropriate tools to treat these freely accessible databases are crucial. To the best of our knowledge, this is the first systematic review on this issue. The existed advantages and drawbacks of chemical databases were analyzed and summarized based on the collected six categories of freely accessible chemical databases from literature in this review. Suggestions on how and in which conditions the usage of these databases could be reasonable were provided. Tools and procedures for building 3D structure chemical libraries were also introduced. In this review, we described the freely accessible chemical database resources for in silico drug discovery. In particular, the chemical information for building chemical database appears as attractive resources for drug design to alleviate experimental pressure. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

2001-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap’99, Human–Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri­tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:11125038

43 CFR 6302.16 - When and how may I gather scientific information about resources in BLM wilderness?

Code of Federal Regulations, 2014 CFR

2014-10-01

... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false When and how may I gather scientific... Penalties Use of Wilderness Areas § 6302.16 When and how may I gather scientific information about resources... natural or cultural resources in wilderness areas, using methods that may cause greater impacts on the...

43 CFR 6302.16 - When and how may I gather scientific information about resources in BLM wilderness?

Code of Federal Regulations, 2013 CFR

2013-10-01

... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false When and how may I gather scientific... Penalties Use of Wilderness Areas § 6302.16 When and how may I gather scientific information about resources... natural or cultural resources in wilderness areas, using methods that may cause greater impacts on the...

43 CFR 6302.16 - When and how may I gather scientific information about resources in BLM wilderness?

Code of Federal Regulations, 2012 CFR

2012-10-01

... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false When and how may I gather scientific... Penalties Use of Wilderness Areas § 6302.16 When and how may I gather scientific information about resources... natural or cultural resources in wilderness areas, using methods that may cause greater impacts on the...

Supporting Middle School Students' Online Reading of Scientific Resources: Moving beyond Cursory, Fragmented, and Opportunistic Reading

ERIC Educational Resources Information Center

Zhang, M.

2013-01-01

The abundant scientific resources on the Web provide great opportunities for students to expand their science learning, yet easy access to information does not ensure learning. Prior research has found that middle school students tend to read Web-based scientific resources in a shallow, superficial manner. A software tool was designed to support…

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.

Emission & Generation Resource Integrated Database (eGRID)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is an integrated source of data on environmental characteristics of electric power generation. Twelve federal databases are represented by eGRID, which provides air emission and resource mix information for thousands of power plants and generating companies. eGRID allows direct comparison of the environmental attributes of electricity from different plants, companies, States, or regions of the power grid.

Open innovation: Towards sharing of data, models and workflows.

PubMed

Conrado, Daniela J; Karlsson, Mats O; Romero, Klaus; Sarr, Céline; Wilkins, Justin J

2017-11-15

Sharing of resources across organisations to support open innovation is an old idea, but which is being taken up by the scientific community at increasing speed, concerning public sharing in particular. The ability to address new questions or provide more precise answers to old questions through merged information is among the attractive features of sharing. Increased efficiency through reuse, and increased reliability of scientific findings through enhanced transparency, are expected outcomes from sharing. In the field of pharmacometrics, efforts to publicly share data, models and workflow have recently started. Sharing of individual-level longitudinal data for modelling requires solving legal, ethical and proprietary issues similar to many other fields, but there are also pharmacometric-specific aspects regarding data formats, exchange standards, and database properties. Several organisations (CDISC, C-Path, IMI, ISoP) are working to solve these issues and propose standards. There are also a number of initiatives aimed at collecting disease-specific databases - Alzheimer's Disease (ADNI, CAMD), malaria (WWARN), oncology (PDS), Parkinson's Disease (PPMI), tuberculosis (CPTR, TB-PACTS, ReSeqTB) - suitable for drug-disease modelling. Organized sharing of pharmacometric executable model code and associated information has in the past been sparse, but a model repository (DDMoRe Model Repository) intended for the purpose has recently been launched. In addition several other services can facilitate model sharing more generally. Pharmacometric workflows have matured over the last decades and initiatives to more fully capture those applied to analyses are ongoing. In order to maximize both the impact of pharmacometrics and the knowledge extracted from clinical data, the scientific community needs to take ownership of and create opportunities for open innovation. Copyright © 2017 Elsevier B.V. All rights reserved.

BRAVO (Brazilian Astrophysical Virtual Observatory): data mining development

NASA Astrophysics Data System (ADS)

De Carvalho, R. R.; Capelato, H. V.; Velho, H. C.

2007-08-01

The primary goal of the BRAVO project is to generate investment in information technology, with particular emphasis on datamining and statistical analysis. From a scientific standpoint, the participants assembled to date are engaged in several scientific projects in various fields of cosmology, astrophysics, and data analysis, with significant contributions from international partners. These scientists conduct research on clusters of galaxies, small groups of galaxies, elliptical galaxies, population synthesis, N-body simulations, and a variety of studies in stellar astrophysics. One of the main aspects of this project is the incorporation of these disparate areas of astrophysical research within the context of the coherent development of database technology.Observational cosmology is one of the branches of science experiencing the largest growth in the past few decades. large photometric and spectroscopic surveys have been carried out in both hemispheres. As a result, an extraordinary amount of data in all portions of the electromagnetic spectrum exists, but without standard techniques for storage and distribution. This project will utilize several specific astronomical databases, created to store data generated by several instruments (including SOAR, Gemini, BDA, etc), uniting them within a common framework and with standard interfaces. We are inviting members of the entire Brazilian astronomical community to partake in this effort. This will certainly impact both education and outreach efforts, as well as the future development of astrophysical research. Finally, this project will provide a constant investment in human resources. First, it will do so by stimulating ongoing short technical visits to Johns Hopkins University and Caltech. These will allow us to bring software technology and expertise in datamining back to Brazil. Second, we will organize the Summer School on Software Technology in Astrophysics, which will be designed to ensure that the Brazilian scientific community can take full advantage of the benefits offered by the VO project

National Vulnerability Database (NVD)

National Institute of Standards and Technology Data Gateway

National Vulnerability Database (NVD) (Web, free access)   NVD is a comprehensive cyber security vulnerability database that integrates all publicly available U.S. Government vulnerability resources and provides references to industry resources. It is based on and synchronized with the CVE vulnerability naming standard.

SciELO, Scientific Electronic Library Online, a Database of Open Access Journals

ERIC Educational Resources Information Center

Meneghini, Rogerio

2013-01-01

This essay discusses SciELO, a scientific journal database operating in 14 countries. It covers over 1000 journals providing open access to full text and table sets of scientometrics data. In Brazil it is responsible for a collection of nearly 300 journals, selected along 15 years as the best Brazilian periodicals in natural and social sciences.…

Human Chromosome Y and Haplogroups; introducing YDHS Database.

PubMed

Tiirikka, Timo; Moilanen, Jukka S

2015-12-01

As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants. The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis. YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.

Host range, host ecology, and distribution of more than 11800 fish parasite species

USGS Publications Warehouse

Strona, Giovanni; Palomares, Maria Lourdes D.; Bailly, Nicholas; Galli, Paolo; Lafferty, Kevin D.

2013-01-01

Our data set includes 38 008 fish parasite records (for Acanthocephala, Cestoda, Monogenea, Nematoda, Trematoda) compiled from the scientific literature, Internet databases, and museum collections paired to the corresponding host ecological, biogeographical, and phylogenetic traits (maximum length, growth rate, life span, age at maturity, trophic level, habitat preference, geographical range size, taxonomy). The data focus on host features, because specific parasite traits are not consistently available across records. For this reason, the data set is intended as a flexible resource able to extend the principles of ecological niche modeling to the host–parasite system, providing researchers with the data to model parasite niches based on their distribution in host species and the associated host features. In this sense, the database offers a framework for testing general ecological, biogeographical, and phylogenetic hypotheses based on the identification of hosts as parasite habitat. Potential applications of the data set are, for example, the investigation of species–area relationships or the taxonomic distribution of host-specificity. The provided host–parasite list is that currently used by Fish Parasite Ecology Software Tool (FishPEST, http://purl.oclc.org/fishpest), which is a website that allows researchers to model several aspects of the relationships between fish parasites and their hosts. The database is intended for researchers who wish to have more freedom to analyze the database than currently possible with FishPEST. However, for readers who have not seen FishPEST, we recommend using this as a starting point for interacting with the database.

Important considerations for feasibility studies in physical activity research involving persons with multiple sclerosis: a scoping systematic review and case study.

PubMed

Learmonth, Yvonne C; Motl, Robert W

2018-01-01

Much research has been undertaken to establish the important benefits of physical activity in persons with multiple sclerosis (MS). There is disagreement regarding the strength of this research, perhaps because the majority of studies on physical activity and its benefits have not undergone initial and systematic feasibility testing. We aim to address the feasibility processes that have been examined within the context of physical activity interventions in MS. A systematic scoping review was conducted based on a literature search of five databases to identify feasibility processes described in preliminary studies of physical activity in MS. We read and extracted methodology from each study based on the following feasibility metrics: process (e.g. recruitment), resource (e.g. monetary costs), management (e.g. personnel time requirements) and scientific outcomes (e.g. clinical/participant reported outcome measures). We illustrate the use of the four feasibility metrics within a randomised controlled trial of a home-based exercise intervention in persons with MS. Twenty-five studies were identified. Resource feasibility (e.g. time and resources) and scientific outcomes feasibility (e.g. clinical outcomes) methodologies were applied and described in many studies; however, these metrics have not been systematically addressed. Metrics related to process feasibility (e.g. recruitment) and management feasibility (e.g. human and data management) are not well described within the literature. Our case study successfully enabled us to address the four feasibility metrics, and we provide new information on management feasibility (i.e. estimate data completeness and estimate data entry) and scientific outcomes feasibility (i.e. determining data collection materials appropriateness). Our review highlights the existing research and provides a case study which assesses important metrics of study feasibility. This review serves as a clarion call for feasibility trials that will substantially strengthen the foundation of research on exercise in MS.

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

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

The designing and implementation of PE teaching information resource database based on broadband network

NASA Astrophysics Data System (ADS)

Wang, Jian

2017-01-01

In order to change traditional PE teaching mode and realize the interconnection, interworking and sharing of PE teaching resources, a distance PE teaching platform based on broadband network is designed and PE teaching information resource database is set up. The designing of PE teaching information resource database takes Windows NT 4/2000Server as operating system platform, Microsoft SQL Server 7.0 as RDBMS, and takes NAS technology for data storage and flow technology for video service. The analysis of system designing and implementation shows that the dynamic PE teaching information resource sharing platform based on Web Service can realize loose coupling collaboration, realize dynamic integration and active integration and has good integration, openness and encapsulation. The distance PE teaching platform based on Web Service and the design scheme of PE teaching information resource database can effectively solve and realize the interconnection, interworking and sharing of PE teaching resources and adapt to the informatization development demands of PE teaching.

Human resources for health: A narrative review of adequacy and distribution of clinical and nonclinical human resources in hospitals of Iran.

PubMed

Nobakht, Samin; Shirdel, Arash; Molavi-Taleghani, Yasamin; Doustmohammadi, Mohammad M; Sheikhbardsiri, Hojjat

2018-03-15

Human resource supply is considered as one of the most vital factors in achieving organizational goals, and human resources are the most valuable factor in the production and delivery of services. Labor shortages and surpluses could downgrade the quality of services offered to patients. Considering the seriousness of this issue, this study aimed to investigate the status of human resources in Iran hospitals. The narrative review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. The key terms "Human Resource," "Human Resource Management," "Staff," "Workforce," "Hospital," "emergency," "staff nursing," "medical," "clinical personnel," "administration," "physician personnel," "non clinical personnel," "hospital personnel," "human development," and "Iran" were used in combination with Boolean operators OR and AND. The Institute for Scientific Information's Web of Science, PubMed, Scopus, ScienceDirect, Ovid, ProQuest, Wiley, Google Scholar, and the Persian database were searched. The research findings revealed that Iran's hospitals have no uniform distribution of human resources. In spite of the concentration of labor forces in some positions (eg, laboratory, radiology, operating room, anesthesia, and midwifery), other positions occupied by physicians and nurses are experiencing serious shortages of human resources, affecting the quality of the provided services. With respect to the study findings, planning to compensate for staff shortages and achieving personnel standard levels as well as providing the grounds for training the heads of wards for proper human resource management and planning would lead to an increase in the efficiency and effectiveness of hospital activities. Copyright © 2018 John Wiley & Sons, Ltd.

Literature searches on Ayurveda: An update.

PubMed

Aggithaya, Madhur G; Narahari, Saravu R

2015-01-01

The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches.

Development of a database of instruments for resource-use measurement: purpose, feasibility, and design.

PubMed

Ridyard, Colin H; Hughes, Dyfrig A

2012-01-01

Health economists frequently rely on methods based on patient recall to estimate resource utilization. Access to questionnaires and diaries, however, is often limited. This study examined the feasibility of establishing an open-access Database of Instruments for Resource-Use Measurement, identified relevant fields for data extraction, and outlined its design. An electronic survey was sent to authors of full UK economic evaluations listed in the National Health Service Economic Evaluation Database (2008-2010), authors of monographs of Health Technology Assessments (1998-2010), and subscribers to the JISCMail health economics e-mailing list. The survey included questions on piloting, validation, recall period, and data capture method. Responses were analyzed and data extracted to generate relevant fields for the database. A total of 143 responses to the survey provided data on 54 resource-use instruments for inclusion in the database. All were reliant on patient or carer recall, and a majority (47) were questionnaires. Thirty-seven were designed for self-completion by the patient, carer, or guardian, and the remainder were designed for completion by researchers or health care professionals while interviewing patients. Methods of development were diverse, particularly in areas such as the planning of resource itemization (evident in 25 instruments), piloting (25), and validation (29). On the basis of the present analysis, we developed a Web-enabled Database of Instruments for Resource-Use Measurement, accessible via www.DIRUM.org. This database may serve as a practical resource for health economists, as well as a means to facilitate further research in the area of resource-use data collection. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

A Global Registry for Scientific Collections: Striking a Balance Between Disciplinary Detail and Interdisciplinary Discoverability

NASA Astrophysics Data System (ADS)

Graham, E.; Schindel, D. E.

2014-12-01

The Global Registry of Scientific Collections (GRSciColl) is an online information resource developed to gather and disseminate basic information on scientific collections. Building on initiatives started for biological collections, GRSciColl expands this framework to encompass all scientific disciplines including earth and space sciences, anthropology, archaeology, biomedicine, and applied fields such as agriculture and technology. The goals of this registry are to (1) provide a single source of synoptic information about the repositories, their component collections, access and use policies, and staff contact information; and (2) facilitate the assignment of identifiers for repositories and their collections that are globally unique across all disciplines. As digitization efforts continue, the importance of globally unique identifiers is paramount to ensuring interoperability across datasets. Search capabilities and web services will significantly increase the web visibility and accessibility of these collections. Institutional records include categorization by governance (e.g., national, state or local governmental, private non-profit) and by scientific discipline (e.g., earth science, biomedical, agricultural). Collection-level metadata categorize the types of contained specimens/samples and modes of preservation. In selecting the level of granularity for these categories, designers sought a compromise that would capture enough information to be useful in searches and inquiries and would complement the detailed archives in specimen-level databases such (which are increasingly digital) hosted by discipline-specific groups (e.g. SESAR) or the repositories themselves (e.g. KE EMu).

CerealsDB 3.0: expansion of resources and data integration.

PubMed

Wilkinson, Paul A; Winfield, Mark O; Barker, Gary L A; Tyrrell, Simon; Bian, Xingdong; Allen, Alexandra M; Burridge, Amanda; Coghill, Jane A; Waterfall, Christy; Caccamo, Mario; Davey, Robert P; Edwards, Keith J

2016-06-24

The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the most important crops in human and livestock diets, and the development of wheat varieties that produce higher yields, combined with increased resistance to pests and resilience to changes in climate, has meant that wheat breeding has become an important focus of scientific research. In an attempt to facilitate these improvements in wheat, plant breeders have employed molecular tools to help them identify genes for important agronomic traits that can be bred into new varieties. Modern molecular techniques have ensured that the rapid and inexpensive characterisation of SNP markers and their validation with modern genotyping methods has produced a valuable resource that can be used in marker assisted selection. CerealsDB was created as a means of quickly disseminating this information to breeders and researchers around the globe. CerealsDB version 3.0 is an online resource that contains a wide range of genomic datasets for wheat that will assist plant breeders and scientists to select the most appropriate markers for use in marker assisted selection. CerealsDB includes a database which currently contains in excess of a million putative varietal SNPs, of which several hundreds of thousands have been experimentally validated. In addition, CerealsDB also contains new data on functional SNPs predicted to have a major effect on protein function and we have constructed a web service to encourage data integration and high-throughput programmatic access. CerealsDB is an open access website that hosts information on SNPs that are considered useful for both plant breeders and research scientists. The recent inclusion of web services designed to federate genomic data resources allows the information on CerealsDB to be more fully integrated with the WheatIS network and other biological databases.

Reef Ecosystem Services and Decision Support Database

EPA Science Inventory

This scientific and management information database utilizes systems thinking to describe the linkages between decisions, human activities, and provisioning of reef ecosystem goods and services. This database provides: (1) Hierarchy of related topics - Click on topics to navigat...

GIS, remote sensing and spatial modeling for conservation of stone forest landscape in Lunan, China

NASA Astrophysics Data System (ADS)

Zhang, Chuanrong

The Lunan Stone Forest is the World's premier pinnacle karst landscape, with considerable scientific and cultural importance. Because of its inherent ecological fragility and ongoing human disruption, especially recently burgeoning tourism development, the landscape is stressed and is in danger of being destroyed. Conservation policies have been implemented by the local and national governments, but many problems remain in the national park. For example, there is no accurate detailed map and no computer system to help authorities manage the natural resources. By integrating GIS, remote sensing and spatial modeling this dissertation investigates the issue of landscape conservation and develops some methodologies to assist in management of the natural resources in the national park. Four elements are involved: (1) To help decision-makers and residents understand the scope of resource exploitation and develop appropriate protective strategies, the dissertation documents how the landscape has been changed by human activities over the past 3 decades; (2) To help authorities scientifically designate different levels of protection in the park and to let the public actively participate in conservation decision making, a web-based Spatial Decision Support System for the conservation of the landscape was developed; (3) To make data sharing and integration easy in the future, a GML-based interoperable database for the park was implemented; and (4) To acquire more information and provide the uncertainty information to landscape conservation decision-makers, spatial land use patterns were modeled and the distributional uncertainty of land cover categories was assessed using a triplex Markov chain (TMC) model approach.

30 CFR 280.11 - What must I do before I may conduct scientific research?

Code of Federal Regulations, 2011 CFR

2011-07-01

... I may conduct scientific research? You may conduct G&G scientific research activities related to... 30 Mineral Resources 2 2011-07-01 2011-07-01 false What must I do before I may conduct scientific research? 280.11 Section 280.11 Mineral Resources BUREAU OF OCEAN ENERGY MANAGEMENT, REGULATION, AND...

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.

Potash: a global overview of evaporate-related potash resources, including spatial databases of deposits, occurrences, and permissive tracts: Chapter S in Global mineral resource assessment

USGS Publications Warehouse

Orris, Greta J.; Cocker, Mark D.; Dunlap, Pamela; Wynn, Jeff C.; Spanski, Gregory T.; Briggs, Deborah A.; Gass, Leila; Bliss, James D.; Bolm, Karen S.; Yang, Chao; Lipin, Bruce R.; Ludington, Stephen; Miller, Robert J.; Słowakiewicz, Mirosław

2014-01-01

This report describes a global, evaporite-related potash deposits and occurrences database and a potash tracts database. Chapter 1 summarizes potash resource history and use. Chapter 2 describes a global potash deposits and occurrences database, which contains more than 900 site records. Chapter 3 describes a potash tracts database, which contains 84 tracts with geology permissive for the presence of evaporite-hosted potash resources, including areas with active evaporite-related potash production, areas with known mineralization that has not been quantified or exploited, and areas with potential for undiscovered potash resources. Chapter 4 describes geographic information system (GIS) data files that include (1) potash deposits and occurrences data, (2) potash tract data, (3) reference databases for potash deposit and tract data, and (4) representative graphics of geologic features related to potash tracts and deposits. Summary descriptive models for stratabound potash-bearing salt and halokinetic potash-bearing salt are included in appendixes A and B, respectively. A glossary of salt- and potash-related terms is contained in appendix C and a list of database abbreviations is given in appendix D. Appendix E describes GIS data files, and appendix F is a guide to using the geodatabase.

Database resources of the National Center for Biotechnology Information

PubMed Central

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. PMID:25398906

Database resources of the National Center for Biotechnology Information

PubMed Central

2016-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:26615191

SAADA: Astronomical Databases Made Easier

NASA Astrophysics Data System (ADS)

Michel, L.; Nguyen, H. N.; Motch, C.

2005-12-01

Many astronomers wish to share datasets with their community but have not enough manpower to develop databases having the functionalities required for high-level scientific applications. The SAADA project aims at automatizing the creation and deployment process of such databases. A generic but scientifically relevant data model has been designed which allows one to build databases by providing only a limited number of product mapping rules. Databases created by SAADA rely on a relational database supporting JDBC and covered by a Java layer including a lot of generated code. Such databases can simultaneously host spectra, images, source lists and plots. Data are grouped in user defined collections whose content can be seen as one unique set per data type even if their formats differ. Datasets can be correlated one with each other using qualified links. These links help, for example, to handle the nature of a cross-identification (e.g., a distance or a likelihood) or to describe their scientific content (e.g., by associating a spectrum to a catalog entry). The SAADA query engine is based on a language well suited to the data model which can handle constraints on linked data, in addition to classical astronomical queries. These constraints can be applied on the linked objects (number, class and attributes) and/or on the link qualifier values. Databases created by SAADA are accessed through a rich WEB interface or a Java API. We are currently developing an inter-operability module implanting VO protocols.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.

PubMed

Hitz, Benjamin C; Rowe, Laurence D; Podduturi, Nikhil R; Glick, David I; Baymuradov, Ulugbek K; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Gabdank, Idan; Narayana, Aditi K; Onate, Kathrina C; Hilton, Jason; Ho, Marcus C; Lee, Brian T; Miyasato, Stuart R; Dreszer, Timothy R; Sloan, Cricket A; Strattan, J Seth; Tanaka, Forrest Y; Hong, Eurie L; Cherry, J Michael

2017-01-01

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package.

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

PubMed Central

Podduturi, Nikhil R.; Glick, David I.; Baymuradov, Ulugbek K.; Malladi, Venkat S.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Narayana, Aditi K.; Onate, Kathrina C.; Hilton, Jason; Ho, Marcus C.; Lee, Brian T.; Miyasato, Stuart R.; Dreszer, Timothy R.; Sloan, Cricket A.; Strattan, J. Seth; Tanaka, Forrest Y.; Hong, Eurie L.; Cherry, J. Michael

2017-01-01

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome Project. The current database exceeds 6500 experiments across more than 450 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the H. sapiens and M. musculus genomes. All ENCODE experimental data, metadata, and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage, unified processing, and distribution to community resources and the scientific community. As the volume of data increases, the identification and organization of experimental details becomes increasingly intricate and demands careful curation. The ENCODE DCC has created a general purpose software system, known as SnoVault, that supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata. The software is fully open-source, code and installation instructions can be found at: http://github.com/ENCODE-DCC/snovault/ (for the generic database) and http://github.com/ENCODE-DCC/encoded/ to store genomic data in the manner of ENCODE. The core database engine, SnoVault (which is completely independent of ENCODE, genomic data, or bioinformatic data) has been released as a separate Python package. PMID:28403240

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

Yesley, M.S.; Ossorio, P.N.

This report updates and expands the second edition of the ELSI Bibliography, published in 1993. The Bibliography and Supplement provides a comprehensive resource for identifying publications on the major topics related to the ethical, legal and social issues (ELSI) of the Human Genome Project. The Bibliography and Supplement are extracted from a database compiled at Los Alamos National Laboratory with the support of the Office of Energy Research, US Department of Energy. The second edition of the ELSI Bibliography was dated May 1993 but included publications added to the database until fall 1993. This Supplement reflects approximately 1,000 entries addedmore » to the database during the past year, bringing the total to approximately 7,000 entries. More than half of the new entries were published in the last year, and the remainder are earlier publications not previously included in the database. Most of the new entries were published in the academic and professional literature. The remainder are press reports from newspapers of record and scientific journals. The topical listing of the second edition has been followed in the Supplement, with a few changes. The topics of Cystic Fibrosis, Huntington`s Disease, and Sickle Cell Anemia have been combined in a single topic, Disorders. Also, all the entries published in the past year are included in a new topic, Publications: September 1993--September 1994, which provides a comprehensive view of recent reporting and commentary on the science and ELSI of genetics.« less

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

PubMed Central

Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

2010-01-01

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718

IRIS Toxicological Review of Ethylene Glycol Mono-Butyl ...

EPA Pesticide Factsheets

EPA has conducted a peer review of the scientific basis supporting the human health hazard and dose-response assessment of ethylene glycol monobutyl ether that will appear on the Integrated Risk Information System (IRIS) database. EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of propionaldehyde that will appear on the Integrated Risk Information System (IRIS) database.

Gene annotation from scientific literature using mappings between keyword systems.

PubMed

Pérez, Antonio J; Perez-Iratxeta, Carolina; Bork, Peer; Thode, Guillermo; Andrade, Miguel A

2004-09-01

The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene. To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%). The algorithm can be publicly accessed and used for the annotation of sequences through a web server at http://www.bork.embl.de/kat

76 FR 17962 - Strengthening the Scientific Understanding of Climate Change Impacts on Freshwater Resources of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-31

... Understanding of Climate Change Impacts on Freshwater Resources of the United States AGENCY: U.S. Geological... Scientific Understanding of Climate Change Impacts on Freshwater Resources of the United States''. The report reviews key issues related to freshwater resource data and climate change and identifies next steps to...

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009–31 January 2010

USDA-ARS?s Scientific Manuscript database

This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primiti...

Annual Review of Database Developments: 1993.

ERIC Educational Resources Information Center

Basch, Reva

1993-01-01

Reviews developments in the database industry for 1993. Topics addressed include scientific and technical information; environmental issues; social sciences; legal information; business and marketing; news services; documentation; databases and document delivery; electronic bulletin boards and the Internet; and information industry organizational…

Database resources of the National Center for Biotechnology Information.

PubMed

Wheeler, David L; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Ostell, James; Miller, Vadim; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Steven T; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene

2007-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Information-seeking behavior and the use of online resources: a snapshot of current health sciences faculty.

PubMed

De Groote, Sandra L; Shultz, Mary; Blecic, Deborah D

2014-07-01

The research assesses the information-seeking behaviors of health sciences faculty, including their use of online databases, journals, and social media. A survey was designed and distributed via email to 754 health sciences faculty at a large urban research university with 6 health sciences colleges. Twenty-six percent (198) of faculty responded. MEDLINE was the primary database utilized, with 78.5% respondents indicating they use the database at least once a week. Compared to MEDLINE, Google was utilized more often on a daily basis. Other databases showed much lower usage. Low use of online databases other than MEDLINE, link-out tools to online journals, and online social media and collaboration tools demonstrates a need for meaningful promotion of online resources and informatics literacy instruction for faculty. Library resources are plentiful and perhaps somewhat overwhelming. Librarians need to help faculty discover and utilize the resources and tools that libraries have to offer.

ODP Legacy

Science.gov Websites

Legacy: Scientific results ODP Legacy: Engineering and science operations ODP Legacy: Samples & ; databases ODP Legacy: Outreach Overview Program Administration | Scientific Results | Engineering &

An Array Library for Microsoft SQL Server with Astrophysical Applications

NASA Astrophysics Data System (ADS)

Dobos, L.; Szalay, A. S.; Blakeley, J.; Falck, B.; Budavári, T.; Csabai, I.

2012-09-01

Today's scientific simulations produce output on the 10-100 TB scale. This unprecedented amount of data requires data handling techniques that are beyond what is used for ordinary files. Relational database systems have been successfully used to store and process scientific data, but the new requirements constantly generate new challenges. Moving terabytes of data among servers on a timely basis is a tough problem, even with the newest high-throughput networks. Thus, moving the computations as close to the data as possible and minimizing the client-server overhead are absolutely necessary. At least data subsetting and preprocessing have to be done inside the server process. Out of the box commercial database systems perform very well in scientific applications from the prospective of data storage optimization, data retrieval, and memory management but lack basic functionality like handling scientific data structures or enabling advanced math inside the database server. The most important gap in Microsoft SQL Server is the lack of a native array data type. Fortunately, the technology exists to extend the database server with custom-written code that enables us to address these problems. We present the prototype of a custom-built extension to Microsoft SQL Server that adds array handling functionality to the database system. With our Array Library, fix-sized arrays of all basic numeric data types can be created and manipulated efficiently. Also, the library is designed to be able to be seamlessly integrated with the most common math libraries, such as BLAS, LAPACK, FFTW, etc. With the help of these libraries, complex operations, such as matrix inversions or Fourier transformations, can be done on-the-fly, from SQL code, inside the database server process. We are currently testing the prototype with two different scientific data sets: The Indra cosmological simulation will use it to store particle and density data from N-body simulations, and the Milky Way Laboratory project will use it to store galaxy simulation data.

30 CFR 280.20 - What must I not do in conducting Geological and Geophysical (G&G) prospecting or scientific...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 2 2011-07-01 2011-07-01 false What must I not do in conducting Geological and Geophysical (G&G) prospecting or scientific research? 280.20 Section 280.20 Mineral Resources BUREAU OF OCEAN...) prospecting or scientific research? While conducting G&G prospecting or scientific research activities under a...

Does bilingualism contribute to cognitive reserve? Cognitive and neural perspectives.

PubMed

Guzmán-Vélez, Edmarie; Tranel, Daniel

2015-01-01

Cognitive reserve refers to how individuals actively utilize neural resources to cope with neuropathology to maintain cognitive functioning. The present review aims to critically examine the literature addressing the relationship between bilingualism and cognitive reserve to elucidate whether bilingualism delays the onset of cognitive and behavioral manifestations of dementia. Potential neural mechanisms behind this relationship are discussed. PubMed and PsycINFO databases were searched (through January 2014) for original research articles in English or Spanish languages. The following search strings were used as keywords for study retrieval: "bilingual AND reserve," "reserve AND neural mechanisms," and "reserve AND multilingualism." Growing scientific evidence suggests that lifelong bilingualism contributes to cognitive reserve and delays the onset of Alzheimer's disease symptoms, allowing bilingual individuals affected by Alzheimer's disease to live an independent and richer life for a longer time than their monolingual counterparts. Lifelong bilingualism is related to more efficient use of brain resources that help individuals maintain cognitive functioning in the presence of neuropathology. We propose multiple putative neural mechanisms through which lifelong bilinguals cope with neuropathology. The roles of immigration status, education, age of onset, proficiency, and frequency of language use on the relationship between cognitive reserve and bilingualism are considered. Implications of these results for preventive practices and future research are discussed. PsycINFO Database Record (c) 2015 APA, all rights reserved.

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease.

PubMed

Eppig, Janan T; Blake, Judith A; Bult, Carol J; Kadin, James A; Richardson, Joel E

2015-01-01

The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse-human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human-Mouse: Disease Connection, allows users to explore gene-phenotype-disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The GHEP–EMPOP collaboration on mtDNA population data—A new resource for forensic casework

PubMed Central

Prieto, L.; Zimmermann, B.; Goios, A.; Rodriguez-Monge, A.; Paneto, G.G.; Alves, C.; Alonso, A.; Fridman, C.; Cardoso, S.; Lima, G.; Anjos, M.J.; Whittle, M.R.; Montesino, M.; Cicarelli, R.M.B.; Rocha, A.M.; Albarrán, C.; de Pancorbo, M.M.; Pinheiro, M.F.; Carvalho, M.; Sumita, D.R.; Parson, W.

2011-01-01

Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP–EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org). PMID:21075696

STI Handbook: Guidelines for Producing, Using, and Managing Scientific and Technical Information in the Department of the Navy. A Handbook for Navy Scientists and Engineers on the Use of Scientific and Technical Information

DTIC Science & Technology

1992-02-01

6 What Information Should Be Included in the TR Database? 2-6 What Types of Media Can Be Used to Submit Information to the TR Database? 2-9 How Is...reports. Contract administration documents. Regulations. Commercially published books. WHAT TYPES OF MEDIA CAN BE USED TO SUBMIT INFORMATION TO THE TR...TOWARD DTIC’S WUIS DATA- BASE ? The WUIS database, used to control and report technical and management data, summarizes ongoing research and technology

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 ...

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

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

Karcher, Sandra; Willighagen, Egon L.; Rumble, John

Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resourcesmore » are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.« less

Computer Databases as an Educational Tool in the Basic Sciences.

ERIC Educational Resources Information Center

Friedman, Charles P.; And Others

1990-01-01

The University of North Carolina School of Medicine developed a computer database, INQUIRER, containing scientific information in bacteriology, and then integrated the database into routine educational activities for first-year medical students in their microbiology course. (Author/MLW)

Hydrological Modeling and WEB-GIS for the Water Resource Management

NASA Astrophysics Data System (ADS)

Pierleoni, A.; Bellezza, M.; Casadei, S.; Manciola, P.

2006-12-01

Water resources are a strategically natural resource although they can be extremely susceptible to degradation. As a matter of fact the increasing demand from multipurpose uses, which often are in competition amongst themselves, seems to affect the concept of sustainability per se', thus highlighting phenomena of quality-quantity degradation of water resources. In this context, the issue of water resource management rises to a more important role, especially when, other then the traditional uses for civil, industrial and agronomic purposes, environmental demands are taken into consideration. In particular, for environmental demands we mean: to preserve minimal flows, to conserve ecosystems and biodiversities, to protect and improve the environment and finally also the recreational facilities. In the present work, two software tools are presented; they combine the scientific aspect of the issues with a feasible and widely accessible application of the mathematical modeling in techno-operative fields within a sustainable management policy of the water resource at the basin scale. The first evaluation model of the available superficial water resource bases its algorithms upon regionalization procedures of flow parameters deduced from the geomorphologic features of the soil of the basin (BFI, Area) and presents, as output, a set of duration curves (DC) of the natural, measurable (natural after withdrawal), and residual (discharge usable for dissipative use) flow. The hydrological modeling combined with a GIS engine allows to process the dataset and regionalize the information of each section of the hydrographic network, in order to attain information about the effect of upriver withdrawals, in terms of evaluation parameters (measurable DC) to maintain an optimal water supply all along the entire downstream network. This model, projected with a WEB interface developed in PERL and connected to a MySQL database, has also been tested at the basin and sub-basin scale as an effective decision support system (DSS). The second software tool is a simulation model of a managed water resource for multipurpose uses. The algorithm is based on a topological sketch of the hydrographic network in terms of "Nodes" and "Links" combined with computation procedures for managing the water resource of big reservoirs. The peculiar feature of this method is that it performs a preliminary budget between the total available amount and the demand over a time span longer than the simulation step (week, month). During the managing phase, four different allocation methods are available: proportional, percentage, priority and balanced priority, hence this tool becomes flexible and allows to simulate many different management policies. This project was developed in JAVA and as a workstation product. Both software tools will be handled in a single system that, combined with a GIS map engine, is an integrated model for managing the water resource at the basin scale. The final aim of this project is to be able to share these scientific tools and hydrological data among many institutional uses. For this purpose, a WEB-based system, under the control of an administrator, provides on the one hand the possibility to easily keep the database up-to-date and on the other, the possibility to share data and retrieve the results of the procedures optimized for managing superficial water resources at the basin scale.

36 CFR 292.43 - Protection and preservation of cultural and paleontological resources.

Code of Federal Regulations, 2011 CFR

2011-07-01

... may also be managed for scientific research, public education and enjoyment. Where interpretation of... scientific research. Paleontological resources may only be disturbed or removed in conjunction with scientific research and only upon the issuance of prior written authorization of the disturbance or removal...

36 CFR 292.43 - Protection and preservation of cultural and paleontological resources.

Code of Federal Regulations, 2010 CFR

2010-07-01

... may also be managed for scientific research, public education and enjoyment. Where interpretation of... scientific research. Paleontological resources may only be disturbed or removed in conjunction with scientific research and only upon the issuance of prior written authorization of the disturbance or removal...

Scientific Communication of Geochemical Data and the Use of Computer Databases.

ERIC Educational Resources Information Center

Le Bas, M. J.; Durham, J.

1989-01-01

Describes a scheme in the United Kingdom that coordinates geochemistry publications with a computerized geochemistry database. The database comprises not only data published in the journals but also the remainder of the pertinent data set. The discussion covers the database design; collection, storage and retrieval of data; and plans for future…

filltex: Automatic queries to ADS and INSPIRE databases to fill LaTex bibliography

NASA Astrophysics Data System (ADS)

Gerosa, Davide; Vallisneri, Michele

2017-05-01

filltex is a simple tool to fill LaTex reference lists with records from the ADS and INSPIRE databases. ADS and INSPIRE are the most common databases used among the theoretical physics and astronomy scientific communities, respectively. filltex automatically looks for all citation labels present in a tex document and, by means of web-scraping, downloads all the required citation records from either of the two databases. filltex significantly speeds up the LaTex scientific writing workflow, as all required actions (compile the tex file, fill the bibliography, compile the bibliography, compile the tex file again) are automated in a single command. We also provide an integration of filltex for the macOS LaTex editor TexShop.

USGS cold-water coral geographic database-Gulf of Mexico and western North Atlantic Ocean, version 1.0

USGS Publications Warehouse

Scanlon, Kathryn M.; Waller, Rhian G.; Sirotek, Alexander R.; Knisel, Julia M.; O'Malley, John; Alesandrini, Stian

2010-01-01

The USGS Cold-Water Coral Geographic Database (CoWCoG) provides a tool for researchers and managers interested in studying, protecting, and/or utilizing cold-water coral habitats in the Gulf of Mexico and western North Atlantic Ocean.  The database makes information about the locations and taxonomy of cold-water corals available to the public in an easy-to-access form while preserving the scientific integrity of the data.  The database includes over 1700 entries, mostly from published scientific literature, museum collections, and other databases.  The CoWCoG database is easy to search in a variety of ways, and data can be quickly displayed in table form and on a map by using only the software included with this publication.  Subsets of the database can be selected on the basis of geographic location, taxonomy, or other criteria and exported to one of several available file formats.  Future versions of the database are being planned to cover a larger geographic area and additional taxa.

The SCEC/UseIT Intern Program: Creating Open-Source Visualization Software Using Diverse Resources

NASA Astrophysics Data System (ADS)

Francoeur, H.; Callaghan, S.; Perry, S.; Jordan, T.

2004-12-01

The Southern California Earthquake Center undergraduate IT intern program (SCEC UseIT) conducts IT research to benefit collaborative earth science research. Through this program, interns have developed real-time, interactive, 3D visualization software using open-source tools. Dubbed LA3D, a distribution of this software is now in use by the seismic community. LA3D enables the user to interactively view Southern California datasets and models of importance to earthquake scientists, such as faults, earthquakes, fault blocks, digital elevation models, and seismic hazard maps. LA3D is now being extended to support visualizations anywhere on the planet. The new software, called SCEC-VIDEO (Virtual Interactive Display of Earth Objects), makes use of a modular, plugin-based software architecture which supports easy development and integration of new data sets. Currently SCEC-VIDEO is in beta testing, with a full open-source release slated for the future. Both LA3D and SCEC-VIDEO were developed using a wide variety of software technologies. These, which included relational databases, web services, software management technologies, and 3-D graphics in Java, were necessary to integrate the heterogeneous array of data sources which comprise our software. Currently the interns are working to integrate new technologies and larger data sets to increase software functionality and value. In addition, both LA3D and SCEC-VIDEO allow the user to script and create movies. Thus program interns with computer science backgrounds have been writing software while interns with other interests, such as cinema, geology, and education, have been making movies that have proved of great use in scientific talks, media interviews, and education. Thus, SCEC UseIT incorporates a wide variety of scientific and human resources to create products of value to the scientific and outreach communities. The program plans to continue with its interdisciplinary approach, increasing the relevance of the software and expanding its use in the scientific community.

Methods for structuring scientific knowledge from many areas related to aging research.

PubMed

Zhavoronkov, Alex; Cantor, Charles R

2011-01-01

Aging and age-related disease represents a substantial quantity of current natural, social and behavioral science research efforts. Presently, no centralized system exists for tracking aging research projects across numerous research disciplines. The multidisciplinary nature of this research complicates the understanding of underlying project categories, the establishment of project relations, and the development of a unified project classification scheme. We have developed a highly visual database, the International Aging Research Portfolio (IARP), available at AgingPortfolio.org to address this issue. The database integrates information on research grants, peer-reviewed publications, and issued patent applications from multiple sources. Additionally, the database uses flexible project classification mechanisms and tools for analyzing project associations and trends. This system enables scientists to search the centralized project database, to classify and categorize aging projects, and to analyze the funding aspects across multiple research disciplines. The IARP is designed to provide improved allocation and prioritization of scarce research funding, to reduce project overlap and improve scientific collaboration thereby accelerating scientific and medical progress in a rapidly growing area of research. Grant applications often precede publications and some grants do not result in publications, thus, this system provides utility to investigate an earlier and broader view on research activity in many research disciplines. This project is a first attempt to provide a centralized database system for research grants and to categorize aging research projects into multiple subcategories utilizing both advanced machine algorithms and a hierarchical environment for scientific collaboration.

Multi-year Content Analysis of User Facility Related Publications

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

Patton, Robert M; Stahl, Christopher G; Hines, Jayson

2013-01-01

Scientific user facilities provide resources and support that enable scientists to conduct experiments or simulations pertinent to their respective research. Consequently, it is critical to have an informed understanding of the impact and contributions that these facilities have on scientific discoveries. Leveraging insight into scientific publications that acknowledge the use of these facilities enables more informed decisions by facility management and sponsors in regard to policy, resource allocation, and influencing the direction of science as well as more effectively understand the impact of a scientific user facility. This work discusses preliminary results of mining scientific publications that utilized resources atmore » the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory (ORNL). These results show promise in identifying and leveraging multi-year trends and providing a higher resolution view of the impact that a scientific user facility may have on scientific discoveries.« less

U.S. Geological Survey mineral databases; MRDS and MAS/MILS

USGS Publications Warehouse

McFaul, E.J.; Mason, G.T.; Ferguson, W.B.; Lipin, B.R.

2000-01-01

These two CD-ROM's contain the latest version of the Mineral Resources Data System (MRDS) database and the Minerals Availability System/Minerals Industry Location System (MAS/MILS) database for coverage of North America and the world outside North America. The records in the MRDS database each contain almost 200 data fields describing metallic and nonmetallic mineral resources, deposits, and commodities. The records in the MAS/MILS database each contain almost 100 data fields describing mines and mineral processing plans.

RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction.

PubMed

Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

2014-07-01

Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. © 2014 Zhang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

PubMed

Kodama, Yuichi; Mashima, Jun; Kaminuma, Eli; Gojobori, Takashi; Ogasawara, Osamu; Takagi, Toshihisa; Okubo, Kousaku; Nakamura, Yasukazu

2012-01-01

The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

The Open Spectral Database: an open platform for sharing and searching spectral data.

PubMed

Chalk, Stuart J

2016-01-01

A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

Natural Partners: Resource-Based and Integrative Learning.

ERIC Educational Resources Information Center

Porter, John R.

1992-01-01

With resource-based learning projects, college students at the Philadelphia College of Pharmacy and Science develop a better sense of the information resources available, the nature of scientific literature, and the characteristics of scientific writing. Faculty motivations, benefits, and disappointments with this approach are addressed.…

Content Is King: Databases Preserve the Collective Information of Science.

PubMed

Yates, John R

2018-04-01

Databases store sequence information experimentally gathered to create resources that further science. In the last 20 years databases have become critical components of fields like proteomics where they provide the basis for large-scale and high-throughput proteomic informatics. Amos Bairoch, winner of the Association of Biomolecular Resource Facilities Frederick Sanger Award, has created some of the important databases proteomic research depends upon for accurate interpretation of data.

MNDR v2.0: an updated resource of ncRNA–disease associations in mammals

PubMed Central

Cui, Tianyu; Zhang, Lin; Huang, Yan; Yi, Ying; Tan, Puwen; Zhao, Yue; Hu, Yongfei

2018-01-01

Abstract Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA–disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA–disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA–disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework. The new developments in MNDR v2.0 include (i) an over 220-fold increase in ncRNA–disease associations enhancement compared with the previous version (including lncRNA, miRNA, piRNA, snoRNA and more than 1400 diseases); (ii) integrating experimental and prediction evidence from 14 resources and prediction algorithms for each ncRNA–disease association; (iii) mapping disease names to the Disease Ontology and Medical Subject Headings (MeSH); (iv) providing a confidence score for each ncRNA–disease association and (v) an increase of species coverage to six mammals. Finally, MNDR v2.0 intends to provide the scientific community with a resource for efficient browsing and extraction of the associations between diverse ncRNAs and diseases, including >260 000 ncRNA–disease associations. PMID:29106639

A New Breed of Database System: Volcano Global Risk Identification and Analysis Project (VOGRIPA)

NASA Astrophysics Data System (ADS)

Crosweller, H. S.; Sparks, R. S.; Siebert, L.

2009-12-01

VOGRIPA originated as part of the Global Risk Identification Programme (GRIP) that is being co-ordinated from the Earth Institute of Columbia University under the auspices of the United Nations and World Bank. GRIP is a five-year programme aiming at improving global knowledge about risk from natural hazards and is part of the international response to the catastrophic 2004 Asian tsunami. VOGRIPA is also a formal IAVCEI project. The objectives of VOGRIPA are to create a global database of volcanic activity, hazards and vulnerability information that can be analysed to identify locations at high risk from volcanism, gaps in knowledge about hazards and risk, and will allow scientists and disaster managers at specific locations to analyse risk within a global context of systematic information. It is this added scope of risk and vulnerability as well as hazard which sets VOGRIPA apart from most previous databases. The University of Bristol is the central coordinating centre for the project, which is an international partnership including the Smithsonian Institution, the Geological Survey of Japan, the Earth Observatory of Singapore (Chris Newhall), the British Geological Survey, the University of Buffalo (SUNY) and Munich Re. The partnership is intended to grow and any individuals or institutions who are able to contribute resources to VOGRIPA objectives are welcome to participate. Work has already begun (funded principally by Munich Re) on populating a database of large magnitude explosive eruptions reaching back to the Quaternary, with extreme-value statistics being used to evaluate the magnitude-frequency relationship of such events, and also an assessment of how the quality of records affect the results. The following 4 years of funding from the European Research Council for VOGRIPA will be used to establish further international collaborations in order to develop different aspects of the database, with the data being accessible online once it is sufficiently complete and analyses have been carried out. It is anticipated that such a resource would be of use to the scientific community, civil authorities with responsibility for mitigating and managing volcanic hazards, and the public.

Mathematical Notation in Bibliographic Databases.

ERIC Educational Resources Information Center

Pasterczyk, Catherine E.

1990-01-01

Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

Establishing lunar resource viability

NASA Astrophysics Data System (ADS)

Carpenter, J.; Fisackerly, R.; Houdou, B.

2016-11-01

Recent research has highlighted the potential of lunar resources as an important element of space exploration but their viability has not been demonstrated. Establishing whether or not they can be considered in future plans is a multidisciplinary effort, requiring scientific expertise and delivering scientific results. To this end various space agencies and private entities are looking to lunar resources, extracted and processed in situ, as a potentially game changing element in future space architectures, with the potential to increase scale and reduce cost. However, before any decisions can be made on the inclusion of resources in exploration roadmaps or future scenarios some big questions need to be answered about the viability of different resource deposits and the processes for extraction and utilisation. The missions and measurements that will be required to answer these questions, and which are being prepared by agencies and others, can only be performed through the engagement and support of the science community. In answering questions about resources, data and knowledge will be generated that is of fundamental scientific importance. In supporting resource prospecting missions the science community will de facto generate new scientific knowledge. Science enables exploration and exploration enables science.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Kenton, David L.; Khovayko, Oleg; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Sherry, Stephen T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Suzek, Tugba O.; Tatusov, Roman; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2006-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Database resources of the National Center for Biotechnology Information

PubMed Central

Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

2014-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429

Database resources of the National Center for Biotechnology

PubMed Central

Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

2003-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941

Operationalizing Semantic Medline for meeting the information needs at point of care.

PubMed

Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

2015-01-01

Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible.

Operationalizing Semantic Medline for meeting the information needs at point of care

PubMed Central

Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

2015-01-01

Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible. PMID:26306259

Questions to Ask Your Doctor

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Systems and methods for automatically identifying and linking names in digital resources

DOEpatents

Parker, Charles T.; Lyons, Catherine M.; Roston, Gerald P.; Garrity, George M.

2017-06-06

The present invention provides systems and methods for automatically identifying name-like-strings in digital resources, matching these name-like-string against a set of names held in an expertly curated database, and for those name-like-strings found in said database, enhancing the content by associating additional matter with the name, wherein said matter includes information about the names that is held within said database and pointers to other digital resources which include the same name and it synonyms.

Scientific Skills and Processes in Curriculum Resources

ERIC Educational Resources Information Center

Kremer, Joe

2017-01-01

Increasingly, the science education community has recognized the need for curriculum resources that support student development of authentic scientific practices, rather than focusing exclusively on content knowledge. This paper proposes a tool for teachers and researchers to assess the degree to which certain curriculum resources and lessons…

Difficulties and challenges associated with literature searches in operating room management, complete with recommendations.

PubMed

Wachtel, Ruth E; Dexter, Franklin

2013-12-01

The purpose of this article is to teach operating room managers, financial analysts, and those with a limited knowledge of search engines, including PubMed, how to locate articles they need in the areas of operating room and anesthesia group management. Many physicians are unaware of current literature in their field and evidence-based practices. The most common source of information is colleagues. Many people making management decisions do not read published scientific articles. Databases such as PubMed are available to search for such articles. Other databases, such as citation indices and Google Scholar, can be used to uncover additional articles. Nevertheless, most people who do not know how to use these databases are reluctant to utilize help resources when they do not know how to accomplish a task. Most people are especially reluctant to use on-line help files. Help files and search databases are often difficult to use because they have been designed for users already familiar with the field. The help files and databases have specialized vocabularies unique to the application. MeSH terms in PubMed are not useful alternatives for operating room management, an important limitation, because MeSH is the default when search terms are entered in PubMed. Librarians or those trained in informatics can be valuable assets for searching unusual databases, but they must possess the domain knowledge relative to the subject they are searching. The search methods we review are especially important when the subject area (e.g., anesthesia group management) is so specific that only 1 or 2 articles address the topic of interest. The materials are presented broadly enough that the reader can extrapolate the findings to other areas of clinical and management issues in anesthesiology.

Physicians utilisation of internet medical databases at the tertiary health institutions in Osun State, south west, Nigeria.

PubMed

Shabi, Iwok N; Shabi, Olabode M; Akewukereke, Modupe A; Udofia, Emem P

2011-12-01

To determine the extent, purpose, determinants and the impact of the utilization of Internet medical databases among the respondents. A descriptive cross sectional survey of 540 randomly selected physicians at the two tertiary health institutions in Osun State, south west, Nigeria. A total of 444 (82.2%) physicians completed the questionnaires. All the respondents have used the internet medical databases within the last 4 weeks of the study. Majority, (53.8%) used the internet resources at least once in 2 weeks, while 12.2% used the resources every day. The online resources are mainly sought for Routine patient care and for Research purposes. pubmed (70.3%), hinari (69.0%), and Free medical journals (60.1%) are the frequently used online databases/digital archives. The internet resources has positively impacted the Clinical practice (40.0%) and Research output (65.5%) of the physicians. There had been considerable increase in the extent and quality of utilization of online medical databases which has positively impacted on the Clinical practice and Research output of the physicians. Ease of finding the needed information and the availability of evidence based resources are the major determinants of the databases utilized. © 2011 The authors. Health Information and Libraries Journal © 2011 Health Libraries Group.

Knowledge production status of Iranian researchers in the gastric cancer area: based on the medline database.

PubMed

Ghojazadeh, Morteza; Naghavi-Behzad, Mohammad; Nasrolah-Zadeh, Raheleh; Bayat-Khajeh, Parvaneh; Piri, Reza; Mirnia, Keyvan; Azami-Aghdash, Saber

2014-01-01

Scientometrics is a useful method for management of financial and human resources and has been applied many times in medical sciences during recent years. The aim of this study was to investigate the status of science production by Iranian scientists in the gastric cancer field based on the Medline database. In this descriptive-cross sectional study Iranian science production concerning gastric cancer during 2000-2011 was investigated based on Medline. After two stages of searching, 121 articles were found, then we reviewed publication date, authors names, journal title, impact factor (IF), and cooperation coefficient between researchers. SPSS.19 was used for statistical analysis. There was a significant increase in published articles about gastric cancer by Iranian researchers in Medline database during 2006-2011. Mean cooperation coefficient between researchers was 6.14±3.29 person per article. Articles of this field were published in 19 countries and 56 journals. Those basex in Thailand, England, and America had the most published Iranian articles. Tehran University of Medical Sciences and Mohammadreza Zali had the most outstanding role in publishing scientific articles. According to results of this study, improving cooperation of researchers in conducting research and scientometric studies about other fields may have an important role in increasing both quality and quantity of published studies.

Network portal: a database for storage, analysis and visualization of biological networks

PubMed Central

Turkarslan, Serdar; Wurtmann, Elisabeth J.; Wu, Wei-Ju; Jiang, Ning; Bare, J. Christopher; Foley, Karen; Reiss, David J.; Novichkov, Pavel; Baliga, Nitin S.

2014-01-01

The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through the inference of networks of interactions among the various cellular components (genes, RNAs, proteins and metabolites). The wider scientific community, however, currently has limited access to tools for network inference, visualization and analysis because these tasks often require advanced computational knowledge and expensive computing resources. We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the storage, visualization and analysis of biological networks. The portal is fully integrated into the Gaggle framework to seamlessly exchange data with desktop and web applications and to allow the user to create, save and modify workspaces, and it includes social networking capabilities for collaborative projects. While the current release of the database contains networks for 13 prokaryotic organisms from diverse phylogenetic clades (4678 co-regulated gene modules, 3466 regulators and 9291 cis-regulatory motifs), it will be rapidly populated with prokaryotic and eukaryotic organisms as relevant data become available in public repositories and through user input. The modular architecture, simple data formats and open API support community development of the portal. PMID:24271392

Acupuncture for chronic prostatitis: A systematic review and meta-analysis protocol.

PubMed

Peng, Tianzhong; Cheng, Ying; Jin, Yuhao; Xu, Na; Guo, Taipin

2018-04-01

Chronic prostatitis (CP) is a prevalent genitourinary condition. Considering its safety profile, acupuncture can be an option treating CP symptoms. The aim of this review is to undertake a systematic review to estimate the effectiveness and safety of acupuncture on CP. We will search all randomized controlled trials for CP in August 2018 in the databases of MEDLINE, Cochrane Library, Web of Science, EMBASE, Springer, WHO International Clinical Trials Registry Platform (ICTRP), China National Knowledge Infrastructure (CNKI), Wan fang, Chinese Biomedical Literature Database (CBM), PsycInfo, Chinese Scientific Journal Database (VIP), and other available resources. Languages are limited as English and Chinese. Search terms used are will "acupuncture," and "chronic prostatitis," "non-bacterial prostatitis," "abacterial prostatitis." And duplicates will be screened. The primary outcomes consisted of improvement rate and pain relief evaluated by The National Institutes of Health Chronic Prostatitis Symptom Index (NIH-CPSI) index. Secondary outcomes include the recurrence rate and side effects, such as pneumothorax, discomforts, and infection. This study will demonstrate an evidence-based review of acupuncture for chronic prostatitis. The study will provide clear evidence to assess the effectiveness and side effects of acupuncture for chronic prostatitis. There is no requirement of ethical approval and it will be in print or disseminated by electronic copies. CRD42018088834.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

PubMed

Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; Blake, Andrew; Bonierbale, Merideth; Brookes, Anthony J; Bucci, Gabriele; Buetti, Iwan; Burge, Sarah; Cabau, Cédric; Carlson, Joseph W; Chelala, Claude; Chrysostomou, Charalambos; Cittaro, Davide; Collin, Olivier; Cordova, Raul; Cutts, Rosalind J; Dassi, Erik; Di Genova, Alex; Djari, Anis; Esposito, Anthony; Estrella, Heather; Eyras, Eduardo; Fernandez-Banet, Julio; Forbes, Simon; Free, Robert C; Fujisawa, Takatomo; Gadaleta, Emanuela; Garcia-Manteiga, Jose M; Goodstein, David; Gray, Kristian; Guerra-Assunção, José Afonso; Haggarty, Bernard; Han, Dong-Jin; Han, Byung Woo; Harris, Todd; Harshbarger, Jayson; Hastings, Robert K; Hayes, Richard D; Hoede, Claire; Hu, Shen; Hu, Zhi-Liang; Hutchins, Lucie; Kan, Zhengyan; Kawaji, Hideya; Keliet, Aminah; Kerhornou, Arnaud; Kim, Sunghoon; Kinsella, Rhoda; Klopp, Christophe; Kong, Lei; Lawson, Daniel; Lazarevic, Dejan; Lee, Ji-Hyun; Letellier, Thomas; Li, Chuan-Yun; Lio, Pietro; Liu, Chu-Jun; Luo, Jie; Maass, Alejandro; Mariette, Jerome; Maurel, Thomas; Merella, Stefania; Mohamed, Azza Mostafa; Moreews, Francois; Nabihoudine, Ibounyamine; Ndegwa, Nelson; Noirot, Céline; Perez-Llamas, Cristian; Primig, Michael; Quattrone, Alessandro; Quesneville, Hadi; Rambaldi, Davide; Reecy, James; Riba, Michela; Rosanoff, Steven; Saddiq, Amna Ali; Salas, Elisa; Sallou, Olivier; Shepherd, Rebecca; Simon, Reinhard; Sperling, Linda; Spooner, William; Staines, Daniel M; Steinbach, Delphine; Stone, Kevin; Stupka, Elia; Teague, Jon W; Dayem Ullah, Abu Z; Wang, Jun; Ware, Doreen; Wong-Erasmus, Marie; Youens-Clark, Ken; Zadissa, Amonida; Zhang, Shi-Jian; Kasprzyk, Arek

2015-07-01

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation.

PubMed

Gao, Tianshun; Liu, Zexian; Wang, Yongbo; Cheng, Han; Yang, Qing; Guo, Anyuan; Ren, Jian; Xue, Yu

2013-01-01

In this work, we developed a family-based database of UUCD (http://uucd.biocuckoo.org) for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes, through a similar E1 (ubiquitin-activating enzyme)-E2 (ubiquitin-conjugating enzyme)-E3 (ubiquitin-protein ligase) enzyme thioester cascade. Although extensive experimental efforts have been taken, an integrative data resource is still not available. From the scientific literature, 26 E1s, 105 E2s, 1003 E3s and 148 deubiquitination enzymes (DUBs) were collected and classified into 1, 3, 19 and 7 families, respectively. To computationally characterize potential enzymes in eukaryotes, we constructed 1, 1, 15 and 6 hidden Markov model (HMM) profiles for E1s, E2s, E3s and DUBs at the family level, separately. Moreover, the ortholog searches were conducted for E3 and DUB families without HMM profiles. Then the UUCD database was developed with 738 E1s, 2937 E2s, 46 631 E3s and 6647 DUBs of 70 eukaryotic species. The detailed annotations and classifications were also provided. The online service of UUCD was implemented in PHP + MySQL + JavaScript + Perl.

Data Intensive Scientific Workflows on a Federated Cloud: CRADA Final Report

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

Garzoglio, Gabriele

The Fermilab Scientific Computing Division and the KISTI Global Science Experimental Data Hub Center have built a prototypical large-scale infrastructure to handle scientific workflows of stakeholders to run on multiple cloud resources. The demonstrations have been in the areas of (a) Data-Intensive Scientific Workflows on Federated Clouds, (b) Interoperability and Federation of Cloud Resources, and (c) Virtual Infrastructure Automation to enable On-Demand Services.

IRIS Toxicological Review of Methanol (Non-Cancer) ...

EPA Pesticide Factsheets

EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of methanol (non-cancer) that when finalized will appear on the Integrated Risk Information System (IRIS) database. EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of methanol (non-cancer) that will appear in the Integrated Risk Information System (IRIS) database.

Esmeralda Energy Company, Final Scientific Technical Report, January 2008. Emigrant Slimhole Drilling Project, DOE GRED III

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

Deymonaz, John; Hulen, Jeffrey B.; Nash, Gregory D.

2008-01-22

The Emigrant Slimhole Drilling Project (ESDP) was a highly successful, phased resource evaluation program designed to evaluate the commercial geothermal potential of the eastern margin of the northern Fish Lake Valley pull-apart basin in west-central Nevada. The program involved three phases: (1) Resource evaluation; (2) Drilling and resource characterization; and (3) Resource testing and assessment. Efforts included detailed geologic mapping; 3-D modeling; compilation of a GIS database; and production of a conceptual geologic model followed by the successful drilling of the 2,938 foot deep 17-31 slimhole (core hole), which encountered commercial geothermal temperatures (327⁰ F) and exhibits an increasing, conductive,more » temperature gradient to total depth; completion of a short injection test; and compilation of a detailed geologic core log and revised geologic cross-sections. Results of the project greatly increased the understanding of the geologic model controlling the Emigrant geothermal resource. Information gained from the 17-31 core hole revealed the existence of commercial temperatures beneath the area in the Silver Peak Core Complex which is composed of formations that exhibit excellent reservoir characteristics. Knowledge gained from the ESDP may lead to the development of a new commercial geothermal field in Nevada. Completion of the 17-31 core hole also demonstrated the cost-effectiveness of deep core drilling as an exploration tool and the unequaled value of core in understanding the geology, mineralogy, evolutional history and structural aspects of a geothermal resource.« less

A database application for wilderness character monitoring

Treesearch

Ashley Adams; Peter Landres; Simon Kingston

2012-01-01

The National Park Service (NPS) Wilderness Stewardship Division, in collaboration with the Aldo Leopold Wilderness Research Institute and the NPS Inventory and Monitoring Program, developed a database application to facilitate tracking and trend reporting in wilderness character. The Wilderness Character Monitoring Database allows consistent, scientifically based...

Monitoring outcomes with relational databases: does it improve quality of care?

PubMed

Clemmer, Terry P

2004-12-01

There are 3 key ingredients in improving quality of medial care: 1) using a scientific process of improvement, 2) executing the process at the lowest possible level in the organization, and 3) measuring the results of any change reliably. Relational databases when used within these guidelines are of great value in these efforts if they contain reliable information that is pertinent to the project and used in a scientific process of quality improvement by a front line team. Unfortunately, the data are frequently unreliable and/or not pertinent to the local process and is used by persons at very high levels in the organization without a scientific process and without reliable measurement of the outcome. Under these circumstances the effectiveness of relational databases in improving care is marginal at best, frequently wasteful and has the potential to be harmful. This article explores examples of these concepts.

Hosting and pulishing astronomical data in SQL databases

NASA Astrophysics Data System (ADS)

Galkin, Anastasia; Klar, Jochen; Riebe, Kristin; Matokevic, Gal; Enke, Harry

2017-04-01

In astronomy, terabytes and petabytes of data are produced by ground instruments, satellite missions and simulations. At Leibniz-Institute for Astrophysics Potsdam (AIP) we host and publish terabytes of cosmological simulation and observational data. The public archive at AIP has now reached a size of 60TB and growing and helps to produce numerous scientific papers. The web framework Daiquiri offers a dedicated web interface for each of the hosted scientific databases. Scientists all around the world run SQL queries which include specific astrophysical functions and get their desired data in reasonable time. Daiquiri supports the scientific projects by offering a number of administration tools such as database and user management, contact messages to the staff and support for organization of meetings and workshops. The webpages can be customized and the Wordpress integration supports the participating scientists in maintaining the documentation and the projects' news sections.

The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.

PubMed

Gifford, Lida K; Carter, Lester G; Gabanyi, Margaret J; Berman, Helen M; Adams, Paul D

2012-06-01

The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.

Better bioinformatics through usability analysis.

PubMed

Bolchini, Davide; Finkelstein, Anthony; Perrone, Vito; Nagl, Sylvia

2009-02-01

Improving the usability of bioinformatics resources enables researchers to find, interact with, share, compare and manipulate important information more effectively and efficiently. It thus enables researchers to gain improved insights into biological processes with the potential, ultimately, of yielding new scientific results. Usability 'barriers' can pose significant obstacles to a satisfactory user experience and force researchers to spend unnecessary time and effort to complete their tasks. The number of online biological databases available is growing and there is an expanding community of diverse users. In this context there is an increasing need to ensure the highest standards of usability. Using 'state-of-the-art' usability evaluation methods, we have identified and characterized a sample of usability issues potentially relevant to web bioinformatics resources, in general. These specifically concern the design of the navigation and search mechanisms available to the user. The usability issues we have discovered in our substantial case studies are undermining the ability of users to find the information they need in their daily research activities. In addition to characterizing these issues, specific recommendations for improvements are proposed leveraging proven practices from web and usability engineering. The methods and approach we exemplify can be readily adopted by the developers of bioinformatics resources.

[Public scientific knowledge distribution in health information, communication and information technology indexed in MEDLINE and LILACS databases].

PubMed

Packer, Abel Laerte; Tardelli, Adalberto Otranto; Castro, Regina Célia Figueiredo

2007-01-01

This study explores the distribution of international, regional and national scientific output in health information and communication, indexed in the MEDLINE and LILACS databases, between 1996 and 2005. A selection of articles was based on the hierarchical structure of Information Science in MeSH vocabulary. Four specific domains were determined: health information, medical informatics, scientific communications on healthcare and healthcare communications. The variables analyzed were: most-covered subjects and journals, author affiliation and publication countries and languages, in both databases. The Information Science category is represented in nearly 5% of MEDLINE and LILACS articles. The four domains under analysis showed a relative annual increase in MEDLINE. The Medical Informatics domain showed the highest number of records in MEDLINE, representing about half of all indexed articles. The importance of Information Science as a whole is more visible in publications from developed countries and the findings indicate the predominance of the United States, with significant growth in scientific output from China and South Korea and, to a lesser extent, Brazil.

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

PubMed Central

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

PubMed

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/

Sismos a l'Ecole : a Seismic Educational Network (FRANCE) linked with Research

NASA Astrophysics Data System (ADS)

Berenguer, J.; Le Puth, J.; Courboulex, F.; Zodmi, B.; Boneff, M.

2007-12-01

Ahead of the quick evolution of our society, in which scientific information has to be accurately understood by a great majority, the promotion of a responsible behaviour coming from educated and trained citizens has become a priority. One of the roles of school is to enable children to understand sciences, these same sciences that were long ago the prerogative of scientific laboratories. The educational network SISMOS à l\\'"Ecole is an example of a project structured on the knowledge of seismic risks through a scientific and technological approach. It develops a teaching method leading to an approach towards the knowledge of natural disasters. The original and innovating feature of this educational network is to enable students to set up a seismograph in their school. The recorded signals - coming from a regional or a worldwide seismic activity - feed an on- line database, which is in fact a real research centre for seismic resources as well as a starting point for educational and scientific activities. The network, that numbers about thirty stations set up in France, in its overseas departments and territories, and in a couple of French schools abroad, is based upon an experience initiated in the French Riviera ten years ago or so. The achievement of the program has from then on gone beyond the simple purpose of conveying seismic data that research and monitoring centres could have recorded. Thanks to the use of scientific measures, students become involved and get into complex notions revolving around geophysics and geosciences. Developing simple tools, setting up concrete experiments combined with an investigate reasoning makes it easier to build up a quality scientific culture as well as an education of citizens to risks.

Userscripts for the life sciences.

PubMed

Willighagen, Egon L; O'Boyle, Noel M; Gopalakrishnan, Harini; Jiao, Dazhi; Guha, Rajarshi; Steinbeck, Christoph; Wild, David J

2007-12-21

The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.

Userscripts for the Life Sciences

PubMed Central

Willighagen, Egon L; O'Boyle, Noel M; Gopalakrishnan, Harini; Jiao, Dazhi; Guha, Rajarshi; Steinbeck, Christoph; Wild, David J

2007-01-01

Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity. PMID:18154664

National Patterns of Science and Technology Resources 1981.

ERIC Educational Resources Information Center

Chirichiello, John; Crowley, Michael

An overview of two science and technology resources (financial support and scientific/technical personnel) is presented, based on a series of National Science Foundation (NSF) surveys on research and development (R&D) resources and scientific/technical personnel in the United States. Areas addressed related to national perspectives of R&D…

"Clicking through" or Learning Concepts

ERIC Educational Resources Information Center

Stidwell, Peter

2005-01-01

The author has developed an innovative science website resource that also shows how engineers use science. As well as addressing scientific facts and concepts, the resource also engages children in the process of scientific enquiry, using graph tools and data interpretation. Part of the resource helps children to understand that much of what they…

Using glycome databases for drug discovery.

PubMed

Aoki-Kinoshita, Kiyoko F

2008-08-01

The glycomics field has made great advancements in the last decade due to technologies for their synthesis and analysis including carbohydrate microarrays. Accordingly, databases for glycomics research have also emerged and been made publicly available by many major institutions worldwide. This review introduces these and other useful databases on which new methods for drug discovery can be developed. The scope of this review covers current documented and accessible databases and resources pertaining to glycomics. These were selected with the expectation that they may be useful for drug discovery research. There is a plethora of glycomics databases that have much potential for drug discovery. This may seem daunting at first but this review helps to put some of these resources into perspective. Additionally, some thoughts on how to integrate these resources to allow more efficient research are presented.

Applications of Precipitation Feature Databases from GPM core and constellation Satellites

NASA Astrophysics Data System (ADS)

Liu, C.

2017-12-01

Using the observations from Global Precipitation Mission (GPM) core and constellation satellites, global precipitation was quantitatively described from the perspective of precipitation systems and their properties. This presentation will introduce the development of precipitation feature databases, and several scientific questions that have been tackled using this database, including the topics of global snow precipitation, extreme intensive convection, hail storms, extreme precipitation, and microphysical properties derived with dual frequency radars at the top of convective cores. As more and more observations of constellation satellites become available, it is anticipated that the precipitation feature approach will help to address a large variety of scientific questions in the future. For anyone who is interested, all the current precipitation feature databases are freely open to public at: http://atmos.tamucc.edu/trmm/.

32 CFR 651.41 - Conditions requiring an EIS.

Code of Federal Regulations, 2010 CFR

2010-07-01

... cultural, archaeological, or scientific resources, public parks and recreation areas, wildlife refuge or... controversial from an environmental standpoint. (j) Cause loss or destruction of significant scientific, cultural, or historical resources. ...

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.

The Vocational Guidance Research Database: A Scientometric Approach

ERIC Educational Resources Information Center

Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

2012-01-01

The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the…

Human Ageing Genomic Resources: new and updated databases

PubMed Central

Tacutu, Robi; Thornton, Daniel; Johnson, Emily; Budovsky, Arie; Barardo, Diogo; Craig, Thomas; Diana, Eugene; Lehmann, Gilad; Toren, Dmitri; Wang, Jingwei; Fraifeld, Vadim E

2018-01-01

Abstract In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/). PMID:29121237

Measuring use patterns of online journals and databases

PubMed Central

De Groote, Sandra L.; Dorsch, Josephine L.

2003-01-01

Purpose: This research sought to determine use of online biomedical journals and databases and to assess current user characteristics associated with the use of online resources in an academic health sciences center. Setting: The Library of the Health Sciences–Peoria is a regional site of the University of Illinois at Chicago (UIC) Library with 350 print journals, more than 4,000 online journals, and multiple online databases. Methodology: A survey was designed to assess online journal use, print journal use, database use, computer literacy levels, and other library user characteristics. A survey was sent through campus mail to all (471) UIC Peoria faculty, residents, and students. Results: Forty-one percent (188) of the surveys were returned. Ninety-eight percent of the students, faculty, and residents reported having convenient access to a computer connected to the Internet. While 53% of the users indicated they searched MEDLINE at least once a week, other databases showed much lower usage. Overall, 71% of respondents indicated a preference for online over print journals when possible. Conclusions: Users prefer online resources to print, and many choose to access these online resources remotely. Convenience and full-text availability appear to play roles in selecting online resources. The findings of this study suggest that databases without links to full text and online journal collections without links from bibliographic databases will have lower use. These findings have implications for collection development, promotion of library resources, and end-user training. PMID:12883574

The Spanish Society of Soil Science: history and future perspectives

NASA Astrophysics Data System (ADS)

Bellinfante, Nicolás; Arbelo, Dolores; Rodríguez, Antonio

2013-04-01

The Spanish Society of Soil Science (SECS; http://www.secs.com.es) has reached sixty years of existence, after being established in 1947 at the Spanish Council for Scientific Research (CSIC) as an initiative of renowned scientists including José María Albareda, Salvador Rivas Goday, Fernando Burriel, Tomás Alvira and others. However, soil studies in Spain began in the first third of XX century, coordinated by Emilio Huguet del Villar, internationally outstanding researcher who was the President of the Subcommittee for the Mediterranean Region of the International Society Soil Science, with the activities of the Forest Research Institute and the Institute of Mediterranean Soils of the Regional Catalonian Government. With the creation of the CSIC and the Spanish Institute of Soil Science and Agrobiology, directed by José M. Albareda, Soil Science research was promoted in all scientific fields and through the Spanish geography. The SECS is considered equally heiress of previously existing organizations, in particular the Spanish Commission of Soil Science and Phytogeography, created in 1925, which was the Spanish voice in various international organizations and meetings related with Soil Science. After these years, Soil Science has developed considerably, showing a great diversification of fields of study and research and its applications, as well as a growing social awareness of the soil degradation processes and the need to implement measures to protect natural resources nonrenewable on a human scale, and an increasing role of universities and CSIC in Soil Science research. Currently, the SECS is a scientific organization dedicated to promoting the study, knowledge, research and protection of soil resources; spread the scientific importance of soil functions as nonrenewable natural resource in society and promote the interest in its protection; and preserve the knowledge about soils, their management and use, both from productive and environmental perspectives. The SECS has helped and sponsored numerous conferences and seminars related to different aspects of Soil Science, and directly organizes the National Congress of Soil Science (since 2004, the Iberian Congress of Soil Science) and National Soil Meetings held annual or biannually without interruption since 1975. Some of the projects currently being carried out include TeSECS (a database of PhD theses), GloSECS (an updated multilingual soil science glossary), promotion of soil museums. Also, the SECS publishes the four-monthly Spanish Journal of Soil Science since 2011 (http://sjss.universia.net).

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

Search strategies on the Internet: general and specific.

PubMed

Bottrill, Krys

2004-06-01

Some of the most up-to-date information on scientific activity is to be found on the Internet; for example, on the websites of academic and other research institutions and in databases of currently funded research studies provided on the websites of funding bodies. Such information can be valuable in suggesting new approaches and techniques that could be applicable in a Three Rs context. However, the Internet is a chaotic medium, not subject to the meticulous classification and organisation of classical information resources. At the same time, Internet search engines do not match the sophistication of search systems used by database hosts. Also, although some offer relatively advanced features, user awareness of these tends to be low. Furthermore, much of the information on the Internet is not accessible to conventional search engines, giving rise to the concept of the "Invisible Web". General strategies and techniques for Internet searching are presented, together with a comparative survey of selected search engines. The question of how the Invisible Web can be accessed is discussed, as well as how to keep up-to-date with Internet content and improve searching skills.

The DrugAge database of aging-related drugs.

PubMed

Barardo, Diogo; Thornton, Daniel; Thoppil, Harikrishnan; Walsh, Michael; Sharifi, Samim; Ferreira, Susana; Anžič, Andreja; Fernandes, Maria; Monteiro, Patrick; Grum, Tjaša; Cordeiro, Rui; De-Souza, Evandro Araújo; Budovsky, Arie; Araujo, Natali; Gruber, Jan; Petrascheck, Michael; Fraifeld, Vadim E; Zhavoronkov, Alexander; Moskalev, Alexey; de Magalhães, João Pedro

2017-06-01

Aging is a major worldwide medical challenge. Not surprisingly, identifying drugs and compounds that extend lifespan in model organisms is a growing research area. Here, we present DrugAge (http://genomics.senescence.info/drugs/), a curated database of lifespan-extending drugs and compounds. At the time of writing, DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. Data were manually curated from 324 publications. Using drug-gene interaction data, we also performed a functional enrichment analysis of targets of lifespan-extending drugs. Enriched terms include various functional categories related to glutathione and antioxidant activity, ion transport and metabolic processes. In addition, we found a modest but significant overlap between targets of lifespan-extending drugs and known aging-related genes, suggesting that some but not most aging-related pathways have been targeted pharmacologically in longevity studies. DrugAge is freely available online for the scientific community and will be an important resource for biogerontologists. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

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

Mouse Tumor Biology (MTB): a database of mouse models for human cancer.

PubMed

Bult, Carol J; Krupke, Debra M; Begley, Dale A; Richardson, Joel E; Neuhauser, Steven B; Sundberg, John P; Eppig, Janan T

2015-01-01

The Mouse Tumor Biology (MTB; http://tumor.informatics.jax.org) database is a unique online compendium of mouse models for human cancer. MTB provides online access to expertly curated information on diverse mouse models for human cancer and interfaces for searching and visualizing data associated with these models. The information in MTB is designed to facilitate the selection of strains for cancer research and is a platform for mining data on tumor development and patterns of metastases. MTB curators acquire data through manual curation of peer-reviewed scientific literature and from direct submissions by researchers. Data in MTB are also obtained from other bioinformatics resources including PathBase, the Gene Expression Omnibus and ArrayExpress. Recent enhancements to MTB improve the association between mouse models and human genes commonly mutated in a variety of cancers as identified in large-scale cancer genomics studies, provide new interfaces for exploring regions of the mouse genome associated with cancer phenotypes and incorporate data and information related to Patient-Derived Xenograft models of human cancers. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach

PubMed Central

2012-01-01

Background Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. Methods We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. Results We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. Conclusions We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data. PMID:22759462

Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach.

PubMed

Ratkovic, Zorana; Golik, Wiktoria; Warnier, Pierre

2012-06-26

Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.

25 Years of GenBank

MedlinePlus

... this page please turn Javascript on. Unique DNA database has helped advance scientific discoveries worldwide Since its origin 25 years ago, the database of nucleic acid sequences known as GenBank has ...

Roadblocks to Scientific Thinking in Educational Decision Making

ERIC Educational Resources Information Center

Yates, Gregory C. R.

2008-01-01

Principles of scientific data accumulation and evidence-based practices are vehicles of professional enhancement. In this article, the author argues that a scientific knowledge base exists descriptive of the relationship between teachers' activities and student learning. This database appears barely recognised however, for reasons including (a)…

How Do You Like Your Science, Wet or Dry? How Two Lab Experiences Influence Student Understanding of Science Concepts and Perceptions of Authentic Scientific Practice.

PubMed

Munn, Maureen; Knuth, Randy; Van Horne, Katie; Shouse, Andrew W; Levias, Sheldon

2017-01-01

This study examines how two kinds of authentic research experiences related to smoking behavior-genotyping human DNA (wet lab) and using a database to test hypotheses about factors that affect smoking behavior (dry lab)-influence students' perceptions and understanding of scientific research and related science concepts. The study used pre and post surveys and a focus group protocol to compare students who conducted the research experiences in one of two sequences: genotyping before database and database before genotyping. Students rated the genotyping experiment to be more like real science than the database experiment, in spite of the fact that they associated more scientific tasks with the database experience than genotyping. Independent of the order of completing the labs, students showed gains in their understanding of science concepts after completion of the two experiences. There was little change in students' attitudes toward science pre to post, as measured by the Scientific Attitude Inventory II. However, on the basis of their responses during focus groups, students developed more sophisticated views about the practices and nature of science after they had completed both research experiences, independent of the order in which they experienced them. © 2017 M. Munn et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Italian polar data center for capacity building associated with the IHY

NASA Astrophysics Data System (ADS)

Damiani, A.; Bendetti, E.; Storini, M.; Rafanelli, C.

The International Heliophysical Year IHY offers a good opportunity to develop and coordinate studies on the Sun-Earth system by using a large variety of simultaneous data obtained by satellite spacecraft and ground based instruments Among these data we recall the ones coming from solar and interplanetary medium observations auroral neutron monitor geomagnetic field ionospheric meteorological and other atmospheric observatories In this context an Information System for the Italian Research in Antarctica SIRIA has started during 2003 aiming to collect information on the scientific research projects funded by the National Antarctic Research Program PNRA of Italy since its birth 1985 It belongs to the Joint Committee on Antarctic Data Management JCADM of SCAR Scientific Committee on Antarctic Research as the Italian Antarctic Data Center SIRIA being the Italian Polar Database gathers also information on research activities conducted in North Pole regions This Information System can be a relevant resource for capacity building associated with the IHY particularly for people involved in interdisciplinary researches We describe the present status of the Italian Polar Data Center and its potential use

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

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

CWA Scientific Documents

EPA Pesticide Factsheets

Summaries and links to scientific documents relevant to the Clean Water Act (CWA) and the protection of wetlands and aquatic resources in the United States, including the National Wetlands Inventory Report, National Resources Inventory Report and others.

Genomics Community Resources | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

To facilitate genomic research and the dissemination of its products, National Human Genome Research Institute (NHGRI) supports genomic resources that are crucial for basic research, disease studies, model organism studies, and other biomedical research.  Awards under this FOA will support the development and distribution of genomic resources that will be valuable for the broad research community, using cost-effective approaches.  Such resources include (but are not limited to) databases and informatics resources (such as human and model organism databases, ontologies, and analysi

The laboratory-clinician team: a professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing.

PubMed

Wain, Karen E; Riggs, Erin; Hanson, Karen; Savage, Melissa; Riethmaier, Darlene; Muirhead, Andrea; Mitchell, Elyse; Packard, Bethanny Smith; Faucett, W Andrew

2012-10-01

The International Standards for Cytogenomic Arrays (ISCA) Consortium is a worldwide collaborative effort dedicated to optimizing patient care by improving the quality of chromosomal microarray testing. The primary effort of the ISCA Consortium has been the development of a database of copy number variants (CNVs) identified during the course of clinical microarray testing. This database is a powerful resource for clinicians, laboratories, and researchers, and can be utilized for a variety of applications, such as facilitating standardized interpretations of certain CNVs across laboratories or providing phenotypic information for counseling purposes when published data is sparse. A recognized limitation to the clinical utility of this database, however, is the quality of clinical information available for each patient. Clinical genetic counselors are uniquely suited to facilitate the communication of this information to the laboratory by virtue of their existing clinical responsibilities, case management skills, and appreciation of the evolving nature of scientific knowledge. We intend to highlight the critical role that genetic counselors play in ensuring optimal patient care through contributing to the clinical utility of the ISCA Consortium's database, as well as the quality of individual patient microarray reports provided by contributing laboratories. Current tools, paper and electronic forms, created to maximize this collaboration are shared. In addition to making a professional commitment to providing complete clinical information, genetic counselors are invited to become ISCA members and to become involved in the discussions and initiatives within the Consortium.

[Exploiture and application of an internet-based Computation Platform for Integrative Pharmacology of Traditional Chinese Medicine].

PubMed

Xu, Hai-Yu; Liu, Zhen-Ming; Fu, Yan; Zhang, Yan-Qiong; Yu, Jian-Jun; Guo, Fei-Fei; Tang, Shi-Huan; Lv, Chuan-Yu; Su, Jin; Cui, Ru-Yi; Yang, Hong-Jun

2017-09-01

Recently, integrative pharmacology(IP) has become a pivotal paradigm for the modernization of traditional Chinese medicines(TCM) and combinatorial drugs discovery, which is an interdisciplinary science for establishing the in vitro and in vivo correlation between absorption, distribution, metabolism, and excretion/pharmacokinetic(ADME/PK) profiles of TCM and the molecular networks of disease by the integration of the knowledge of multi-disciplinary and multi-stages. In the present study, an internet-based Computation Platform for IP of TCM(TCM-IP, www.tcmip.cn) is established to promote the development of the emerging discipline. Among them, a big data of TCM is an important resource for TCM-IP including Chinese Medicine Formula Database, Chinese Medical Herbs Database, Chemical Database of Chinese Medicine, Target Database for Disease and Symptoms, et al. Meanwhile, some data mining and bioinformatics approaches are critical technology for TCM-IP including the identification of the TCM constituents, ADME prediction, target prediction for the TCM constituents, network construction and analysis, et al. Furthermore, network beautification and individuation design are employed to meet the consumer's requirement. We firmly believe that TCM-IP is a very useful tool for the identification of active constituents of TCM and their involving potential molecular mechanism for therapeutics, which would wildly applied in quality evaluation, clinical repositioning, scientific discovery based on original thinking, prescription compatibility and new drug of TCM, et al. Copyright© by the Chinese Pharmaceutical Association.

Transitioning Newborns from NICU to Home: Family Information Packet

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Next Steps After Your Diagnosis: Finding Information and Support

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Blood Thinner Pills: Your Guide to Using Them Safely

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Question Builder: Be Prepared for Your Next Medical Appointment

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Academic Entrepreneurship and Exchange of Scientific Resources: Material Transfer in Life and Materials Sciences in Japanese Universities

ERIC Educational Resources Information Center

Shibayama, Sotaro; Walsh, John P.; Baba, Yasunori

2012-01-01

This study uses a sample of Japanese university scientists in life and materials sciences to examine how academic entrepreneurship has affected the norms and behaviors of academic scientists regarding sharing scientific resources. Results indicate that high levels of academic entrepreneurship in a scientific field are associated with less reliance…

The Modular Modeling System (MMS): A modeling framework for water- and environmental-resources management

USGS Publications Warehouse

Leavesley, G.H.; Markstrom, S.L.; Viger, R.J.

2004-01-01

The interdisciplinary nature and increasing complexity of water- and environmental-resource problems require the use of modeling approaches that can incorporate knowledge from a broad range of scientific disciplines. The large number of distributed hydrological and ecosystem models currently available are composed of a variety of different conceptualizations of the associated processes they simulate. Assessment of the capabilities of these distributed models requires evaluation of the conceptualizations of the individual processes, and the identification of which conceptualizations are most appropriate for various combinations of criteria, such as problem objectives, data constraints, and spatial and temporal scales of application. With this knowledge, "optimal" models for specific sets of criteria can be created and applied. The U.S. Geological Survey (USGS) Modular Modeling System (MMS) is an integrated system of computer software that has been developed to provide these model development and application capabilities. MMS supports the integration of models and tools at a variety of levels of modular design. These include individual process models, tightly coupled models, loosely coupled models, and fully-integrated decision support systems. A variety of visualization and statistical tools are also provided. MMS has been coupled with the Bureau of Reclamation (BOR) object-oriented reservoir and river-system modeling framework, RiverWare, under a joint USGS-BOR program called the Watershed and River System Management Program. MMS and RiverWare are linked using a shared relational database. The resulting database-centered decision support system provides tools for evaluating and applying optimal resource-allocation and management strategies to complex, operational decisions on multipurpose reservoir systems and watersheds. Management issues being addressed include efficiency of water-resources management, environmental concerns such as meeting flow needs for endangered species, and optimizing operations within the constraints of multiple objectives such as power generation, irrigation, and water conservation. This decision support system approach is being developed, tested, and implemented in the Gunni-son, Yakima, San Juan, Rio Grande, and Truckee River basins of the western United States. Copyright ASCE 2004.

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. PMID:22180823

Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

NASA Astrophysics Data System (ADS)

Ehlmann, Bryon K.

Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

Database Software Selection for the Egyptian National STI Network.

ERIC Educational Resources Information Center

Slamecka, Vladimir

The evaluation and selection of information/data management system software for the Egyptian National Scientific and Technical (STI) Network are described. An overview of the state-of-the-art of database technology elaborates on the differences between information retrieval and database management systems (DBMS). The desirable characteristics of…

[New bibliometric indicators for the scientific literature: an evolving panorama].

PubMed

La Torre, G; Sciarra, I; Chiappetta, M; Monteduro, A

2017-01-01

Bibliometrics is a science which evaluates the impact of the scientific work of a journal or of an author, using mathematical and statistical tools. Impact Factor (IF) is the first bibliometric parameter created, and after it many others have been progressively conceived in order to go beyond its limits. Currently bibliometric indexes are used for academic purposes, among them to evaluate the eligibility of a researcher to compete for the National Scientific Qualification, in order to access to competitive exams to become professor. Aim of this study is to identify the most relevant bibliometric indexes and to summarized their characteristics. A revision of bibliometric indexes as been conducted, starting from the classic ones and completing with the most recent ones. The two most used bibliometric indexes are the IF, which measures the scientific impact of a periodical and bases on Web of Science citation database, and the h-index, which measures the impact of the scientific work of a researcher, basing on Scopus database. Besides them other indexes have been created more recently, such as the SCImago Journal Rank Indicator (SJR), the Source Normalised Impact per Paper (SNIP) and the CiteScore index. They are all based on Scopus database and evaluate, in different ways, the citational impact of a periodic. The i10-index instead is provided from Google Scholar database and allows to evaluate the impact of the scientific production of a researcher. Recently two softwares have been introduced: the first one, Publish or Perish, allows to evaluate the scientific work of a researcher, through the assessment of many indexes; the second one, Altmetric, measure the use in the Web of the academic papers, instead of measuring citations, by means of alternative metrics respect to the traditional ones. Each analized index shows advantages but also criticalities. Therefore the combined use of more than one indexes, citational and not, should be preferred, in order to correctly evaluate the work of reserchers and to finally improve the quality and the development of scientific research.

Replicability and other features of a high-quality science: Toward a balanced and empirical approach.

PubMed

Finkel, Eli J; Eastwick, Paul W; Reis, Harry T

2017-08-01

Finkel, Eastwick, and Reis (2015; FER2015) argued that psychological science is better served by responding to apprehensions about replicability rates with contextualized solutions than with one-size-fits-all solutions. Here, we extend FER2015's analysis to suggest that much of the discussion of best research practices since 2011 has focused on a single feature of high-quality science-replicability-with insufficient sensitivity to the implications of recommended practices for other features, like discovery, internal validity, external validity, construct validity, consequentiality, and cumulativeness. Thus, although recommendations for bolstering replicability have been innovative, compelling, and abundant, it is difficult to evaluate their impact on our science as a whole, especially because many research practices that are beneficial for some features of scientific quality are harmful for others. For example, FER2015 argued that bigger samples are generally better, but also noted that very large samples ("those larger than required for effect sizes to stabilize"; p. 291) could have the downside of commandeering resources that would have been better invested in other studies. In their critique of FER2015, LeBel, Campbell, and Loving (2016) concluded, based on simulated data, that ever-larger samples are better for the efficiency of scientific discovery (i.e., that there are no tradeoffs). As demonstrated here, however, this conclusion holds only when the replicator's resources are considered in isolation. If we widen the assumptions to include the original researcher's resources as well, which is necessary if the goal is to consider resource investment for the field as a whole, the conclusion changes radically-and strongly supports a tradeoff-based analysis. In general, as psychologists seek to strengthen our science, we must complement our much-needed work on increasing replicability with careful attention to the other features of a high-quality science. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

PubMed Central

Shimoyama, Mary; Smith, Jennifer R.; De Pons, Jeff; Tutaj, Marek; Khampang, Pawjai; Hong, Wenzhou; Erbe, Christy B.; Ehrlich, Garth D.; Bakaletz, Lauren O.; Kerschner, Joseph E.

2016-01-01

The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease. Database URL: http://crrd.mcw.edu PMID:27173523

A 5-year scientometric analysis of research centers affiliated to Tehran University of Medical Sciences.

PubMed

Yazdani, Kamran; Rahimi-Movaghar, Afarin; Nedjat, Saharnaz; Ghalichi, Leila; Khalili, Malahat

2015-01-01

Since Tehran University of Medical Sciences (TUMS) has the oldest and highest number of research centers among all Iranian medical universities, this study was conducted to evaluate scientific output of research centers affiliated to Tehran University of Medical Sciences (TUMS) using scientometric indices and the affecting factors. Moreover, a number of scientometric indicators were introduced. This cross-sectional study was performed to evaluate a 5-year scientific performance of research centers of TUMS. Data were collected through questionnaires, annual evaluation reports of the Ministry of Health, and also from Scopus database. We used appropriate measures of central tendency and variation for descriptive analyses. Moreover, uni-and multi-variable linear regression were used to evaluate the effect of independent factors on the scientific output of the centers. The medians of the numbers of papers and books during a 5-year period were 150.5 and 2.5 respectively. The median of the "articles per researcher" was 19.1. Based on multiple linear regression, younger age centers (p=0.001), having a separate budget line (p=0.016), and number of research personnel (p<0.001) had a direct significant correlation with the number of articles while real properties had a reverse significant correlation with it (p=0.004). The results can help policy makers and research managers to allocate sufficient resources to improve current situation of the centers. Newly adopted and effective scientometric indices are is suggested to be used to evaluate scientific outputs and functions of these centers.

Scientific integrity resource guide: Efforts by federal agencies, foundations, nonprofit organizations, professional societies, and academia in the United States

PubMed Central

Kretser, Alison; Murphy, Delia; Dwyer, Johanna

2017-01-01

ABSTRACT Scientific integrity is at the forefront of the scientific research enterprise. This paper provides an overview of key existing efforts on scientific integrity by federal agencies, foundations, nonprofit organizations, professional societies, and academia from 1989 to April 2016. It serves as a resource for the scientific community on scientific integrity work and helps to identify areas in which more action is needed. Overall, there is tremendous activity in this area and there are clear linkages among the efforts of the five sectors. All the same, scientific integrity needs to remain visible in the scientific community and evolve along with new research paradigms. High priority in instilling these values falls upon all stakeholders. PMID:27748637

Database resources of the National Center for Biotechnology Information

PubMed Central

Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Madden, Thomas L; Maglott, Donna R; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Yaschenko, Eugene; Ye, Jian

2009-01-01

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Exploring Cloud Computing for Large-scale Scientific Applications

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

Lin, Guang; Han, Binh; Yin, Jian

This paper explores cloud computing for large-scale data-intensive scientific applications. Cloud computing is attractive because it provides hardware and software resources on-demand, which relieves the burden of acquiring and maintaining a huge amount of resources that may be used only once by a scientific application. However, unlike typical commercial applications that often just requires a moderate amount of ordinary resources, large-scale scientific applications often need to process enormous amount of data in the terabyte or even petabyte range and require special high performance hardware with low latency connections to complete computation in a reasonable amount of time. To address thesemore » challenges, we build an infrastructure that can dynamically select high performance computing hardware across institutions and dynamically adapt the computation to the selected resources to achieve high performance. We have also demonstrated the effectiveness of our infrastructure by building a system biology application and an uncertainty quantification application for carbon sequestration, which can efficiently utilize data and computation resources across several institutions.« less

RPA tree-level database users guide

Treesearch

Patrick D. Miles; Scott A. Pugh; Brad Smith; Sonja N. Oswalt

2014-01-01

The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974 calls for a periodic assessment of the Nation's renewable resources. The Forest Inventory and Analysis (FIA) program of the U.S. Forest Service supports the RPA effort by providing information on the forest resources of the United States. The RPA tree-level database (RPAtreeDB) was generated...

RNAcentral: A vision for an international database of RNA sequences

PubMed Central

Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian

2011-01-01

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

Be More Involved in Your Health Care: Tips for Patients

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

[Utilization suitability of forest resources in typical forest zone of Changbai Mountains].

PubMed

Hao, Zhanqing; Yu, Deyong; Xiong, Zaiping; Ye, Ji

2004-10-01

Conservation of natural forest does not simply equal to no logging. The Northeast China Forest Region has a logging quota of mature forest as part of natural forest conservation project. How to determine the logging spots rationally and scientifically is very important. Recent scientific theories of forest resources management advocate that the utilization of forest resources should stick to the principle of sustaining use, and pay attention to the ecological function of forest resources. According to the logging standards, RS and GIS techniques can be used to detect the precise location of forest resources and obtain information of forest areas and types, and thus, provide more rational and scientific support for space choice about future utilization of forest resources. In this paper, the Lushuihe Forest Bureau was selected as a typical case in Changbai Mountains Forest Region to assess the utilization conditions of forest resources, and some advices on spatial choice for future management of forest resources in the study area were offered.

Neuromas

MedlinePlus

... and Reimbursement Basics APMA Career Center Your APMA Leadership Opportunities Early Career Resources Academic and Scientific Resources Practice Management & Reimbursement Coding Resources Coding Resource Center Reimbursement Resources ...

Literature searches on Ayurveda: An update

PubMed Central

Aggithaya, Madhur G.; Narahari, Saravu R.

2015-01-01

Introduction: The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. Aims: To update on Ayurveda literature search and strategy to retrieve maximum publications. Methods: Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Results: Five among 46 databases are now relevant – AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. “The Researches in Ayurveda” and “Ayurvedic Research Database” (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. Conclusion: AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches. PMID:27313409

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

Foot Surgery

MedlinePlus

... and Reimbursement Basics APMA Career Center Your APMA Leadership Opportunities Early Career Resources Academic and Scientific Resources Practice Management & Reimbursement Coding Resources Coding Resource Center Reimbursement Resources ...

Athlete's Foot

MedlinePlus

... and Reimbursement Basics APMA Career Center Your APMA Leadership Opportunities Early Career Resources Academic and Scientific Resources Practice Management & Reimbursement Coding Resources Coding Resource Center Reimbursement Resources ...

Heel Pain

MedlinePlus

... and Reimbursement Basics APMA Career Center Your APMA Leadership Opportunities Early Career Resources Academic and Scientific Resources Practice Management & Reimbursement Coding Resources Coding Resource Center Reimbursement Resources ...

To ontologise or not to ontologise: An information model for a geospatial knowledge infrastructure

NASA Astrophysics Data System (ADS)

Stock, Kristin; Stojanovic, Tim; Reitsma, Femke; Ou, Yang; Bishr, Mohamed; Ortmann, Jens; Robertson, Anne

2012-08-01

A geospatial knowledge infrastructure consists of a set of interoperable components, including software, information, hardware, procedures and standards, that work together to support advanced discovery and creation of geoscientific resources, including publications, data sets and web services. The focus of the work presented is the development of such an infrastructure for resource discovery. Advanced resource discovery is intended to support scientists in finding resources that meet their needs, and focuses on representing the semantic details of the scientific resources, including the detailed aspects of the science that led to the resource being created. This paper describes an information model for a geospatial knowledge infrastructure that uses ontologies to represent these semantic details, including knowledge about domain concepts, the scientific elements of the resource (analysis methods, theories and scientific processes) and web services. This semantic information can be used to enable more intelligent search over scientific resources, and to support new ways to infer and visualise scientific knowledge. The work describes the requirements for semantic support of a knowledge infrastructure, and analyses the different options for information storage based on the twin goals of semantic richness and syntactic interoperability to allow communication between different infrastructures. Such interoperability is achieved by the use of open standards, and the architecture of the knowledge infrastructure adopts such standards, particularly from the geospatial community. The paper then describes an information model that uses a range of different types of ontologies, explaining those ontologies and their content. The information model was successfully implemented in a working geospatial knowledge infrastructure, but the evaluation identified some issues in creating the ontologies.

43 CFR 6302.16 - When and how may I gather scientific information about resources in BLM wilderness?

Code of Federal Regulations, 2011 CFR

2011-10-01

... natural or cultural resources in wilderness areas, using methods that may cause greater impacts on the... CONSERVATION (6000) MANAGEMENT OF DESIGNATED WILDERNESS AREAS Use of Wilderness Areas, Prohibited Acts, and Penalties Use of Wilderness Areas § 6302.16 When and how may I gather scientific information about resources...