Cosmos: An Information Retrieval System that Works.

ERIC Educational Resources Information Center

Clay, Katherine; Grossman, Alvin

1980-01-01

Briefly described is the County of San Mateo Online System (COSMOS) which was developed and is used by the San Mateo Educational Resources Center (SMERC) to access the Educational Resources Information Center (ERIC) and Fugitive Information Data Organizer (FIDO) databases as well as the curriculum guides housed at SMERC. (TG)

Resourcing the clinical complementary medicine information needs of Australian medical students: Results of a grounded theory study.

PubMed

Templeman, Kate; Robinson, Anske; McKenna, Lisa

2016-09-01

The aim of this study was to identify Australian medical students' complementary medicine information needs. Thirty medical students from 10 medical education faculties across Australian universities were recruited. Data were generated using in-depth semi-structured interviews and constructivist grounded theory method was used to analyze and construct data. Students sought complementary medicine information from a range of inadequate sources, such as pharmacological texts, Internet searches, peer-reviewed medical journals, and drug databases. The students identified that many complementary medicine resources may not be regarded as objective, reliable, differentiated, or comprehensive, leaving much that medical education needs to address. Most students sought succinct, easily accessible, evidence-based information to inform safe and appropriate clinical decisions about complementary medicines. A number of preferred resources were identified that can be recommended and actively promoted to medical students. Therefore, specific, evidence-based complementary medicine databases and secondary resources should be subscribed and recommended to medical schools and students, to assist meeting professional responsibilities regarding complementary medicines. These findings may help inform the development of appropriate medical information resources regarding complementary medicines. © 2016 John Wiley & Sons Australia, Ltd.

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.

Oral cancer databases: A comprehensive review.

PubMed

Sarode, Gargi S; Sarode, Sachin C; Maniyar, Nikunj; Anand, Rahul; Patil, Shankargouda

2017-11-29

Cancer database is a systematic collection and analysis of information on various human cancers at genomic and molecular level that can be utilized to understand various steps in carcinogenesis and for therapeutic advancement in cancer field. Oral cancer is one of the leading causes of morbidity and mortality all over the world. The current research efforts in this field are aimed at cancer etiology and therapy. Advanced genomic technologies including microarrays, proteomics, transcrpitomics, and gene sequencing development have culminated in generation of extensive data and subjection of several genes and microRNAs that are distinctively expressed and this information is stored in the form of various databases. Extensive data from various resources have brought the need for collaboration and data sharing to make effective use of this new knowledge. The current review provides comprehensive information of various publicly accessible databases that contain information pertinent to oral squamous cell carcinoma (OSCC) and databases designed exclusively for OSCC. The databases discussed in this paper are Protein-Coding Gene Databases and microRNA Databases. This paper also describes gene overlap in various databases, which will help researchers to reduce redundancy and focus on only those genes, which are common to more than one databases. We hope such introduction will promote awareness and facilitate the usage of these resources in the cancer research community, and researchers can explore the molecular mechanisms involved in the development of cancer, which can help in subsequent crafting of therapeutic strategies. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Design research about coastal zone planning and management information system based on GIS and database technologies

NASA Astrophysics Data System (ADS)

Huang, Pei; Wu, Sangyun; Feng, Aiping; Guo, Yacheng

2008-10-01

As littoral areas in possession of concentrated population, abundant resources, developed industry and active economy, the coastal areas are bound to become the forward positions and supported regions for marine exploitation. In the 21st century, the pressure that coastal zones are faced with is as follows: growth of population and urbanization, rise of sea level and coastal erosion, shortage of freshwater resource and deterioration of water resource, and degradation of fishery resource and so on. So the resources of coastal zones should be programmed and used reasonably for the sustainable development of economy and environment. This paper proposes a design research on the construction of coastal zone planning and management information system based on GIS and database technologies. According to this system, the planning results of coastal zones could be queried and displayed expediently through the system interface. It is concluded that the integrated application of GIS and database technologies provides a new modern method for the management of coastal zone resources, and makes it possible to ensure the rational development and utilization of the coastal zone resources, along with the sustainable development of economy and environment.

Computing and Communications Infrastructure for Network-Centric Warfare: Exploiting COTS, Assuring Performance

DTIC Science & Technology

2004-06-01

remote databases, has seen little vendor acceptance. Each database ( Oracle , DB2, MySQL , etc.) has its own client- server protocol. Therefore each...existing standards – SQL , X.500/LDAP, FTP, etc. • View information dissemination as selective replication – State-oriented vs . message-oriented...allowing the 8 application to start. The resource management system would serve as a broker to the resources, making sure that resources are not

Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources

PubMed Central

2013-01-01

Background Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities. Description Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436bacterial, fungal and archaea species from 52 collections in 25 countries and regions. A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM. Conclusion A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the activities of microbiologists world-wide, who work in both public and industrial research centres. This database is available from http://gcm.wfcc.info. PMID:24377417

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.

Directory of On-Line Networks, Databases and Bulletin Boards on Assistive Technology. Second Edition. RESNA Technical Assistance Project.

ERIC Educational Resources Information Center

RESNA: Association for the Advancement of Rehabilitation Technology, Washington, DC.

This resource directory provides a selective listing of electronic networks, online databases, and bulletin boards that highlight technology-related services and products. For each resource, the following information is provided: name, address, and telephone number; description; target audience; hardware/software needs to access the system;…

Preference vs. Authority: A Comparison of Student Searching in a Subject-Specific Indexing and Abstracting Database and a Customized Discovery Layer

ERIC Educational Resources Information Center

Dahlen, Sarah P. C.; Hanson, Kathlene

2017-01-01

Discovery layers provide a simplified interface for searching library resources. Libraries with limited finances make decisions about retaining indexing and abstracting databases when similar information is available in discovery layers. These decisions should be informed by student success at finding quality information as well as satisfaction…

MIPSPlantsDB—plant database resource for integrative and comparative plant genome research

PubMed Central

Spannagl, Manuel; Noubibou, Octave; Haase, Dirk; Yang, Li; Gundlach, Heidrun; Hindemitt, Tobias; Klee, Kathrin; Haberer, Georg; Schoof, Heiko; Mayer, Klaus F. X.

2007-01-01

Genome-oriented plant research delivers rapidly increasing amount of plant genome data. Comprehensive and structured information resources are required to structure and communicate genome and associated analytical data for model organisms as well as for crops. The increase in available plant genomic data enables powerful comparative analysis and integrative approaches. PlantsDB aims to provide data and information resources for individual plant species and in addition to build a platform for integrative and comparative plant genome research. PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato. Complementary data resources for cis elements, repetive elements and extensive cross-species comparisons are implemented. The PlantsDB portal can be reached at . PMID:17202173

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.

USGS Mineral Resources Program; national maps and datasets for research and land planning

USGS Publications Warehouse

Nicholson, S.W.; Stoeser, D.B.; Ludington, S.D.; Wilson, Frederic H.

2001-01-01

The U.S. Geological Survey, the Nation’s leader in producing and maintaining earth science data, serves as an advisor to Congress, the Department of the Interior, and many other Federal and State agencies. Nationwide datasets that are easily available and of high quality are critical for addressing a wide range of land-planning, resource, and environmental issues. Four types of digital databases (geological, geophysical, geochemical, and mineral occurrence) are being compiled and upgraded by the Mineral Resources Program on regional and national scales to meet these needs. Where existing data are incomplete, new data are being collected to ensure national coverage. Maps and analyses produced from these databases provide basic information essential for mineral resource assessments and environmental studies, as well as fundamental information for regional and national land-use studies. Maps and analyses produced from the databases are instrumental to ongoing basic research, such as the identification of mineral deposit origins, determination of regional background values of chemical elements with known environmental impact, and study of the relationships between toxic elements or mining practices to human health. As datasets are completed or revised, the information is made available through a variety of media, including the Internet. Much of the available information is the result of cooperative activities with State and other Federal agencies. The upgraded Mineral Resources Program datasets make geologic, geophysical, geochemical, and mineral occurrence information at the state, regional, and national scales available to members of Congress, State and Federal government agencies, researchers in academia, and the general public. The status of the Mineral Resources Program datasets is outlined below.

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

PubMed Central

Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria; García‐Sastre, Adolfo; Macken, Catherine; Baumgarth, Nicole; Suarez, David; Pickett, Brett E.; Zhang, Yun; Larsen, Christopher N.; Ramsey, Alvin; Zhou, Liwei; Zaremba, Sam; Kumar, Sanjeev; Deitrich, Jon; Klem, Edward; Scheuermann, Richard H.

2012-01-01

Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses 6(6), 404–416. Background  The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design  The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly‐accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user‐friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in‐protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results  To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross‐protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions  The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics. PMID:22260278

Aquatic information and retrieval (AQUIRE) database system

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

Hunter, R.; Niemi, G.; Pilli, A.

The AQUIRE database system is one of the foremost international resources for finding aquatic toxicity information. Information in the system is organized around the concept of an 'aquatic toxicity test.' A toxicity test record contains information about the chemical, species, endpoint, endpoint concentrations, and test conditions under which the toxicity test was conducted. For the past 10 years aquatic literature has been reviewed and entered into the system. Currently, the AQUIRE database system contains data on more than 2,400 species, 160 endpoints, 5,000 chemicals, 6,000 references, and 104,000 toxicity tests.

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database.

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful AOP-DB user interface in...

AOP-DB Frontend: A user interface for the Adverse Outcome Pathways Database

EPA Science Inventory

The EPA Adverse Outcome Pathway Database (AOP-DB) is a database resource that aggregates association relationships between AOPs, genes, chemicals, diseases, pathways, species orthology information, ontologies. The AOP-DB frontend is a simple yet powerful user interface in the for...

ADAPTmap: International coordinated data resource for improving goat production effiency

USDA-ARS?s Scientific Manuscript database

Goats provide vital food and economic security, particularly in developing countries. We created a database that is a nexus for all performance, type, geographic information system (GIS), production environment, and genome information on goats. This resource provides a platform for meta-analysis tha...

Forest Vegetation Simulator translocation techniques with the Bureau of Land Management's Forest Vegetation Information system database

Treesearch

Timothy A. Bottomley

2008-01-01

The BLM uses a database, called the Forest Vegetation Information System (FORVIS), to store, retrieve, and analyze forest resource information on a majority of their forested lands. FORVIS also has the capability of easily transferring appropriate data electronically into Forest Vegetation Simulator (FVS) for simulation runs. Only minor additional data inputs or...

NetMap: a new tool in support of watershed science and resource management.

Treesearch

L. Benda; D. Miller; K. Andras; P. Bigelow; G. Reeves; D. Michael

2007-01-01

In this paper, we show how application of principles of river ecology can guide use of a comprehensive terrain database within geographic information system (GIS) to facilitate watershed analysis relevant to natural resource management. We present a unique arrangement of a terrain database, GIS, and principles of riverine ecology for the purpose of advancing watershed...

Online bibliographic sources in hydrology

USGS Publications Warehouse

Wild, Emily C.; Havener, W. Michael

2001-01-01

Traditional commercial bibliographic databases and indexes provide some access to hydrology materials produced by the government; however, these sources do not provide comprehensive coverage of relevant hydrologic publications. This paper discusses bibliographic information available from the federal government and state geological surveys, water resources agencies, and depositories. In addition to information in these databases, the paper describes the scope, styles of citing, subject terminology, and the ways these information sources are currently being searched, formally and informally, by hydrologists. Information available from the federal and state agencies and from the state depositories might be missed by limiting searches to commercially distributed databases.

Analyzing legacy U.S. Geological Survey geochemical databases using GIS: applications for a national mineral resource assessment

USGS Publications Warehouse

Yager, Douglas B.; Hofstra, Albert H.; Granitto, Matthew

2012-01-01

This report emphasizes geographic information system analysis and the display of data stored in the legacy U.S. Geological Survey National Geochemical Database for use in mineral resource investigations. Geochemical analyses of soils, stream sediments, and rocks that are archived in the National Geochemical Database provide an extensive data source for investigating geochemical anomalies. A study area in the Egan Range of east-central Nevada was used to develop a geographic information system analysis methodology for two different geochemical datasets involving detailed (Bureau of Land Management Wilderness) and reconnaissance-scale (National Uranium Resource Evaluation) investigations. ArcGIS was used to analyze and thematically map geochemical information at point locations. Watershed-boundary datasets served as a geographic reference to relate potentially anomalous sample sites with hydrologic unit codes at varying scales. The National Hydrography Dataset was analyzed with Hydrography Event Management and ArcGIS Utility Network Analyst tools to delineate potential sediment-sample provenance along a stream network. These tools can be used to track potential upstream-sediment-contributing areas to a sample site. This methodology identifies geochemically anomalous sample sites, watersheds, and streams that could help focus mineral resource investigations in the field.

The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics.

PubMed Central

Ellis, L B; Hershberger, C D; Wackett, L P

1999-01-01

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes. PMID:9847233

Expert searching in public health

PubMed Central

Alpi, Kristine M.

2005-01-01

Objective: The article explores the characteristics of public health information needs and the resources available to address those needs that distinguish it as an area of searching requiring particular expertise. Methods: Public health searching activities from reference questions and literature search requests at a large, urban health department library were reviewed to identify the challenges in finding relevant public health information. Results: The terminology of the information request frequently differed from the vocabularies available in the databases. Searches required the use of multiple databases and/or Web resources with diverse interfaces. Issues of the scope and features of the databases relevant to the search questions were considered. Conclusion: Expert searching in public health differs from other types of expert searching in the subject breadth and technical demands of the databases to be searched, the fluidity and lack of standardization of the vocabulary, and the relative scarcity of high-quality investigations at the appropriate level of geographic specificity. Health sciences librarians require a broad exposure to databases, gray literature, and public health terminology to perform as expert searchers in public health. PMID:15685281

TryTransDB: A web-based resource for transport proteins in Trypanosomatidae.

PubMed

Sonar, Krushna; Kabra, Ritika; Singh, Shailza

2018-03-12

TryTransDB is a web-based resource that stores transport protein data which can be retrieved using a standalone BLAST tool. We have attempted to create an integrated database that can be a one-stop shop for the researchers working with transport proteins of Trypanosomatidae family. TryTransDB (Trypanosomatidae Transport Protein Database) is a web based comprehensive resource that can fire a BLAST search against most of the transport protein sequences (protein and nucleotide) from Trypanosomatidae family organisms. This web resource further allows to compute a phylogenetic tree by performing multiple sequence alignment (MSA) using CLUSTALW suite embedded in it. Also, cross-linking to other databases helps in gathering more information for a certain transport protein in a single website.

New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

PubMed

Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

2013-07-01

Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

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

PubMed Central

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

2015-01-01

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

Development of a conceptual integrated traffic safety problem identification database

DOT National Transportation Integrated Search

1999-12-01

The project conceptualized a traffic safety risk management information system and statistical database for improved problem-driver identification, countermeasure development, and resource allocation. The California Department of Motor Vehicles Drive...

When Money Matters: How Educational Expenditures Improve Student Performance and How They Don't. A Policy Information Perspective.

ERIC Educational Resources Information Center

Wenglinsky, Harold

Little agreement exists on which school expenditures and resources are most likely to improve student resources or whether resources really matter at all. This study compiles a national database of school finance information and analyzes the data to address the importance of school expenditures. Data were collected from the National Assessment of…

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.

ACToR: Aggregated Computational Toxicology Resource (T)

EPA Science Inventory

The EPA Aggregated Computational Toxicology Resource (ACToR) is a set of databases compiling information on chemicals in the environment from a large number of public and in-house EPA sources. ACToR has 3 main goals: (1) The serve as a repository of public toxicology information ...

The development of an Ada programming support environment database: SEAD (Software Engineering and Ada Database), user's manual

NASA Technical Reports Server (NTRS)

Liaw, Morris; Evesson, Donna

1988-01-01

This is a manual for users of the Software Engineering and Ada Database (SEAD). SEAD was developed to provide an information resource to NASA and NASA contractors with respect to Ada-based resources and activities that are available or underway either in NASA or elsewhere in the worldwide Ada community. The sharing of such information will reduce the duplication of effort while improving quality in the development of future software systems. The manual describes the organization of the data in SEAD, the user interface from logging in to logging out, and concludes with a ten chapter tutorial on how to use the information in SEAD. Two appendices provide quick reference for logging into SEAD and using the keyboard of an IBM 3270 or VT100 computer terminal.

Practice databases and their uses in clinical research.

PubMed

Tierney, W M; McDonald, C J

1991-04-01

A few large clinical information databases have been established within larger medical information systems. Although they are smaller than claims databases, these clinical databases offer several advantages: accurate and timely data, rich clinical detail, and continuous parameters (for example, vital signs and laboratory results). However, the nature of the data vary considerably, which affects the kinds of secondary analyses that can be performed. These databases have been used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation, resource use, quality assurance, and decision analysis. In addition, practice databases can be used to identify subjects for prospective studies. Further methodologic developments are necessary to deal with the prevalent problems of missing data and various forms of bias if such databases are to grow and contribute valuable clinical information.

The Animal Genetic Resource Information Network (AnimalGRIN) Database: A Database Design & Implementation Case

ERIC Educational Resources Information Center

Irwin, Gretchen; Wessel, Lark; Blackman, Harvey

2012-01-01

This case describes a database redesign project for the United States Department of Agriculture's National Animal Germplasm Program (NAGP). The case provides a valuable context for teaching and practicing database analysis, design, and implementation skills, and can be used as the basis for a semester-long team project. The case demonstrates the…

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

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

77 FR 67657 - Request for Public Comment: 30-Day Proposed Information Collection: Indian Health Service (IHS...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-13

... Practice, and Local Effort (BPPPLE) Form.'' Need and Use of Information Collection: The IHS goal is to.../Disease Prevention, Nursing, and Dental) have developed a centralized program database of best practices, promising Practices and local efforts and resources. This database was previously referred as OSCAR, but the...

CD-ROMS Step by Step.

ERIC Educational Resources Information Center

Nath, Herbert

This manual consists of sets of guides for six CD-ROM databases: (1) ABI/INFORM, a business administration CD-ROM published by UMI; (2) Books in Print (an outstanding tool for compiling bibliographies on any subject); (3) ERIC (Educational Resources Information Center), an education database in the version published by SilverPlatter; (4) MLA, a…

Using sampling theory as the basis for a conceptual data model

Treesearch

Fred C. Martin; Tonya Baggett; Tom Wolfe

2000-01-01

Greater demands on forest resources require that larger amounts of information be readily available to decisionmakers. To provide more information faster, databases must be developed that are more comprehensive and easier to use. Data modeling is a process for building more complete and flexible databases by emphasizing fundamental relationships over existing or...

New Access Points to ERIC--CD-ROM Versions. ERIC Digest.

ERIC Educational Resources Information Center

McLaughlin, Pamela W.

This digest reviews three CD-ROM (compact disc-read only memory) versions of the ERIC (Educational Resources Information Center) database currently being delivered or tested and provides information for comparison. However, no attempt is made to recommend any one product. The advantages and disadvantages of the acquisition of CD-ROM databases are…

An Index to PGE-Ni-Cr Deposits and Occurrences in Selected Mineral-Occurrence Databases

USGS Publications Warehouse

Causey, J. Douglas; Galloway, John P.; Zientek, Michael L.

2009-01-01

Databases of mineral deposits and occurrences are essential to conducting assessments of undiscovered mineral resources. In the USGS's (U.S. Geological Survey) global assessment of undiscovered resources of copper, potash, and the platinum-group elements (PGE), only a few mineral deposit types will be evaluated. For example, only porphyry-copper and sediment-hosted copper deposits will be considered for the copper assessment. To support the global assessment, the USGS prepared comprehensive compilations of the occurrences of these two deposit types in order to develop grade and tonnage models and delineate permissive areas for undiscovered deposits of those types. This publication identifies previously published databases and database records that describe PGE, nickel, and chromium deposits and occurrences. Nickel and chromium were included in this overview because of the close association of PGE with nickel and chromium mineralization. Users of this database will need to refer to the original databases for detailed information about the deposits and occurrences. This information will be used to develop a current and comprehensive global database of PGE deposits and occurrences.

Towards a Global Service Registry for the World-Wide LHC Computing Grid

NASA Astrophysics Data System (ADS)

Field, Laurence; Alandes Pradillo, Maria; Di Girolamo, Alessandro

2014-06-01

The World-Wide LHC Computing Grid encompasses a set of heterogeneous information systems; from central portals such as the Open Science Grid's Information Management System and the Grid Operations Centre Database, to the WLCG information system, where the information sources are the Grid services themselves. Providing a consistent view of the information, which involves synchronising all these informations systems, is a challenging activity that has lead the LHC virtual organisations to create their own configuration databases. This experience, whereby each virtual organisation's configuration database interfaces with multiple information systems, has resulted in the duplication of effort, especially relating to the use of manual checks for the handling of inconsistencies. The Global Service Registry aims to address this issue by providing a centralised service that aggregates information from multiple information systems. It shows both information on registered resources (i.e. what should be there) and available resources (i.e. what is there). The main purpose is to simplify the synchronisation of the virtual organisation's own configuration databases, which are used for job submission and data management, through the provision of a single interface for obtaining all the information. By centralising the information, automated consistency and validation checks can be performed to improve the overall quality of information provided. Although internally the GLUE 2.0 information model is used for the purpose of integration, the Global Service Registry in not dependent on any particular information model for ingestion or dissemination. The intention is to allow the virtual organisation's configuration databases to be decoupled from the underlying information systems in a transparent way and hence simplify any possible future migration due to the evolution of those systems. This paper presents the Global Service Registry architecture, its advantages compared to the current situation and how it can support the evolution of information systems.

The Universal Protein Resource (UniProt): an expanding universe of protein information.

PubMed

Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

2006-01-01

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

The Importance of Biological Databases in Biological Discovery.

PubMed

Baxevanis, Andreas D; Bateman, Alex

2015-06-19

Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. Copyright © 2015 John Wiley & Sons, Inc.

Environment Online: The Greening of Databases. Part 2. Scientific and Technical Databases.

ERIC Educational Resources Information Center

Alston, Patricia Gayle

1991-01-01

This second in a series of articles about online sources of environmental information describes scientific and technical databases that are useful for searching environmental data. Topics covered include chemicals and hazardous substances; agriculture; pesticides; water; forestry, oil, and energy resources; air; environmental and occupational…

Explore Arctic Health.

PubMed

Lebow, Mahria

2014-04-01

The Arctic Health web site is a portal to Arctic-specific, health related content. The site provides expertly organized and annotated resources pertinent to northern peoples and places, including health information, research publications and environmental information. This site also features the Arctic Health Publications Database, which indexes an array of Arctic-related resources.

The Implications of Well-Formedness on Web-Based Educational Resources.

ERIC Educational Resources Information Center

Mohler, James L.

Within all institutions, Web developers are beginning to utilize technologies that make sites more than static information resources. Databases such as XML (Extensible Markup Language) and XSL (Extensible Stylesheet Language) are key technologies that promise to extend the Web beyond the "information storehouse" paradigm and provide…

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.

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

PubMed Central

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads

2017-01-01

Abstract Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. Database URL: http://www.midasfieldguide.org PMID:28365734

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors.

PubMed

Gayali, Saurabh; Acharya, Shankar; Lande, Nilesh Vikram; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan

2016-07-29

Transcription factor (TF) databases are major resource for systematic studies of TFs in specific species as well as related family members. Even though there are several publicly available multi-species databases, the information on the amount and diversity of TFs within individual species is fragmented, especially for newly sequenced genomes of non-model species of agricultural significance. We constructed CicerTransDB (Cicer Transcription Factor Database), the first database of its kind, which would provide a centralized putatively complete list of TFs in a food legume, chickpea. CicerTransDB, available at www.cicertransdb.esy.es , is based on chickpea (Cicer arietinum L.) annotation v 1.0. The database is an outcome of genome-wide domain study and manual classification of TF families. This database not only provides information of the gene, but also gene ontology, domain and motif architecture. CicerTransDB v 1.0 comprises information of 1124 genes of chickpea and enables the user to not only search, browse and download sequences but also retrieve sequence features. CicerTransDB also provides several single click interfaces, transconnecting to various other databases to ease further analysis. Several webAPI(s) integrated in the database allow end-users direct access of data. A critical comparison of CicerTransDB with PlantTFDB (Plant Transcription Factor Database) revealed 68 novel TFs in the chickpea genome, hitherto unexplored. Database URL: http://www.cicertransdb.esy.es.

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.

The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

PubMed

Chen, Yi-Bu; Chattopadhyay, Ansuman; Bergen, Phillip; Gadd, Cynthia; Tannery, Nancy

2007-01-01

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc).

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.

PubMed

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. © The Author(s) 2014. Published by Oxford University Press.

A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework.

PubMed

Cachat, Jonathan; Bandrowski, Anita; Grethe, Jeffery S; Gupta, Amarnath; Astakhov, Vadim; Imam, Fahim; Larson, Stephen D; Martone, Maryann E

2012-01-01

The number of available neuroscience resources (databases, tools, materials, and networks) available via the Web continues to expand, particularly in light of newly implemented data sharing policies required by funding agencies and journals. However, the nature of dense, multifaceted neuroscience data and the design of classic search engine systems make efficient, reliable, and relevant discovery of such resources a significant challenge. This challenge is especially pertinent for online databases, whose dynamic content is largely opaque to contemporary search engines. The Neuroscience Information Framework was initiated to address this problem of finding and utilizing neuroscience-relevant resources. Since its first production release in 2008, NIF has been surveying the resource landscape for the neurosciences, identifying relevant resources and working to make them easily discoverable by the neuroscience community. In this chapter, we provide a survey of the resource landscape for neuroscience: what types of resources are available, how many there are, what they contain, and most importantly, ways in which these resources can be utilized by the research community to advance neuroscience research. Copyright © 2012 Elsevier Inc. All rights reserved.

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

Laramore, G.E.; Griffin, B.R.; Spence, A.

The purpose of this work is to establish and maintain a database for patients from the United States who have received BNCT in Japan for malignant gliomas of the brain. This database will serve as a resource for the DOE to aid in decisions relating to BNCT research in the United States, as well as assisting the design and implementation of clinical trials of BNCT for brain cancer patients in this country. The database will also serve as an information resource for patients with brain tumors and their families who are considering this form of therapy.

ERIC: Sphinx or Golden Griffin?

ERIC Educational Resources Information Center

Lopez, Manuel D.

1989-01-01

Evaluates the Educational Resources Information Center (ERIC) database. Summarizes ERIC's history and organization, and discusses criticisms concerning access, currency, and database content. Reviews role of component clearinghouses, indexing practices, thesaurus structure, international coverage, and comparative studies. Finds ERIC a valuable…

77 FR 52748 - 60-Day Proposed Information Collection: Indian Health Service (IHS) Sharing What Works-Best...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... Form (OMB Form No. 0917-0034). Need and Use of Information Collection: The IHS goal is to raise the... Prevention (HP/DP), Nursing, and Dental) have developed a centralized program database of Best/Promising Practices and Local Efforts (BPPPLE) and resources. The purpose of this collection is to develop a database...

Conversion of environmental data to a digital-spatial database, Puget Sound area, Washington

USGS Publications Warehouse

Uhrich, M.A.; McGrath, T.S.

1997-01-01

Data and maps from the Puget Sound Environmental Atlas, compiled for the U.S. Environmental Protection Agency, the Puget Sound Water Quality Authority, and the U.S. Army Corps of Engineers, have been converted into a digital-spatial database using a geographic information system. Environmental data for the Puget Sound area,collected from sources other than the Puget SoundEnvironmental Atlas by different Federal, State, andlocal agencies, also have been converted into thisdigital-spatial database. Background on the geographic-information-system planning process, the design and implementation of the geographic information-system database, and the reasons for conversion to this digital-spatial database are included in this report. The Puget Sound Environmental Atlas data layers include information about seabird nesting areas, eelgrass and kelp habitat, marine mammal and fish areas, and shellfish resources and bed certification. Data layers, from sources other than the Puget Sound Environmental Atlas, include the Puget Sound shoreline, the water-body system, shellfish growing areas, recreational shellfish beaches, sewage-treatment outfalls, upland hydrography,watershed and political boundaries, and geographicnames. The sources of data, descriptions of the datalayers, and the steps and errors of processing associated with conversion to a digital-spatial database used in development of the Puget Sound Geographic Information System also are included in this report. The appendixes contain data dictionaries for each of the resource layers and error values for the conversion of Puget SoundEnvironmental Atlas data.

Integrating In Silico Resources to Map a Signaling Network

PubMed Central

Liu, Hanqing; Beck, Tim N.; Golemis, Erica A.; Serebriiskii, Ilya G.

2013-01-01

The abundance of publicly available life science databases offer a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol to building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

Implementing the EuroFIR Document and Data Repositories as accessible resources of food composition information.

PubMed

Unwin, Ian; Jansen-van der Vliet, Martine; Westenbrink, Susanne; Presser, Karl; Infanger, Esther; Porubska, Janka; Roe, Mark; Finglas, Paul

2016-02-15

The EuroFIR Document and Data Repositories are being developed as accessible collections of source documents, including grey literature, and the food composition data reported in them. These Repositories will contain source information available to food composition database compilers when selecting their nutritional data. The Document Repository was implemented as searchable bibliographic records in the Europe PubMed Central database, which links to the documents online. The Data Repository will contain original data from source documents in the Document Repository. Testing confirmed the FoodCASE food database management system as a suitable tool for the input, documentation and quality assessment of Data Repository information. Data management requirements for the input and documentation of reported analytical results were established, including record identification and method documentation specifications. Document access and data preparation using the Repositories will provide information resources for compilers, eliminating duplicated work and supporting unambiguous referencing of data contributing to their compiled data. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

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

2012-06-01

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

A Resource Center for the Stimulation of Post Secondary Education Innovation via Computer Network.

ERIC Educational Resources Information Center

Savin, William

The goal of the project described here was to improve the quality of postsecondary education by offering institutions of higher learning information on currently funded educational projects through an interactive database, the Educational Resources Directory (ERD), which contains information on new methods, curricula, and educational technology.…

The Next Step in Educational Program Budgets and Information Resource Management: Integrated Data Structures.

ERIC Educational Resources Information Center

Jackowski, Edward M.

1988-01-01

Discusses the role that information resource management (IRM) plays in educational program-oriented budgeting (POB), and presents a theoretical IRM model. Highlights include design considerations for integrated data systems; database management systems (DBMS); and how POB data can be integrated to enhance its value and use within an educational…

Uniform Resource Locators (URLs): Powerful Reference Tools for Librarians and Information Professionals.

ERIC Educational Resources Information Center

Smith, Teresa S.

The Internet is a network of networks which continually accumulates and amasses information, much of which is without organization and evaluation. This study addresses the need for establishing a database of Uniform Resource Locators (URLs), and for collecting, organizing, indexing, and publishing catalogs of URLs. Librarians and information…

The research and development of water resources management information system based on ArcGIS

NASA Astrophysics Data System (ADS)

Cui, Weiqun; Gao, Xiaoli; Li, Yuzhi; Cui, Zhencai

According to that there are large amount of data, complexity of data type and format in the water resources management, we built the water resources calculation model and established the water resources management information system based on the advanced ArcGIS and Visual Studio.NET development platform. The system can integrate the spatial data and attribute data organically, and manage them uniformly. It can analyze spatial data, inquire by map and data bidirectionally, provide various charts and report forms automatically, link multimedia information, manage database etc. . So it can provide spatial and static synthetical information services for study, management and decision of water resources, regional geology and eco-environment etc..

BIRS - Bioterrorism Information Retrieval System.

PubMed

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. The database is freely available at http://www.bioterrorism.biowaves.org.

Insect barcode information system.

PubMed

Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

2014-01-01

Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. http://www.nabg-nbaii.res.in/barcode.

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

PubMed

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

2009-05-04

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

Quality tools and resources to support organisational improvement integral to high-quality primary care: a systematic review of published and grey literature.

PubMed

Janamian, Tina; Upham, Susan J; Crossland, Lisa; Jackson, Claire L

2016-04-18

To conduct a systematic review of the literature to identify existing online primary care quality improvement tools and resources to support organisational improvement related to the seven elements in the Primary Care Practice Improvement Tool (PC-PIT), with the identified tools and resources to progress to a Delphi study for further assessment of relevance and utility. Systematic review of the international published and grey literature. CINAHL, Embase and PubMed databases were searched in March 2014 for articles published between January 2004 and December 2013. GreyNet International and other relevant websites and repositories were also searched in March-April 2014 for documents dated between 1992 and 2012. All citations were imported into a bibliographic database. Published and unpublished tools and resources were included in the review if they were in English, related to primary care quality improvement and addressed any of the seven PC-PIT elements of a high-performing practice. Tools and resources that met the eligibility criteria were then evaluated for their accessibility, relevance, utility and comprehensiveness using a four-criteria appraisal framework. We used a data extraction template to systematically extract information from eligible tools and resources. A content analysis approach was used to explore the tools and resources and collate relevant information: name of the tool or resource, year and country of development, author, name of the organisation that provided access and its URL, accessibility information or problems, overview of each tool or resource and the quality improvement element(s) it addresses. If available, a copy of the tool or resource was downloaded into the bibliographic database, along with supporting evidence (published or unpublished) on its use in primary care. This systematic review identified 53 tools and resources that can potentially be provided as part of a suite of tools and resources to support primary care practices in improving the quality of their practice, to achieve improved health outcomes.

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

AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.

PubMed

Major, Sylvia M; Nishizuka, Satoshi; Morita, Daisaku; Rowland, Rick; Sunshine, Margot; Shankavaram, Uma; Washburn, Frank; Asin, Daniel; Kouros-Mehr, Hosein; Kane, David; Weinstein, John N

2006-04-06

Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different tissues of origin. AbMiner is a relational database that provides extensive information from our own laboratory and other sources on more than 600 available antibodies and the genes that encode the antibodies' antigens. The data will be made freely available at http://discover.nci.nih.gov/abminer.

MIPS: curated databases and comprehensive secondary data resources in 2010.

PubMed

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

MIPS: curated databases and comprehensive secondary data resources in 2010

PubMed Central

Mewes, H. Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F.X.; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de). PMID:21109531

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.

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

PubMed

Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

2015-01-01

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

Information-seeking behavior of basic science researchers: implications for library services.

PubMed

Haines, Laura L; Light, Jeanene; O'Malley, Donna; Delwiche, Frances A

2010-01-01

This study examined the information-seeking behaviors of basic science researchers to inform the development of customized library services. A qualitative study using semi-structured interviews was conducted on a sample of basic science researchers employed at a university medical school. The basic science researchers used a variety of information resources ranging from popular Internet search engines to highly technical databases. They generally relied on basic keyword searching, using the simplest interface of a database or search engine. They were highly collegial, interacting primarily with coworkers in their laboratories and colleagues employed at other institutions. They made little use of traditional library services and instead performed many traditional library functions internally. Although the basic science researchers expressed a positive attitude toward the library, they did not view its resources or services as integral to their work. To maximize their use by researchers, library resources must be accessible via departmental websites. Use of library services may be increased by cultivating relationships with key departmental administrative personnel. Despite their self-sufficiency, subjects expressed a desire for centralized information about ongoing research on campus and shared resources, suggesting a role for the library in creating and managing an institutional repository.

Information-seeking behavior of basic science researchers: implications for library services

PubMed Central

Haines, Laura L.; Light, Jeanene; O'Malley, Donna; Delwiche, Frances A.

2010-01-01

Objectives: This study examined the information-seeking behaviors of basic science researchers to inform the development of customized library services. Methods: A qualitative study using semi-structured interviews was conducted on a sample of basic science researchers employed at a university medical school. Results: The basic science researchers used a variety of information resources ranging from popular Internet search engines to highly technical databases. They generally relied on basic keyword searching, using the simplest interface of a database or search engine. They were highly collegial, interacting primarily with coworkers in their laboratories and colleagues employed at other institutions. They made little use of traditional library services and instead performed many traditional library functions internally. Conclusions: Although the basic science researchers expressed a positive attitude toward the library, they did not view its resources or services as integral to their work. To maximize their use by researchers, library resources must be accessible via departmental websites. Use of library services may be increased by cultivating relationships with key departmental administrative personnel. Despite their self-sufficiency, subjects expressed a desire for centralized information about ongoing research on campus and shared resources, suggesting a role for the library in creating and managing an institutional repository. PMID:20098658

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.

PubMed

Wang, Julia; Al-Ouran, Rami; Hu, Yanhui; Kim, Seon-Young; Wan, Ying-Wooi; Wangler, Michael F; Yamamoto, Shinya; Chao, Hsiao-Tuan; Comjean, Aram; Mohr, Stephanie E; Perrimon, Norbert; Liu, Zhandong; Bellen, Hugo J

2017-06-01

One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

BioSYNTHESIS: access to a knowledge network of health sciences databases.

PubMed

Broering, N C; Hylton, J S; Guttmann, R; Eskridge, D

1991-04-01

Users of the IAIMS Knowledge Network at the Georgetown University Medical Center have access to multiple in-house and external databases from a single point of entry through BioSYNTHESIS. The IAIMS project has developed a rich environment of biomedical information resources that represent a medical decision support system for campus physicians and students. The BioSYNTHESIS system is an information navigator that provides transparent access to a Knowledge Network of over a dozen databases. These multiple health sciences databases consist of bibliographic, informational, diagnostic, and research systems which reside on diverse computers such as DEC VAXs, SUN 490, AT&T 3B2s, Macintoshes, IBM PC/PS2s and the AT&T ISN and SYTEK network systems. Ethernet and TCP/IP protocols are used in the network architecture. BioSYNTHESIS also provides network links to the other campus libraries and to external institutions. As additional knowledge resources and technological advances have become available. BioSYNTHESIS has evolved from a two phase to a three phase program. Major components of the system including recent achievements and future plans are described.

Chemical Informatics and the Drug Discovery Knowledge Pyramid

PubMed Central

Lushington, Gerald H.; Dong, Yinghua; Theertham, Bhargav

2012-01-01

The magnitude of the challenges in preclinical drug discovery is evident in the large amount of capital invested in such efforts in pursuit of a small static number of eventually successful marketable therapeutics. An explosion in the availability of potentially drug-like compounds and chemical biology data on these molecules can provide us with the means to improve the eventual success rates for compounds being considered at the preclinical level, but only if the community is able to access available information in an efficient and meaningful way. Thus, chemical database resources are critical to any serious drug discovery effort. This paper explores the basic principles underlying the development and implementation of chemical databases, and examines key issues of how molecular information may be encoded within these databases so as to enhance the likelihood that users will be able to extract meaningful information from data queries. In addition to a broad survey of conventional data representation and query strategies, key enabling technologies such as new context-sensitive chemical similarity measures and chemical cartridges are examined, with recommendations on how such resources may be integrated into a practical database environment. PMID:23782037

TMDL TRACKING SYSTEM

EPA Science Inventory

Resource Purpose:The TMDL Tracking System database contains information on the waters listed under section 303(d) of the Clean Water Act and to track those listed waters through TMDL development. The purpose of the database is to allow EPA, the States/Territories/Tribes, ...

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.

Conversion of a traditional image archive into an image resource on compact disc.

PubMed Central

Andrew, S M; Benbow, E W

1997-01-01

The conversion of a traditional archive of pathology images was organised on 35 mm slides into a database of images stored on compact disc (CD-ROM), and textual descriptions were added to each image record. Students on a didactic pathology course found this resource useful as an aid to revision, despite relative computer illiteracy, and it is anticipated that students on a new problem based learning course, which incorporates experience with information technology, will benefit even more readily when they use the database as an educational resource. A text and image database on CD-ROM can be updated repeatedly, and the content manipulated to reflect the content and style of the courses it supports. Images PMID:9306931

Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

ERIC Educational Resources Information Center

Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

2016-01-01

Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

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.

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1996

1996-01-01

This annotated list includes media-related resources classified under the following headings: artificial intelligence and robotics, CD-ROM, computer-assisted instruction, databases and online searching, distance education, educational research, educational technology, electronic publishing, information science and technology, instructional design…

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1997

1997-01-01

This annotated list includes media-related resources classified under the following headings: artificial intelligence and robotics, CD-ROM, computer-assisted instruction, databases and online searching, distance education, educational research, educational technology, electronic publishing, information science and technology, instructional design…

Real-time Geographic Information System (GIS) for Monitoring the Area of Potential Water Level Using Rule Based System

NASA Astrophysics Data System (ADS)

Anugrah, Wirdah; Suryono; Suseno, Jatmiko Endro

2018-02-01

Management of water resources based on Geographic Information System can provide substantial benefits to water availability settings. Monitoring the potential water level is needed in the development sector, agriculture, energy and others. In this research is developed water resource information system using real-time Geographic Information System concept for monitoring the potential water level of web based area by applying rule based system method. GIS consists of hardware, software, and database. Based on the web-based GIS architecture, this study uses a set of computer that are connected to the network, run on the Apache web server and PHP programming language using MySQL database. The Ultrasound Wireless Sensor System is used as a water level data input. It also includes time and geographic location information. This GIS maps the five sensor locations. GIS is processed through a rule based system to determine the level of potential water level of the area. Water level monitoring information result can be displayed on thematic maps by overlaying more than one layer, and also generating information in the form of tables from the database, as well as graphs are based on the timing of events and the water level values.

RESIS-II: An Updated Version of the Original Reservoir Sedimentation Survey Information System (RESIS) Database

USGS Publications Warehouse

Ackerman, Katherine V.; Mixon, David M.; Sundquist, Eric T.; Stallard, Robert F.; Schwarz, Gregory E.; Stewart, David W.

2009-01-01

The Reservoir Sedimentation Survey Information System (RESIS) database, originally compiled by the Soil Conservation Service (now the Natural Resources Conservation Service) in collaboration with the Texas Agricultural Experiment Station, is the most comprehensive compilation of data from reservoir sedimentation surveys throughout the conterminous United States (U.S.). The database is a cumulative historical archive that includes data from as early as 1755 and as late as 1993. The 1,823 reservoirs included in the database range in size from farm ponds to the largest U.S. reservoirs (such as Lake Mead). Results from 6,617 bathymetric surveys are available in the database. This Data Series provides an improved version of the original RESIS database, termed RESIS-II, and a report describing RESIS-II. The RESIS-II relational database is stored in Microsoft Access and includes more precise location coordinates for most of the reservoirs than the original database but excludes information on reservoir ownership. RESIS-II is anticipated to be a template for further improvements in the database.

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

PubMed

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

2015-09-01

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

ERIC Annual Report, 1999: Summarizing the Recent Accomplishments of the Educational Resources Information Center.

ERIC Educational Resources Information Center

Smarte, Lynn

This 1999 annual report, summarizing the accomplishments of the Educational Resources Information System (ERIC) system in 1998, begins with a section that highlights progress towards meeting goals, as well as selected statistics. The second section, comprising the bulk of the report, provides an overview of ERIC, including the ERIC database, user…

ERIC Annual Report, 2000: Summarizing the Recent Accomplishments of the Educational Resources Information Center.

ERIC Educational Resources Information Center

Smarte, Lynn

This 2000 annual report, summarizing the accomplishments of the Educational Resources Information Center (ERIC) system in 1999, begins with a section that highlights progress towards meeting goals, as well as selected statistics. The second section, comprising the bulk of the report, provides an overview of ERIC, including the ERIC database, user…

Development of an Ada programming support environment database SEAD (Software Engineering and Ada Database) administration manual

NASA Technical Reports Server (NTRS)

Liaw, Morris; Evesson, Donna

1988-01-01

Software Engineering and Ada Database (SEAD) was developed to provide an information resource to NASA and NASA contractors with respect to Ada-based resources and activities which are available or underway either in NASA or elsewhere in the worldwide Ada community. The sharing of such information will reduce duplication of effort while improving quality in the development of future software systems. SEAD data is organized into five major areas: information regarding education and training resources which are relevant to the life cycle of Ada-based software engineering projects such as those in the Space Station program; research publications relevant to NASA projects such as the Space Station Program and conferences relating to Ada technology; the latest progress reports on Ada projects completed or in progress both within NASA and throughout the free world; Ada compilers and other commercial products that support Ada software development; and reusable Ada components generated both within NASA and from elsewhere in the free world. This classified listing of reusable components shall include descriptions of tools, libraries, and other components of interest to NASA. Sources for the data include technical newletters and periodicals, conference proceedings, the Ada Information Clearinghouse, product vendors, and project sponsors and contractors.

Mashup of Geo and Space Science Data Provided via Relational Databases in the Semantic Web

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, J. S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2014-12-01

The use of RDBMS for the storage and management of geo and space science data and/or metadata is very common. Although the information stored in tables is based on a data model and therefore well organized and structured, a direct mashup with RDF based data stored in triple stores is not possible. One solution of the problem consists in the transformation of the whole content into RDF structures and storage in triple stores. Another interesting way is the use of a specific system/service, such as e.g. D2RQ, for the access to relational database content as virtual, read only RDF graphs. The Semantic Web based -proof of concept- GFZ ISDC uses the triple store Virtuoso for the storage of general context information/metadata to geo and space science satellite and ground station data. There is information about projects, platforms, instruments, persons, product types, etc. available but no detailed metadata about the data granuals itself. Such important information, as e.g. start or end time or the detailed spatial coverage of a single measurement is stored in RDBMS tables of the ISDC catalog system only. In order to provide a seamless access to all available information about the granuals/data products a mashup of the different data resources (triple store and RDBMS) is necessary. This paper describes the use of D2RQ for a Semantic Web/SPARQL based mashup of relational databases used for ISDC data server but also for the access to IUGONET and/or ESPAS and further geo and space science data resources. RDBMS Relational Database Management System RDF Resource Description Framework SPARQL SPARQL Protocol And RDF Query Language D2RQ Accessing Relational Databases as Virtual RDF Graphs GFZ ISDC German Research Centre for Geosciences Information System and Data Center IUGONET Inter-university Upper Atmosphere Global Observation Network (Japanese project) ESPAS Near earth space data infrastructure for e-science (European Union funded project)

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.

Effects of soil water holding capacity on evapotranspiration and irrigation scheduling

USDA-ARS?s Scientific Manuscript database

The USDA Natural Resources Conservation Service (NRCS), through the National Cooperative Soil Survey, developed three soil geographic databases that are appropriate for acquiring soil information at the national, regional, and local scales. These relational databases include the National Soil Geogra...

Development of the acquisition model of online information resources at Faculty of Medicine Library, Khon Kaen University.

PubMed

Thanapaisal, Soodjai; Thanapaisal, Chaiwit

2013-09-01

Faculty of Medicine Library, Khon Kaen University started to acquire online information resources since 2001 with the subscriptions to 2 databases. Nowadays it has 29 items of subscriptions and the expenses on online information resources reach to 17 million baht, more than 70 percent of the information resources budget, serving the academic purposes of the Faculty of Medicine. The problems of online information resources acquisition fall into 4 categories, and lead to 4 aspects conforming the model of the acquisition, comparing or benchmarking with the 4 selected medical school libraries in Bangkok, Chiang Mai, and Songkhla, and discussion with some other Thai and foreign libraries. The acquisition model of online information resources is developed from those problems and proposed for Faculty of Medicine Library, Khon Kaen University as well as for any medical libraries which prefer.

Drill hole data for coal beds in the Powder River Basin, Montana and Wyoming

USGS Publications Warehouse

Haacke, Jon E.; Scott, David C.

2013-01-01

This report by the U.S. Geological Survey (USGS) of the Powder River Basin (PRB) of Montana and Wyoming is part of the U.S. Coal Resources and Reserves Assessment Project. Essential to that project was the creation of a comprehensive drill hole database that was used for coal bed correlation and for coal resource and reserve assessments in the PRB. This drill hole database was assembled using data from the USGS National Coal Resources Data System, several other Federal and State agencies, and selected mining companies. Additionally, USGS personnel manually entered lithologic picks into the database from geophysical logs of coalbed methane, oil, and gas wells. Of the 29,928 drill holes processed, records of 21,393 are in the public domain and are included in this report. The database contains location information, lithology, and coal bed names for each drill hole.

MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors

PubMed Central

Muvva, Charuvaka; Patra, Sanjukta; Venkatesan, Subramanian

2016-01-01

Matrix metalloproteinases (MMPs) are a family of zinc-dependent proteinases involved in the regulation of the extracellular signaling and structural matrix environment of cells and tissues. MMPs are considered as promising targets for the treatment of many diseases. Therefore, creation of database on the inhibitors of MMP would definitely accelerate the research activities in this area due to its implication in above-mentioned diseases and associated limitations in the first and second generation inhibitors. In this communication, we report the development of a new MMpI database which provides resourceful information for all researchers working in this field. It is a web-accessible, unique resource that contains detailed information on the inhibitors of MMP including small molecules, peptides and MMP Drug Leads. The database contains entries of ~3000 inhibitors including ~72 MMP Drug Leads and ~73 peptide based inhibitors. This database provides the detailed molecular and structural details which are necessary for the drug discovery and development. The MMpI database contains physical properties, 2D and 3D structures (mol2 and pdb format files) of inhibitors of MMP. Other data fields are hyperlinked to PubChem, ChEMBL, BindingDB, DrugBank, PDB, MEROPS and PubMed. The database has extensive searching facility with MMpI ID, IUPAC name, chemical structure and with the title of research article. The MMP inhibitors provided in MMpI database are optimized using Python-based Hierarchical Environment for Integrated Xtallography (Phenix) software. MMpI Database is unique and it is the only public database that contains and provides the complete information on the inhibitors of MMP. Database URL: http://clri.res.in/subramanian/databases/mmpi/index.php. PMID:27509041

Information resources at the National Center for Biotechnology Information.

PubMed Central

Woodsmall, R M; Benson, D A

1993-01-01

The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, was established in 1988 to perform basic research in the field of computational molecular biology as well as build and distribute molecular biology databases. The basic research has led to new algorithms and analysis tools for interpreting genomic data and has been instrumental in the discovery of human disease genes for neurofibromatosis and Kallmann syndrome. The principal database responsibility is the National Institutes of Health (NIH) genetic sequence database, GenBank. NCBI, in collaboration with international partners, builds, distributes, and provides online and CD-ROM access to over 112,000 DNA sequences. Another major program is the integration of multiple sequences databases and related bibliographic information and the development of network-based retrieval systems for Internet access. PMID:8374583

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

dbCPG: A web resource for cancer predisposition genes.

PubMed

Wei, Ran; Yao, Yao; Yang, Wu; Zheng, Chun-Hou; Zhao, Min; Xia, Junfeng

2016-06-21

Cancer predisposition genes (CPGs) are genes in which inherited mutations confer highly or moderately increased risks of developing cancer. Identification of these genes and understanding the biological mechanisms that underlie them is crucial for the prevention, early diagnosis, and optimized management of cancer. Over the past decades, great efforts have been made to identify CPGs through multiple strategies. However, information on these CPGs and their molecular functions is scattered. To address this issue and provide a comprehensive resource for researchers, we developed the Cancer Predisposition Gene Database (dbCPG, Database URL: http://bioinfo.ahu.edu.cn:8080/dbCPG/index.jsp), the first literature-based gene resource for exploring human CPGs. It contains 827 human (724 protein-coding, 23 non-coding, and 80 unknown type genes), 637 rats, and 658 mouse CPGs. Furthermore, data mining was performed to gain insights into the understanding of the CPGs data, including functional annotation, gene prioritization, network analysis of prioritized genes and overlap analysis across multiple cancer types. A user-friendly web interface with multiple browse, search, and upload functions was also developed to facilitate access to the latest information on CPGs. Taken together, the dbCPG database provides a comprehensive data resource for further studies of cancer predisposition genes.

Using a spatial and tabular database to generate statistics from terrain and spectral data for soil surveys

USGS Publications Warehouse

Horvath , E.A.; Fosnight, E.A.; Klingebiel, A.A.; Moore, D.G.; Stone, J.E.; Reybold, W.U.; Petersen, G.W.

1987-01-01

A methodology has been developed to create a spatial database by referencing digital elevation, Landsat multispectral scanner data, and digitized soil premap delineations of a number of adjacent 7.5-min quadrangle areas to a 30-m Universal Transverse Mercator projection. Slope and aspect transformations are calculated from elevation data and grouped according to field office specifications. An unsupervised classification is performed on a brightness and greenness transformation of the spectral data. The resulting spectral, slope, and aspect maps of each of the 7.5-min quadrangle areas are then plotted and submitted to the field office to be incorporated into the soil premapping stages of a soil survey. A tabular database is created from spatial data by generating descriptive statistics for each data layer within each soil premap delineation. The tabular data base is then entered into a data base management system to be accessed by the field office personnel during the soil survey and to be used for subsequent resource management decisions.Large amounts of data are collected and archived during resource inventories for public land management. Often these data are stored as stacks of maps or folders in a file system in someone's office, with the maps in a variety of formats, scales, and with various standards of accuracy depending on their purpose. This system of information storage and retrieval is cumbersome at best when several categories of information are needed simultaneously for analysis or as input to resource management models. Computers now provide the resource scientist with the opportunity to design increasingly complex models that require even more categories of resource-related information, thus compounding the problem.Recently there has been much emphasis on the use of geographic information systems (GIS) as an alternative method for map data archives and as a resource management tool. Considerable effort has been devoted to the generation of tabular databases, such as the U.S. Department of Agriculture's SCS/S015 (Soil Survey Staff, 1983), to archive the large amounts of information that are collected in conjunction with mapping of natural resources in an easily retrievable manner.During the past 4 years the U.S. Geological Survey's EROS Data Center, in a cooperative effort with the Bureau of Land Management (BLM) and the Soil Conservation Service (SCS), developed a procedure that uses spatial and tabular databases to generate elevation, slope, aspect, and spectral map products that can be used during soil premapping. The procedure results in tabular data, residing in a database management system, that are indexed to the final soil delineations and help quantify soil map unit composition.The procedure was developed and tested on soil surveys on over 600 000 ha in Wyoming, Nevada, and Idaho. A transfer of technology from the EROS Data Center to the BLM will enable the Denver BLM Service Center to use this procedure in soil survey operations on BLM lands. Also underway is a cooperative effort between the EROS Data Center and SCS to define and evaluate maps that can be produced as derivatives of digital elevation data for 7.5-min quadrangle areas, such as those used during the premapping stage of the soil surveys mentioned above, the idea being to make such products routinely available.The procedure emphasizes the applications of digital elevation and spectral data to order-three soil surveys on rangelands, and will:Incorporate digital terrain and spectral data into a spatial database for soil surveys.Provide hardcopy products (that can be generated from digital elevation model and spectral data) that are useful during the soil pre-mapping process.Incorporate soil premaps into a spatial database that can be accessed during the soil survey process along with terrain and spectral data.Summarize useful quantitative information for soil mapping and for making interpretations for resource management.

Uniform standards for genome databases in forest and fruit trees

USDA-ARS?s Scientific Manuscript database

TreeGenes and tfGDR serve the international forestry and fruit tree genomics research communities, respectively. These databases hold similar sequence data and provide resources for the submission and recovery of this information in order to enable comparative genomics research. Large-scale genotype...

Pharmacoepidemiology resources in Ireland-an introduction to pharmacy claims data.

PubMed

Sinnott, Sarah-Jo; Bennett, Kathleen; Cahir, Caitriona

2017-11-01

Administrative health data, such as pharmacy claims data, present a valuable resource for conducting pharmacoepidemiological and health services research. Often, data are available for whole populations allowing population level analyses. Moreover, their routine collection ensures that the data reflect health care utilisation in the real-world setting compared to data collected in clinical trials. The Irish Health Service Executive-Primary Care Reimbursement Service (HSE-PCRS) community pharmacy claims database is described. The availability of demographic variables and drug-related information is discussed. The strengths and limitations associated using this database for conducting research are presented, in particular, internal and external validity. Examples of recently conducted research using the HSE-PCRS pharmacy claims database are used to illustrate the breadth of its use. The HSE-PCRS national pharmacy claims database is a large, high-quality, valid and accurate data source for measuring drug exposure in specific populations in Ireland. The main limitation is the lack of generalisability for those aged <70 years and the lack of information on indication or outcome.

GlycoRDF: an ontology to standardize glycomics data in RDF.

PubMed

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-03-15

Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Annotated checklist and database for vascular plants of the Jemez Mountains

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

Foxx, T. S.; Pierce, L.; Tierney, G. D.

Studies done in the last 40 years have provided information to construct a checklist of the Jemez Mountains. The present database and checklist builds on the basic list compiled by Teralene Foxx and Gail Tierney in the early 1980s. The checklist is annotated with taxonomic information, geographic and biological information, economic uses, wildlife cover, revegetation potential, and ethnographic uses. There are nearly 1000 species that have been noted for the Jemez Mountains. This list is cross-referenced with the US Department of Agriculture Natural Resource Conservation Service PLANTS database species names and acronyms. All information will soon be available on amore » Web Page.« less

Marketing ITS infrastructure in the public interest

DOT National Transportation Integrated Search

2000-10-01

This guide, Volume 4 - Bibliographic and Non-bibliographic databases, is part of the International Guide to Highway Transportation Information - a multi-volume set of guides that provides highway transportation information resources for domestic and ...

National Center for Biotechnology Information Celebrates 25th Anniversary | NIH MedlinePlus the Magazine

MedlinePlus

... is a national and international resource for molecular biology information. It creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and ...

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

A Bibliography of Publications about the Educational Resources Information Center (Covering the Period 1985-1988).

ERIC Educational Resources Information Center

Brandhorst, Ted, Ed.

The result of a comprehensive search for writings about the Educational Resources Information Center (ERIC) published between 1985 and 1988, this annotated bibliography lists 107 documents and journal articles about ERIC that were entered in the ERIC database during that period. The 1964-1978 edition cited 269 items. The 1979-1984 edition cited…

MIPS PlantsDB: a database framework for comparative plant genome research.

PubMed

Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

MIPS PlantsDB: a database framework for comparative plant genome research

PubMed Central

Nussbaumer, Thomas; Martis, Mihaela M.; Roessner, Stephan K.; Pfeifer, Matthias; Bader, Kai C.; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB. PMID:23203886

USGS national surveys and analysis projects: Preliminary compilation of integrated geological datasets for the United States

USGS Publications Warehouse

Nicholson, Suzanne W.; Stoeser, Douglas B.; Wilson, Frederic H.; Dicken, Connie L.; Ludington, Steve

2007-01-01

The growth in the use of Geographic nformation Systems (GS) has highlighted the need for regional and national digital geologic maps attributed with age and rock type information. Such spatial data can be conveniently used to generate derivative maps for purposes that include mineral-resource assessment, metallogenic studies, tectonic studies, human health and environmental research. n 1997, the United States Geological Survey’s Mineral Resources Program initiated an effort to develop national digital databases for use in mineral resource and environmental assessments. One primary activity of this effort was to compile a national digital geologic map database, utilizing state geologic maps, to support mineral resource studies in the range of 1:250,000- to 1:1,000,000-scale. Over the course of the past decade, state databases were prepared using a common standard for the database structure, fields, attributes, and data dictionaries. As of late 2006, standardized geological map databases for all conterminous (CONUS) states have been available on-line as USGS Open-File Reports. For Alaska and Hawaii, new state maps are being prepared, and the preliminary work for Alaska is being released as a series of 1:500,000-scale regional compilations. See below for a list of all published databases.

MIPS: analysis and annotation of proteins from whole genomes in 2005

PubMed Central

Mewes, H. W.; Frishman, D.; Mayer, K. F. X.; Münsterkötter, M.; Noubibou, O.; Pagel, P.; Rattei, T.; Oesterheld, M.; Ruepp, A.; Stümpflen, V.

2006-01-01

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (). PMID:16381839

MIPS: analysis and annotation of proteins from whole genomes in 2005.

PubMed

Mewes, H W; Frishman, D; Mayer, K F X; Münsterkötter, M; Noubibou, O; Pagel, P; Rattei, T; Oesterheld, M; Ruepp, A; Stümpflen, V

2006-01-01

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein-protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.gsf.de).

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

PubMed

Yokochi, Masashi; Kobayashi, Naohiro; Ulrich, Eldon L; Kinjo, Akira R; Iwata, Takeshi; Ioannidis, Yannis E; Livny, Miron; Markley, John L; Nakamura, Haruki; Kojima, Chojiro; Fujiwara, Toshimichi

2016-05-05

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

A comprehensive view of the web-resources related to sericulture

PubMed Central

Singh, Deepika; Chetia, Hasnahana; Kabiraj, Debajyoti; Sharma, Swagata; Kumar, Anil; Sharma, Pragya; Deka, Manab; Bora, Utpal

2016-01-01

Recent progress in the field of sequencing and analysis has led to a tremendous spike in data and the development of data science tools. One of the outcomes of this scientific progress is development of numerous databases which are gaining popularity in all disciplines of biology including sericulture. As economically important organism, silkworms are studied extensively for their numerous applications in the field of textiles, biomaterials, biomimetics, etc. Similarly, host plants, pests, pathogens, etc. are also being probed to understand the seri-resources more efficiently. These studies have led to the generation of numerous seri-related databases which are extremely helpful for the scientific community. In this article, we have reviewed all the available online resources on silkworm and its related organisms, including databases as well as informative websites. We have studied their basic features and impact on research through citation count analysis, finally discussing the role of emerging sequencing and analysis technologies in the field of seri-data science. As an outcome of this review, a web portal named SeriPort, has been created which will act as an index for the various sericulture-related databases and web resources available in cyberspace. Database URL: http://www.seriport.in/ PMID:27307138

BIRS – Bioterrorism Information Retrieval System

PubMed Central

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. Availability The database is freely available at http://www.bioterrorism.biowaves.org PMID:23390356

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/

The Human Ageing Genomic Resources: online databases and tools for biogerontologists

PubMed Central

de Magalhães, João Pedro; Budovsky, Arie; Lehmann, Gilad; Costa, Joana; Li, Yang; Fraifeld, Vadim; Church, George M.

2009-01-01

Summary Ageing is a complex, challenging phenomenon that will require multiple, interdisciplinary approaches to unravel its puzzles. To assist basic research on ageing, we developed the Human Ageing Genomic Resources (HAGR). This work provides an overview of the databases and tools in HAGR and describes how the gerontology research community can employ them. Several recent changes and improvements to HAGR are also presented. The two centrepieces in HAGR are GenAge and AnAge. GenAge is a gene database featuring genes associated with ageing and longevity in model organisms, a curated database of genes potentially associated with human ageing, and a list of genes tested for their association with human longevity. A myriad of biological data and information is included for hundreds of genes, making GenAge a reference for research that reflects our current understanding of the genetic basis of ageing. GenAge can also serve as a platform for the systems biology of ageing, and tools for the visualization of protein-protein interactions are also included. AnAge is a database of ageing in animals, featuring over 4,000 species, primarily assembled as a resource for comparative and evolutionary studies of ageing. Longevity records, developmental and reproductive traits, taxonomic information, basic metabolic characteristics, and key observations related to ageing are included in AnAge. Software is also available to aid researchers in the form of Perl modules to automate numerous tasks and as an SPSS script to analyse demographic mortality data. The Human Ageing Genomic Resources are available online at http://genomics.senescence.info. PMID:18986374

The Cancer Epidemiology Descriptive Cohort Database: A Tool to Support Population-Based Interdisciplinary Research

PubMed Central

Kennedy, Amy E.; Khoury, Muin J.; Ioannidis, John P.A.; Brotzman, Michelle; Miller, Amy; Lane, Crystal; Lai, Gabriel Y.; Rogers, Scott D.; Harvey, Chinonye; Elena, Joanne W.; Seminara, Daniela

2017-01-01

Background We report on the establishment of a web-based Cancer Epidemiology Descriptive Cohort Database (CEDCD). The CEDCD’s goals are to enhance awareness of resources, facilitate interdisciplinary research collaborations, and support existing cohorts for the study of cancer-related outcomes. Methods Comprehensive descriptive data were collected from large cohorts established to study cancer as primary outcome using a newly developed questionnaire. These included an inventory of baseline and follow-up data, biospecimens, genomics, policies, and protocols. Additional descriptive data extracted from publicly available sources were also collected. This information was entered in a searchable and publicly accessible database. We summarized the descriptive data across cohorts and reported the characteristics of this resource. Results As of December 2015, the CEDCD includes data from 46 cohorts representing more than 6.5 million individuals (29% ethnic/racial minorities). Overall, 78% of the cohorts have collected blood at least once, 57% at multiple time points, and 46% collected tissue samples. Genotyping has been performed by 67% of the cohorts, while 46% have performed whole-genome or exome sequencing in subsets of enrolled individuals. Information on medical conditions other than cancer has been collected in more than 50% of the cohorts. More than 600,000 incident cancer cases and more than 40,000 prevalent cases are reported, with 24 cancer sites represented. Conclusions The CEDCD assembles detailed descriptive information on a large number of cancer cohorts in a searchable database. Impact Information from the CEDCD may assist the interdisciplinary research community by facilitating identification of well-established population resources and large-scale collaborative and integrative research. PMID:27439404

A new database on contaminant exposure and effects in terrestrial vertebrates for natural resource managers

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Garrett, L.J.; Erwin, R.M.; Walz, A.; Ottinger, M.A.; Barrett, H.R.

1997-01-01

The Biomonitoring of Environmental Status and Trends (BEST) program of the Department of the Interior is focused to identify and understand effects of contaminant stressors on biological resources under their stewardship. Despite the desire of many to continuously monitor the environmental health of our estuaries, much can be learned by summarizing existing temporal, geographic, and phylogenetic contaminant information. To this end, retrospective contaminant exposure and effects data for amphibians, reptiles, birds, and mammals residing within 30 km of Atlantic coast estuaries are being assembled through searches of published literature (e.g., Fisheries Review, Wildlife Review, BIOSIS Previews) and databases (e.g., US EPA Ecological Incident Information System; USGS Diagnostic and Epizootic Databases), and compilation of summary data from unpublished reports of government natural resource agencies, private conservation groups, and universities. These contaminant exposure and effect data for terrestrial vertebrates (CEE-TV) are being summarized using Borland dBASE in a 96- field format, including species, collection time and site coordinates, sample matrix, contaminant concentration, biomarker and bioindicator responses, and source of information (N>1500 records). This CEE-TV database has been imported into the ARC/INFO geographic information system (GIS), for purposes of examining geographic coverage and trends, and to identify critical data gaps. A preliminary risk assessment will be conducted to identify and characterize contaminants and other stressors potentially affecting terrestrial vertebrates that reside, migrate through or reproduce in these estuaries. Evaluations are underway, using specific measurement and assessment endpoints, to rank and prioritize estuarine ecosystems in which terrestrial vertebrates are potentially at risk for purposes of prediction and focusing future biomonitoring efforts.

MIPS plant genome information resources.

PubMed

Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

2007-01-01

The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

75 FR 46943 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

...-capturing process. SAMHSA will place Web site registration information into a Knowledge Management database... September 3, 2010 to: SAMHSA Desk Officer, Human Resources and Housing Branch, Office of Management and...

Information literacy in science writing: how students find, identify, and use scientific literature

NASA Astrophysics Data System (ADS)

Klucevsek, Kristin M.; Brungard, Allison B.

2016-11-01

For undergraduate students to achieve science literacy, they must first develop information literacy skils. These skills align with Information Literacy Standards and include determining appropriate databases, distinguishing among resource types, and citing resources ethically. To effectively improve information literacy and science literacy, we must identify how students interact with authentic scientific texts. In this case study, we addressed this aim by embedding a science librarian into a science writing course, where students wrote a literature review on a research topic of their choice. Library instruction was further integrated through the use of an online guide and outside assistance. To evaluate the evolution of information literacy in our students and provide evidence of student practices, we used task-scaffolded writing assessments, a reflection, and surveys. We found that students improved their ability and confidence in finding research articles using discipline-specific databases as well as their ability to distinguish primary from secondary research articles. We also identified ways students improperly used and cited resources in their writing assignments. While our results reveal a better understanding of how students find and approach scientific research articles, additional research is needed to develop effective strategies to improve long-term information literacy in the sciences.

The Advent of Portals.

ERIC Educational Resources Information Center

Jackson, Mary E.

2002-01-01

Explains portals as tools that gather a variety of electronic information resources, including local library resources, into a single Web page. Highlights include cross-database searching; integration with university portals and course management software; the ARL (Association of Research Libraries) Scholars Portal Initiative; and selected vendors…

The Tropical Biominer Project: mining old sources for new drugs.

PubMed

Artiguenave, François; Lins, André; Maciel, Wesley Dias; Junior, Antonio Celso Caldeira; Nacif-Coelho, Carla; de Souza Linhares, Maria Margarida Ribeiro; de Oliveira, Guilherme Correa; Barbosa, Luis Humberto Rezende; Lopes, Júlio César Dias; Junior, Claudionor Nunes Coelho

2005-01-01

The Tropical Biominer Project is a recent initiative from the Federal University of Minas Gerais (UFMG) and the Oswaldo Cruz foundation, with the participation of the Biominas Foundation (Belo Horizonte, Minas Gerais, Brazil) and the start-up Homologix. The main objective of the project is to build a new resource for the chemogenomics research, on chemical compounds, with a strong emphasis on natural molecules. Adopted technologies include the search of information from structured, semi-structured, and non-structured documents (the last two from the web) and datamining tools in order to gather information from different sources. The database is the support for developing applications to find new potential treatments for parasitic infections by using virtual screening tools. We present here the midpoint of the project: the conception and implementation of the Tropical Biominer Database. This is a Federated Database designed to store data from different resources. Connected to the database, a web crawler is able to gather information from distinct, patented web sites and store them after automatic classification using datamining tools. Finally, we demonstrate the interest of the approach, by formulating new hypotheses on specific targets of a natural compound, violacein, using inferences from a Virtual Screening procedure.

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

PubMed

Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

2016-07-04

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

[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.

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

Identifying and Synchronizing Health Information Technology (HIT) Events from FDA Medical Device Reports.

PubMed

Kang, Hong; Wang, Frank; Zhou, Sicheng; Miao, Qi; Gong, Yang

2017-01-01

Health information technology (HIT) events, a subtype of patient safety events, pose a major threat and barrier toward a safer healthcare system. It is crucial to gain a better understanding of the nature of the errors and adverse events caused by current HIT systems. The scarcity of HIT event-exclusive databases and event reporting systems indicates the challenge of identifying the HIT events from existing resources. FDA Manufacturer and User Facility Device Experience (MAUDE) database is a potential resource for HIT events. However, the low proportion and the rapid evolvement of HIT-related events present challenges for distinguishing them from other equipment failures and hazards. We proposed a strategy to identify and synchronize HIT events from MAUDE by using a filter based on structured features and classifiers based on unstructured features. The strategy will help us develop and grow an HIT event-exclusive database, keeping pace with updates to MAUDE toward shared learning.

VitisExpDB: a database resource for grape functional genomics.

PubMed

Doddapaneni, Harshavardhan; Lin, Hong; Walker, M Andrew; Yao, Jiqiang; Civerolo, Edwin L

2008-02-28

The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic information on different Vitis species and cultivars, including the European grape vine, Vitis vinifera. Our goal is to develop a comprehensive web data source for Vitaceae. VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for V. vinifera and non-vinifera grape species and varieties. Currently, the database stores approximately 320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of approximately 20,000 non-redundant set of ESTs. Finally, the database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online bioinformatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database. The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website http://cropdisease.ars.usda.gov/vitis_at/main-page.htm.

VitisExpDB: A database resource for grape functional genomics

PubMed Central

Doddapaneni, Harshavardhan; Lin, Hong; Walker, M Andrew; Yao, Jiqiang; Civerolo, Edwin L

2008-01-01

Background The family Vitaceae consists of many different grape species that grow in a range of climatic conditions. In the past few years, several studies have generated functional genomic information on different Vitis species and cultivars, including the European grape vine, Vitis vinifera. Our goal is to develop a comprehensive web data source for Vitaceae. Description VitisExpDB is an online MySQL-PHP driven relational database that houses annotated EST and gene expression data for V. vinifera and non-vinifera grape species and varieties. Currently, the database stores ~320,000 EST sequences derived from 8 species/hybrids, their annotation (BLAST top match) details and Gene Ontology based structured vocabulary. Putative homologs for each EST in other species and varieties along with information on their percent nucleotide identities, phylogenetic relationship and common primers can be retrieved. The database also includes information on probe sequence and annotation features of the high density 60-mer gene expression chip consisting of ~20,000 non-redundant set of ESTs. Finally, the database includes 14 processed global microarray expression profile sets. Data from 12 of these expression profile sets have been mapped onto metabolic pathways. A user-friendly web interface with multiple search indices and extensively hyperlinked result features that permit efficient data retrieval has been developed. Several online bioinformatics tools that interact with the database along with other sequence analysis tools have been added. In addition, users can submit their ESTs to the database. Conclusion The developed database provides genomic resource to grape community for functional analysis of genes in the collection and for the grape genome annotation and gene function identification. The VitisExpDB database is available through our website . PMID:18307813

PIECE 2.0: an update for the plant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparision and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in ...

Cyber-Community for Housing, Consumer Economics Created

ERIC Educational Resources Information Center

Manley, Kelly Shannon; Sweaney, Anne L.

2007-01-01

This article discusses a curriculum resource database project for housing and consumer economics educators. This database, along with message boards, an event calendar, and discipline-related articles, is available at www.GetYourFACtS.com (Sweaney, Manley, Valente, & Black, 2002). Given the overwhelming volume of information available on the…

EROS Main Image File: A Picture Perfect Database for Landsat Imagery and Aerial Photography.

ERIC Educational Resources Information Center

Jack, Robert F.

1984-01-01

Describes Earth Resources Observation System online database, which provides access to computerized images of Earth obtained via satellite. Highlights include retrieval system and commands, types of images, search strategies, other online functions, and interpretation of accessions. Satellite information, sources and samples of accessions, and…

Toxicities of oils, dispersants and dispersed oils to algae and aquatic plants: review and database value to resource sustainability

EPA Science Inventory

Published toxicity results are reviewed for oils, dispersants and dispersed oils and aquatic plants. The historical phytotoxicity database consists largely of results from a patchwork of research conducted after oil spills to marine waters. Toxicity information is available for ...

Database Marketplace 2010: Feast and Famine

ERIC Educational Resources Information Center

Tenopir, Carol; Baker, Gayle; Grogg, Jill

2010-01-01

With fancy new software developments and growth in both the richness of content and delivery options for information resources, the Database Marketplace 2010 is a feast for buyers. Unfortunately, institutional budget cuts may force more of a famine mentality--with belt-tightening for most, and only purchases that are life-sustaining being served…

FEMA Database Requirements Assessment and Resource Directory Model.

DTIC Science & Technology

1982-05-01

File (NRCM) -- WContains information on organizations that are information resources on virtually any subject. * NEW YORK TIMES ONLINE -- Full text...version of the New York Times. * Newsearch: The Daily Index (Newsearch) -- Daily indexing of the periodicals in Magazine Index, newspapers in National...a NEXIS -- Full text of all general and business news covered in a variety of news - papers, magazines and wire services. 0 Oceanic Abstracts

Proceedings of the Annual Military Librarians Workshop (33rd) Held in San Antonio, Texas on 18-20 October 1989

DTIC Science & Technology

1992-12-01

Revolution," ONLINE (1989 July):75. 6. Ibid., 76. 7. Ibid., 77. 17 HYPERMEDIA: INTERFACING IN THE INFORMATION AGE J . Wesley Regian Air Force Human...Resources Laboratory (AFSC) Brooks Air Force Base, Texas 19 HYPERMEDIA: INTERFACING IN THE INFORMATION AGE J . Wesley Regian Air Force Human Resources...AUTOMATION SYSTEM DISTRIBUTED INFORMATION ACCESS: RETRIEVAL DATABASE INTERFACE MANAGEMENT James J . Young, President Ann R Tinker Sirsi Corporation Huntsville

Quantum Search in Hilbert Space

NASA Technical Reports Server (NTRS)

Zak, Michail

2003-01-01

A proposed quantum-computing algorithm would perform a search for an item of information in a database stored in a Hilbert-space memory structure. The algorithm is intended to make it possible to search relatively quickly through a large database under conditions in which available computing resources would otherwise be considered inadequate to perform such a task. The algorithm would apply, more specifically, to a relational database in which information would be stored in a set of N complex orthonormal vectors, each of N dimensions (where N can be exponentially large). Each vector would constitute one row of a unitary matrix, from which one would derive the Hamiltonian operator (and hence the evolutionary operator) of a quantum system. In other words, all the stored information would be mapped onto a unitary operator acting on a quantum state that would represent the item of information to be retrieved. Then one could exploit quantum parallelism: one could pose all search queries simultaneously by performing a quantum measurement on the system. In so doing, one would effectively solve the search problem in one computational step. One could exploit the direct- and inner-product decomposability of the unitary matrix to make the dimensionality of the memory space exponentially large by use of only linear resources. However, inasmuch as the necessary preprocessing (the mapping of the stored information into a Hilbert space) could be exponentially expensive, the proposed algorithm would likely be most beneficial in applications in which the resources available for preprocessing were much greater than those available for searching.

Technology for Independent Living: Sourcebook.

ERIC Educational Resources Information Center

Enders, Alexandra, Ed.

This sourcebook provides information for the practical implementation of independent living technology in the everyday rehabilitation process. "Information Services and Resources" lists databases, clearinghouses, networks, research and development programs, toll-free telephone numbers, consumer protection caveats, selected publications, and…

Marine and Hydrokinetic (MHK) Databases and Systems

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

None

2015-01-01

The online information resources included in this fact sheet were developed with support from the U.S. Department of Energy, and are designed to provide the public access to information pertaining to MHK technologies, projects, and research.

Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources

USDA-ARS?s Scientific Manuscript database

Fully annotated genome sequences of many microorganisms are publicly available as a resource. However, in-depth analysis of these genomes using specialized tools is required to derive meaningful information. We describe here the utility of three powerful publicly available genome databases and ana...

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

Resources for Functional Genomics Studies in Drosophila melanogaster

PubMed Central

Mohr, Stephanie E.; Hu, Yanhui; Kim, Kevin; Housden, Benjamin E.; Perrimon, Norbert

2014-01-01

Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, “meta” information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally. PMID:24653003

Technologies and standards in the information systems of the soil-geographic database of Russia

NASA Astrophysics Data System (ADS)

Golozubov, O. M.; Rozhkov, V. A.; Alyabina, I. O.; Ivanov, A. V.; Kolesnikova, V. M.; Shoba, S. A.

2015-01-01

The achievements, problems, and challenges of the modern stage of the development of the Soil-Geographic Database of Russia (SGDBR) and the history of this project are outlined. The structure of the information system of the SGDBR as an internet-based resource to collect data on soil profiles and to integrate the geographic and attribute databases on the same platform is described. The pilot project in Rostov oblast illustrates the inclusion of regional information in the SGDBR and its application for solving practical problems. For the first time in Russia, the GeoRSS standard based on the structured hypertext representation of the geographic and attribute information has been applied in the state system for the agromonitoring of agricultural lands in Rostov oblast and information exchange through the internet.

Presence and Accuracy of Drug Dosage Recommendations for Continuous Renal Replacement Therapy in Tertiary Drug Information References

PubMed Central

Gorman, Sean K; Slavik, Richard S; Lam, Stefanie

2012-01-01

Background: Clinicians commonly rely on tertiary drug information references to guide drug dosages for patients who are receiving continuous renal replacement therapy (CRRT). It is unknown whether the dosage recommendations in these frequently used references reflect the most current evidence. Objective: To determine the presence and accuracy of drug dosage recommendations for patients undergoing CRRT in 4 drug information references. Methods: Medications commonly prescribed during CRRT were identified from an institutional medication inventory database, and evidence-based dosage recommendations for this setting were developed from the primary and secondary literature. The American Hospital Formulary System—Drug Information (AHFS–DI), Micromedex 2.0 (specifically the DRUGDEX and Martindale databases), and the 5th edition of Drug Prescribing in Renal Failure (DPRF5) were assessed for the presence of drug dosage recommendations in the CRRT setting. The dosage recommendations in these tertiary references were compared with the recommendations derived from the primary and secondary literature to determine concordance. Results: Evidence-based drug dosage recommendations were developed for 33 medications administered in patients undergoing CRRT. The AHFS–DI provided no dosage recommendations specific to CRRT, whereas the DPRF5 provided recommendations for 27 (82%) of the medications and the Micromedex 2.0 application for 20 (61%) (13 [39%] in the DRUGDEX database and 16 [48%] in the Martindale database, with 9 medications covered by both). The dosage recommendations were in concordance with evidence-based recommendations for 12 (92%) of the 13 medications in the DRUGDEX database, 26 (96%) of the 27 in the DPRF5, and all 16 (100%) of those in the Martindale database. Conclusions: One prominent tertiary drug information resource provided no drug dosage recommendations for patients undergoing CRRT. However, 2 of the databases in an Internet-based medical information application and the latest edition of a renal specialty drug information resource provided recommendations for a majority of the medications investigated. Most dosage recommendations were similar to those derived from the primary and secondary literature. The most recent edition of the DPRF is the preferred source of information when prescribing dosage regimens for patients receiving CRRT. PMID:22783029

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups.

PubMed

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca; Nierychlo, Marta; Kristensen, Jannie Munk; Karst, Søren Michael; Albertsen, Mads; Nielsen, Per Halkjær

2017-01-01

Wastewater is increasingly viewed as a resource, with anaerobic digester technology being routinely implemented for biogas production. Characterising the microbial communities involved in wastewater treatment facilities and their anaerobic digesters is considered key to their optimal design and operation. Amplicon sequencing of the 16S rRNA gene allows high-throughput monitoring of these systems. The MiDAS field guide is a public resource providing amplicon sequencing protocols and an ecosystem-specific taxonomic database optimized for use with wastewater treatment facility samples. The curated taxonomy endeavours to provide a genus-level-classification for abundant phylotypes and the online field guide links this identity to published information regarding their ecology, function and distribution. This article describes the expansion of the database resources to cover the organisms of the anaerobic digester systems fed primary sludge and surplus activated sludge. The updated database includes descriptions of the abundant genus-level-taxa in influent wastewater, activated sludge and anaerobic digesters. Abundance information is also included to allow assessment of the role of emigration in the ecology of each phylotype. MiDAS is intended as a collaborative resource for the progression of research into the ecology of wastewater treatment, by providing a public repository for knowledge that is accessible to all interested in these biotechnologically important systems. http://www.midasfieldguide.org. © The Author(s) 2017. Published by Oxford University Press.

EVITHERM: The Virtual Institute of Thermal Metrology

NASA Astrophysics Data System (ADS)

Redgrove, J.; Filtz, J.-R.; Fischer, J.; Le Parlouër, P.; Mathot, V.; Nesvadba, P.; Pavese, F.

2007-12-01

Evitherm is a web-based thermal resource centre, resulting from a 3-year project partly funded by the EU’s GROWTH programme (2002 05). Evitherm links together the widely distributed centres of excellence (NMIs, research and teaching institutes, consultants, etc.) and others concerned with thermal measurements and technology to provide a focal point for information exchange and knowledge transfer between all these organizations and industry. To facilitate the quick and easy flow of thermal knowledge to users of thermal technologies, evitherm has a website (www.evitherm.org) through which it disseminates information and by which it also provides access to resources such as training, property data, measurements and experts. Among the resources available from the website are (1) thermal property data—offering access to some of the world’s leading databases; (2) expertise— evitherm has a database of consultants, an Advice line, a public Forum and a unique Consultancy Brokering Service whereby users are linked to the expert they need to solve their thermal industrial problems; (3) industry resources—thermal information for particular industry sectors; (4) services—information directories on thermal property measurement, training, equipment supply, reference materials, etc.; (5) literature—links to books, papers, standards, etc.; (6) events—conferences, meetings, seminars, organizations and networks, what’s happening. A user only has to register (for free) to gain access to all the information on the evitherm website. Much of the thermal property data can be accessed for free and in a few cases we have negotiated affordable rates for access to some leading databases, such as CINDAS, THERSYST and NELFOOD. This article illustrates the aims and structure of the evitherm Society, how it is directed, and how it serves the thermal community worldwide in its need for quick and easy access to the resources needed to help ensure a well resourced industrial work force and clean and efficient thermal processes.

dbCPG: A web resource for cancer predisposition genes

PubMed Central

Wei, Ran; Yao, Yao; Yang, Wu; Zheng, Chun-Hou; Zhao, Min; Xia, Junfeng

2016-01-01

Cancer predisposition genes (CPGs) are genes in which inherited mutations confer highly or moderately increased risks of developing cancer. Identification of these genes and understanding the biological mechanisms that underlie them is crucial for the prevention, early diagnosis, and optimized management of cancer. Over the past decades, great efforts have been made to identify CPGs through multiple strategies. However, information on these CPGs and their molecular functions is scattered. To address this issue and provide a comprehensive resource for researchers, we developed the Cancer Predisposition Gene Database (dbCPG, Database URL: http://bioinfo.ahu.edu.cn:8080/dbCPG/index.jsp), the first literature-based gene resource for exploring human CPGs. It contains 827 human (724 protein-coding, 23 non-coding, and 80 unknown type genes), 637 rats, and 658 mouse CPGs. Furthermore, data mining was performed to gain insights into the understanding of the CPGs data, including functional annotation, gene prioritization, network analysis of prioritized genes and overlap analysis across multiple cancer types. A user-friendly web interface with multiple browse, search, and upload functions was also developed to facilitate access to the latest information on CPGs. Taken together, the dbCPG database provides a comprehensive data resource for further studies of cancer predisposition genes. PMID:27192119

GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2009-06-01

We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

ARMOUR - A Rice miRNA: mRNA Interaction Resource.

PubMed

Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita; Shukla, Rohit N; Vasudevan, Madavan; Goswami, Hitesh

2018-01-01

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Information system of mineral deposits in Slovenia

NASA Astrophysics Data System (ADS)

Hribernik, K.; Rokavec, D.; Šinigioj, J.; Šolar, S.

2010-03-01

At the Geologic Survey of Slovenia the need for complex overview and control of the deposits of available non-metallic mineral raw materials and of their exploitations became urgent. In the framework of the Geologic Information System we established the Database of non-metallic mineral deposits comprising all important data of deposits and concessionars. Relational database is built with program package MS Access, but in year 2008 we plan to transfer it on SQL server. In the evidence there is 272 deposits and 200 concessionars. The mineral resources information system of Slovenia, which was started back in 2002, consists of two integrated parts, mentioned relational database of mineral deposits, which relates information in tabular way so that rules of relational algebra can be applied, and geographic information system (GIS), which relates spatial information of deposits. . The complex relationships between objects and the concepts of normalized data structures, lead to the practical informative and useful data model, transparent to the user and to better decision-making by allowing future scenarios to be developed and inspected. Computerized storage, and display system is as already said, developed and managed under the support of Geological Survey of Slovenia, which conducts research on the occurrence, quality, quantity, and availability of mineral resources in order to help the Nation make informed decisions using earth-science information. Information about deposit is stored in records in approximately hundred data fields. A numeric record number uniquely identifies each site. The data fields are grouped under principal categories. Each record comprise elementary data of deposit (name, type, location, prospect, rock), administrative data (concessionar, number of decree in official paper, object of decree, number of contract and its duration) and data of mineral resource produced amount and size of exploration area). The data can also be searched, sorted and printed using any of these fields. New records are being added annually, and existing records updated or upgraded. Relational database is connected with scanned exploration/exploitation areas of deposits, defined on the base of digital ortofoto. Register of those areas is indispensable because of spatial planning and spatial municipal and regional strategy development. Database is also part of internet application for quick search and review of data and part of web page of mineral resources of Slovenia. The technology chosen for internet application is ESRI's ArcIMS Internet Map Server. ArcIMS allows users to readily and easily display, analyze, and interpret spatial data from desktop using a Web browser connected to the Internet. We believe that there is an opportunity for cooperation within this activity. We can offer a single location where users can come to browse relatively simply for geoscience-related digital data sets.

Resource Sharing: A Necessity for the '80s.

ERIC Educational Resources Information Center

Lavo, Barbara, Comp.

Papers presented at a 1981 seminar on library resource sharing covered topics related to Australasian databases, Australian and New Zealand document delivery systems, and shared acquisition and cataloging for special libraries. The papers included: (1) "AUSINET: Australasia's Information Network?" by Ian McCallum; (2) "Australia/New…

The Internet Compendium: Subject Guides to Humanities Resources.

ERIC Educational Resources Information Center

Rosenfeld, Louis; And Others

This guide describes and evaluates the Internet's humanities resources by subject. It offers information on a multitude of listservs; Usenet newsgroups; forums; electronic journals; topical mailing lists; text archives; Freenets; bulletin boards; FAQs; newsletters; real-time chats; databases; and library catalogs. Internet users can draw upon…

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

Piece2.0: an update for the pant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...

Library Instruction in Communication Disorders: Which Databases Should Be Prioritized?

ERIC Educational Resources Information Center

Grabowsky, Adelia

2015-01-01

The field of communication disorders encompasses the health science disciplines of both speech-­language pathology and audiology. Pertinent literature for communication disorders can be found in a number of databases. Librarians providing information literacy instruction may not have the time to cover more than a few resources. This study develops…

The Weaknesses of Full-Text Searching

ERIC Educational Resources Information Center

Beall, Jeffrey

2008-01-01

This paper provides a theoretical critique of the deficiencies of full-text searching in academic library databases. Because full-text searching relies on matching words in a search query with words in online resources, it is an inefficient method of finding information in a database. This matching fails to retrieve synonyms, and it also retrieves…

Successful Keyword Searching: Initiating Research on Popular Topics Using Electronic Databases.

ERIC Educational Resources Information Center

MacDonald, Randall M.; MacDonald, Susan Priest

Students are using electronic resources more than ever before to locate information for assignments. Without the proper search terms, results are incomplete, and students are frustrated. Using the keywords, key people, organizations, and Web sites provided in this book and compiled from the most commonly used databases, students will be able to…

The Cancer Epidemiology Descriptive Cohort Database: A Tool to Support Population-Based Interdisciplinary Research.

PubMed

Kennedy, Amy E; Khoury, Muin J; Ioannidis, John P A; Brotzman, Michelle; Miller, Amy; Lane, Crystal; Lai, Gabriel Y; Rogers, Scott D; Harvey, Chinonye; Elena, Joanne W; Seminara, Daniela

2016-10-01

We report on the establishment of a web-based Cancer Epidemiology Descriptive Cohort Database (CEDCD). The CEDCD's goals are to enhance awareness of resources, facilitate interdisciplinary research collaborations, and support existing cohorts for the study of cancer-related outcomes. Comprehensive descriptive data were collected from large cohorts established to study cancer as primary outcome using a newly developed questionnaire. These included an inventory of baseline and follow-up data, biospecimens, genomics, policies, and protocols. Additional descriptive data extracted from publicly available sources were also collected. This information was entered in a searchable and publicly accessible database. We summarized the descriptive data across cohorts and reported the characteristics of this resource. As of December 2015, the CEDCD includes data from 46 cohorts representing more than 6.5 million individuals (29% ethnic/racial minorities). Overall, 78% of the cohorts have collected blood at least once, 57% at multiple time points, and 46% collected tissue samples. Genotyping has been performed by 67% of the cohorts, while 46% have performed whole-genome or exome sequencing in subsets of enrolled individuals. Information on medical conditions other than cancer has been collected in more than 50% of the cohorts. More than 600,000 incident cancer cases and more than 40,000 prevalent cases are reported, with 24 cancer sites represented. The CEDCD assembles detailed descriptive information on a large number of cancer cohorts in a searchable database. Information from the CEDCD may assist the interdisciplinary research community by facilitating identification of well-established population resources and large-scale collaborative and integrative research. Cancer Epidemiol Biomarkers Prev; 25(10); 1392-401. ©2016 AACR. ©2016 American Association for Cancer Research.

Modernization of the International Volcanic Ash Website - a global resource for ashfall preparedness and impact guidance.

NASA Astrophysics Data System (ADS)

Wallace, K.; Leonard, G.; Stewart, C.; Wilson, T. M.; Randall, M.; Stovall, W. K.

2015-12-01

The internationally collaborative volcanic ash website (http://volcanoes.usgs.gov/ash/) has been an important global information resource for ashfall preparedness and impact guidance since 2004. Recent volcanic ashfalls with significant local, regional, and global impacts highlighted the need to improve the website to make it more accessible and pertinent to users worldwide. Recently, the Volcanic Ash Impacts Working Group (Cities and Volcanoes Commission of IAVCEI) redesigned and modernized the website. Improvements include 1) a database-driven back end, 2) reorganized menu navigation, 3) language translation, 4) increased downloadable content, 5) addition of ash-impact case studies, 7) expanded and updated references , 8) an image database, and 9) inclusion of cooperating organization's logos. The database-driven platform makes the website more dynamic and efficient to operate and update. New menus provide information about specific impact topics (buildings, transportation, power, health, agriculture, water and waste water, equipment and communications, clean up) and updated content has been added throughout all topics. A new "for scientists" menu includes information on ash collection and analysis. Website translation using Google translate will significantly increase user base. Printable resources (e.g. checklists, pamphlets, posters) provide information to people without Internet access. Ash impact studies are used to improve mitigation measures during future eruptions, and links to case studies will assist communities' preparation and response plans. The Case Studies menu is intended to be a living topic area, growing as new case studies are published. A database of all images from the website allows users to access larger resolution images and additional descriptive details. Logos clarify linkages among key contributors and assure users that the site is authoritative and science-based.

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

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

ERIC Educational Resources Information Center

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

2002-01-01

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

Preliminary Integrated Geologic Map Databases for the United States: Connecticut, Maine, Massachusetts, New Hampshire, New Jersey, Rhode Island and Vermont

USGS Publications Warehouse

Nicholson, Suzanne W.; Dicken, Connie L.; Horton, John D.; Foose, Michael P.; Mueller, Julia A.L.; Hon, Rudi

2006-01-01

The rapid growth in the use of Geographic Information Systems (GIS) has highlighted the need for regional and national scale digital geologic maps that have standardized information about geologic age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. Although two digital geologic maps (Schruben and others, 1994; Reed and Bush, 2004) of the United States currently exist, their scales (1:2,500,000 and 1:5,000,000) are too general for many regional applications. Most states have digital geologic maps at scales of about 1:500,000, but the databases are not comparably structured and, thus, it is difficult to use the digital database for more than one state at a time. This report describes the result for a seven state region of an effort by the U.S. Geological Survey to produce a series of integrated and standardized state geologic map databases that cover the entire United States. In 1997, the United States Geological Survey's Mineral Resources Program initiated the National Surveys and Analysis (NSA) Project to develop national digital databases. One primary activity of this project was to compile a national digital geologic map database, utilizing state geologic maps, to support studies in the range of 1:250,000- to 1:1,000,000-scale. To accomplish this, state databases were prepared using a common standard for the database structure, fields, attribution, and data dictionaries. For Alaska and Hawaii new state maps are being prepared and the preliminary work for Alaska is being released as a series of 1:250,000 scale quadrangle reports. This document provides background information and documentation for the integrated geologic map databases of this report. This report is one of a series of such reports releasing preliminary standardized geologic map databases for the United States. The data products of the project consist of two main parts, the spatial databases and a set of supplemental tables relating to geologic map units. The datasets serve as a data resource to generate a variety of stratigraphic, age, and lithologic maps. This documentation is divided into four main sections: (1) description of the set of data files provided in this report, (2) specifications of the spatial databases, (3) specifications of the supplemental tables, and (4) an appendix containing the data dictionaries used to populate some fields of the spatial database and supplemental tables.

TDR Targets: a chemogenomics resource for neglected diseases.

PubMed

Magariños, María P; Carmona, Santiago J; Crowther, Gregory J; Ralph, Stuart A; Roos, David S; Shanmugam, Dhanasekaran; Van Voorhis, Wesley C; Agüero, Fernán

2012-01-01

The TDR Targets Database (http://tdrtargets.org) has been designed and developed as an online resource to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data (e.g. expression, phylogeny, essentiality) for genes collected from various sources, including literature curation. This information can be browsed and queried using an extensive web interface with functionalities for combining, saving, exporting and sharing the query results. Target genes can be ranked and prioritized using numerical weights assigned to the criteria used for querying. In this report we describe recent updates to the TDR Targets database, including the addition of new genomes (specifically helminths), and integration of chemical structure, property and bioactivity information for biological ligands, drugs and inhibitors and cheminformatic tools for querying and visualizing these chemical data. These changes greatly facilitate exploration of linkages (both known and predicted) between genes and small molecules, yielding insight into whether particular proteins may be druggable, effectively allowing the navigation of chemical space in a genomics context.

TDR Targets: a chemogenomics resource for neglected diseases

PubMed Central

Magariños, María P.; Carmona, Santiago J.; Crowther, Gregory J.; Ralph, Stuart A.; Roos, David S.; Shanmugam, Dhanasekaran; Van Voorhis, Wesley C.; Agüero, Fernán

2012-01-01

The TDR Targets Database (http://tdrtargets.org) has been designed and developed as an online resource to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data (e.g. expression, phylogeny, essentiality) for genes collected from various sources, including literature curation. This information can be browsed and queried using an extensive web interface with functionalities for combining, saving, exporting and sharing the query results. Target genes can be ranked and prioritized using numerical weights assigned to the criteria used for querying. In this report we describe recent updates to the TDR Targets database, including the addition of new genomes (specifically helminths), and integration of chemical structure, property and bioactivity information for biological ligands, drugs and inhibitors and cheminformatic tools for querying and visualizing these chemical data. These changes greatly facilitate exploration of linkages (both known and predicted) between genes and small molecules, yielding insight into whether particular proteins may be druggable, effectively allowing the navigation of chemical space in a genomics context. PMID:22116064

Instruments of scientific visual representation in atomic databases

NASA Astrophysics Data System (ADS)

Kazakov, V. V.; Kazakov, V. G.; Meshkov, O. I.

2017-10-01

Graphic tools of spectral data representation provided by operating information systems on atomic spectroscopy—ASD NIST, VAMDC, SPECTR-W3, and Electronic Structure of Atoms—for the support of scientific-research and human-resource development are presented. Such tools of visual representation of scientific data as those of the spectrogram and Grotrian diagram plotting are considered. The possibility of comparative analysis of the experimentally obtained spectra and reference spectra of atomic systems formed according to the database of a resource is described. The access techniques to the mentioned graphic tools are presented.

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

PubMed

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

2011-01-01

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

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

PubMed Central

Huala, Eva; Dickerman, Allan W.; Garcia-Hernandez, Margarita; Weems, Danforth; Reiser, Leonore; LaFond, Frank; Hanley, David; Kiphart, Donald; Zhuang, Mingzhe; Huang, Wen; Mueller, Lukas A.; Bhattacharyya, Debika; Bhaya, Devaki; Sobral, Bruno W.; Beavis, William; Meinke, David W.; Town, Christopher D.; Somerville, Chris; Rhee, Seung Yon

2001-01-01

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org). PMID:11125061

The Internet Compendium: Subject Guides to Health and Science Resources.

ERIC Educational Resources Information Center

Rosenfeld, Louis; And Others

This guide describes and evaluates the Internet's health and science resources by subject. It offers information on a multitude of listservs; Usenet newsgroups; forums; electronic journals; topical mailing lists; text archives; Freenets; bulletin boards; FAQs; newsletters; real-time chats; databases; and library catalogs. From alternative medicine…

Selected Sources on the Internet.

ERIC Educational Resources Information Center

Scott, Ralph Lee; And Others

1994-01-01

Five articles describe specific Internet resources, including geoscience and science databases; economic and statistical information; the JANET (Joint Academic Network) Bulletin Board for Librarians; and White House communications. A sixth article describes how practical applications of Internet information create new roles for reference…

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.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

Resources monitoring and automatic management system for multi-VO distributed computing system

NASA Astrophysics Data System (ADS)

Chen, J.; Pelevanyuk, I.; Sun, Y.; Zhemchugov, A.; Yan, T.; Zhao, X. H.; Zhang, X. M.

2017-10-01

Multi-VO supports based on DIRAC have been set up to provide workload and data management for several high energy experiments in IHEP. To monitor and manage the heterogeneous resources which belong to different Virtual Organizations in a uniform way, a resources monitoring and automatic management system based on Resource Status System(RSS) of DIRAC has been presented in this paper. The system is composed of three parts: information collection, status decision and automatic control, and information display. The information collection includes active and passive way of gathering status from different sources and stores them in databases. The status decision and automatic control is used to evaluate the resources status and take control actions on resources automatically through some pre-defined policies and actions. The monitoring information is displayed on a web portal. Both the real-time information and historical information can be obtained from the web portal. All the implementations are based on DIRAC framework. The information and control including sites, policies, web portal for different VOs can be well defined and distinguished within DIRAC user and group management infrastructure.

mHealthApps: A Repository and Database of Mobile Health Apps.

PubMed

Xu, Wenlong; Liu, Yin

2015-03-18

The market of mobile health (mHealth) apps has rapidly evolved in the past decade. With more than 100,000 mHealth apps currently available, there is no centralized resource that collects information on these health-related apps for researchers in this field to effectively evaluate the strength and weakness of these apps. The objective of this study was to create a centralized mHealth app repository. We expect the analysis of information in this repository to provide insights for future mHealth research developments. We focused on apps from the two most established app stores, the Apple App Store and the Google Play Store. We extracted detailed information of each health-related app from these two app stores via our python crawling program, and then stored the information in both a user-friendly array format and a standard JavaScript Object Notation (JSON) format. We have developed a centralized resource that provides detailed information of more than 60,000 health-related apps from the Apple App Store and the Google Play Store. Using this information resource, we analyzed thousands of apps systematically and provide an overview of the trends for mHealth apps. This unique database allows the meta-analysis of health-related apps and provides guidance for research designs of future apps in the mHealth field.

Geotherm: the U.S. geological survey geothermal information system

USGS Publications Warehouse

Bliss, J.D.; Rapport, A.

1983-01-01

GEOTHERM is a comprehensive system of public databases and software used to store, locate, and evaluate information on the geology, geochemistry, and hydrology of geothermal systems. Three main databases address the general characteristics of geothermal wells and fields, and the chemical properties of geothermal fluids; the last database is currently the most active. System tasks are divided into four areas: (1) data acquisition and entry, involving data entry via word processors and magnetic tape; (2) quality assurance, including the criteria and standards handbook and front-end data-screening programs; (3) operation, involving database backups and information extraction; and (4) user assistance, preparation of such items as application programs, and a quarterly newsletter. The principal task of GEOTHERM is to provide information and research support for the conduct of national geothermal-resource assessments. The principal users of GEOTHERM are those involved with the Geothermal Research Program of the U.S. Geological Survey. Information in the system is available to the public on request. ?? 1983.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA.

PubMed

Hendrickx, Diana M; Boyles, Rebecca R; Kleinjans, Jos C S; Dearry, Allen

2014-12-01

A joint US-EU workshop on enhancing data sharing and exchange in toxicogenomics was held at the National Institute for Environmental Health Sciences. Currently, efficient reuse of data is hampered by problems related to public data availability, data quality, database interoperability (the ability to exchange information), standardization and sustainability. At the workshop, experts from universities and research institutes presented databases, studies, organizations and tools that attempt to deal with these problems. Furthermore, a case study showing that combining toxicogenomics data from multiple resources leads to more accurate predictions in risk assessment was presented. All participants agreed that there is a need for a web portal describing the diverse, heterogeneous data resources relevant for toxicogenomics research. Furthermore, there was agreement that linking more data resources would improve toxicogenomics data analysis. To outline a roadmap to enhance interoperability between data resources, the participants recommend collecting user stories from the toxicogenomics research community on barriers in data sharing and exchange currently hampering answering to certain research questions. These user stories may guide the prioritization of steps to be taken for enhancing integration of toxicogenomics databases.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

PubMed

Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

2018-01-04

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

The immune epitope database: a historical retrospective of the first decade.

PubMed

Salimi, Nima; Fleri, Ward; Peters, Bjoern; Sette, Alessandro

2012-10-01

As the amount of biomedical information available in the literature continues to increase, databases that aggregate this information continue to grow in importance and scope. The population of databases can occur either through fully automated text mining approaches or through manual curation by human subject experts. We here report our experiences in populating the National Institute of Allergy and Infectious Diseases sponsored Immune Epitope Database and Analysis Resource (IEDB, http://iedb.org), which was created in 2003, and as of 2012 captures the epitope information from approximately 99% of all papers published to date that describe immune epitopes (with the exception of cancer and HIV data). This was achieved using a hybrid model based on automated document categorization and extensive human expert involvement. This task required automated scanning of over 22 million PubMed abstracts followed by classification and curation of over 13 000 references, including over 7000 infectious disease-related manuscripts, over 1000 allergy-related manuscripts, roughly 4000 related to autoimmunity, and 1000 transplant/alloantigen-related manuscripts. The IEDB curation involves an unprecedented level of detail, capturing for each paper the actual experiments performed for each different epitope structure. Key to enabling this process was the extensive use of ontologies to ensure rigorous and consistent data representation as well as interoperability with other bioinformatics resources, including the Protein Data Bank, Chemical Entities of Biological Interest, and the NIAID Bioinformatics Resource Centers. A growing fraction of the IEDB data derives from direct submissions by research groups engaged in epitope discovery, and is being facilitated by the implementation of novel data submission tools. The present explosion of information contained in biological databases demands effective query and display capabilities to optimize the user experience. Accordingly, the development of original ways to query the database, on the basis of ontologically driven hierarchical trees, and display of epitope data in aggregate in a biologically intuitive yet rigorous fashion is now at the forefront of the IEDB efforts. We also highlight advances made in the realm of epitope analysis and predictive tools available in the IEDB. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

Socioeconomic resources in medicine: review of the literature.

PubMed Central

Austin, T

1984-01-01

In this era of intense competition in medicine, it is essential for health sciences librarians to keep abreast of the new and varied socioeconomic influences in the medical environment. A list of socioeconomic resources is provided to help meet this objective. A citation analysis of the Socioeconomic Bibliographic Information (SIB) database was used as a selection criterion. An annotated list of ninety journals, newspapers, and newsletters is included, which provides title of publication, publisher, cost, index information, and special characteristics. In addition, publishers and associations that provide socioeconomic information are listed, and an annotated list of standard statistical resource books is given. PMID:6378285

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples

PubMed Central

Galli, Joakim; Oelrich, Johan; Taussig, Michael J.; Andreasson, Ulrika; Ortega-Paino, Eva; Landegren, Ulf

2015-01-01

We report the development of a new database of technology services and products for analysis of biobank samples in biomedical research. BARCdb, the Biobanking Analysis Resource Catalogue (http://www.barcdb.org), is a freely available web resource, listing expertise and molecular resource capabilities of research centres and biotechnology companies. The database is designed for researchers who require information on how to make best use of valuable biospecimens from biobanks and other sample collections, focusing on the choice of analytical techniques and the demands they make on the type of samples, pre-analytical sample preparation and amounts needed. BARCdb has been developed as part of the Swedish biobanking infrastructure (BBMRI.se), but now welcomes submissions from service providers throughout Europe. BARCdb can help match resource providers with potential users, stimulating transnational collaborations and ensuring compatibility of results from different labs. It can promote a more optimal use of European resources in general, both with respect to standard and more experimental technologies, as well as for valuable biobank samples. This article describes how information on service and reagent providers of relevant technologies is made available on BARCdb, and how this resource may contribute to strengthening biomedical research in academia and in the biotechnology and pharmaceutical industries. PMID:25336620

Technology-based management of environmental organizations using an Environmental Management Information System (EMIS): Design and development

NASA Astrophysics Data System (ADS)

Kouziokas, Georgios N.

2016-01-01

The adoption of Information and Communication Technologies (ICT) in environmental management has become a significant demand nowadays with the rapid growth of environmental information. This paper presents a prototype Environmental Management Information System (EMIS) that was developed to provide a systematic way of managing environmental data and human resources of an environmental organization. The system was designed using programming languages, a Database Management System (DBMS) and other technologies and programming tools and combines information from the relational database in order to achieve the principal goals of the environmental organization. The developed application can be used to store and elaborate information regarding: human resources data, environmental projects, observations, reports, data about the protected species, environmental measurements of pollutant factors or other kinds of analytical measurements and also the financial data of the organization. Furthermore, the system supports the visualization of spatial data structures by using geographic information systems (GIS) and web mapping technologies. This paper describes this prototype software application, its structure, its functions and how this system can be utilized to facilitate technology-based environmental management and decision-making process.

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

ACToR: Aggregated Computational Toxicology Resource (T) ...

EPA Pesticide Factsheets

The EPA Aggregated Computational Toxicology Resource (ACToR) is a set of databases compiling information on chemicals in the environment from a large number of public and in-house EPA sources. ACToR has 3 main goals: (1) The serve as a repository of public toxicology information on chemicals of interest to the EPA, and in particular to be a central source for the testing data on all chemicals regulated by all EPA programs; (2) To be a source of in vivo training data sets for building in vitro to in vivo computational models; (3) To serve as a central source of chemical structure and identity information for the ToxCastTM and Tox21 programs. There are 4 main databases, all linked through a common set of chemical information and a common structure linking chemicals to assay data: the public ACToR system (available at http://actor.epa.gov), the ToxMiner database holding ToxCast and Tox21 data, along with results form statistical analyses on these data; the Tox21 chemical repository which is managing the ordering and sample tracking process for the larger Tox21 project; and the public version of ToxRefDB. The public ACToR system contains information on ~500K compounds with toxicology, exposure and chemical property information from >400 public sources. The web site is visited by ~1,000 unique users per month and generates ~1,000 page requests per day on average. The databases are built on open source technology, which has allowed us to export them to a number of col

Porphyry copper assessment of northeast Asia: Far East Russia and northeasternmost China: Chapter W in Global mineral resource assessment

USGS Publications Warehouse

Mihalasky, Mark J.; Ludington, Stephen; Alexeiev, Dmitriy V.; Frost, Thomas P.; Light, Thomas D.; Briggs, Deborah A.; Hammarstrom, Jane M.; Wallis, John C.; Bookstrom, Arthur A.; Panteleyev, Andre

2015-01-01

The database of known deposits, significant prospects, and prospects includes an inventory of mineral resources in two known porphyry copper deposits, as well as key characteristics derived from available exploration reports for 70 significant porphyry copper prospects and 86 other prospects. Resource and exploration and development activity are updated with information current through February 2013.

The Internet as an Information Source for Environmental Chemicals--First Results of the Evaluation of the Meta-Database of Internet Resources.

ERIC Educational Resources Information Center

Voigt, Kristina; Benz, Joachim; Bruggemann, Rainer

An evaluation approach using the mathematical method of the Hasse diagram technique is applied on 20 environmental and chemical Internet resources. The data for this evaluation procedure are taken out of a metadatabase called DAIN (Metadatabase of Internet Resources for Environmental Chemicals) which is set up by the GSF Research Centre for…

ATtRACT-a database of RNA-binding proteins and associated motifs.

PubMed

Giudice, Girolamo; Sánchez-Cabo, Fátima; Torroja, Carlos; Lara-Pezzi, Enrique

2016-01-01

RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es. © The Author(s) 2016. Published by Oxford University Press.

DBGC: A Database of Human Gastric Cancer

PubMed Central

Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

2015-01-01

The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

Phynx: an open source software solution supporting data management and web-based patient-level data review for drug safety studies in the general practice research database and other health care databases.

PubMed

Egbring, Marco; Kullak-Ublick, Gerd A; Russmann, Stefan

2010-01-01

To develop a software solution that supports management and clinical review of patient data from electronic medical records databases or claims databases for pharmacoepidemiological drug safety studies. We used open source software to build a data management system and an internet application with a Flex client on a Java application server with a MySQL database backend. The application is hosted on Amazon Elastic Compute Cloud. This solution named Phynx supports data management, Web-based display of electronic patient information, and interactive review of patient-level information in the individual clinical context. This system was applied to a dataset from the UK General Practice Research Database (GPRD). Our solution can be setup and customized with limited programming resources, and there is almost no extra cost for software. Access times are short, the displayed information is structured in chronological order and visually attractive, and selected information such as drug exposure can be blinded. External experts can review patient profiles and save evaluations and comments via a common Web browser. Phynx provides a flexible and economical solution for patient-level review of electronic medical information from databases considering the individual clinical context. It can therefore make an important contribution to an efficient validation of outcome assessment in drug safety database studies.

Multiresource inventories incorporating GIS, GPS, and database management systems

Treesearch

Loukas G. Arvanitis; Balaji Ramachandran; Daniel P. Brackett; Hesham Abd-El Rasol; Xuesong Du

2000-01-01

Large-scale natural resource inventories generate enormous data sets. Their effective handling requires a sophisticated database management system. Such a system must be robust enough to efficiently store large amounts of data and flexible enough to allow users to manipulate a wide variety of information. In a pilot project, related to a multiresource inventory of the...

Social Gerontology--Integrative and Territorial Aspects: A Citation Analysis of Subject Scatter and Database Coverage

ERIC Educational Resources Information Center

Lasda Bergman, Elaine M.

2011-01-01

To determine the mix of resources used in social gerontology research, a citation analysis was conducted. A representative sample of citations was selected from three prominent gerontology journals and information was added to determine subject scatter and database coverage for the cited materials. Results indicate that a significant portion of…

End User Information Searching on the Internet: How Do Users Search and What Do They Search For? (SIG USE)

ERIC Educational Resources Information Center

Saracevic, Tefko

2000-01-01

Summarizes a presentation that discussed findings and implications of research projects using an Internet search service and Internet-accessible vendor databases, representing the two sides of public database searching: query formulation and resource utilization. Presenters included: Tefko Saracevic, Amanda Spink, Dietmar Wolfram and Hong Xie.…

Research resources for Drosophila: the expanding universe.

PubMed

Matthews, Kathleen A; Kaufman, Thomas C; Gelbart, William M

2005-03-01

Drosophila melanogaster has been the subject of research into central questions about biological mechanisms for almost a century. The experimental tools and resources that are available or under development for D. melanogaster and its related species, particularly those for genomic analysis, are truly outstanding. Here we review three types of resource that have been developed for D. melanogaster research: databases and other sources of information, biological materials and experimental services. These resources are there to be exploited and we hope that this guide will encourage new uses for D. melanogaster information, materials and services, both by those new to flies and by experienced D. melanogaster researchers.

Update on Genomic Databases and Resources at the National Center for Biotechnology Information.

PubMed

Tatusova, Tatiana

2016-01-01

The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data.

An Information System for European culture collections: the way forward.

PubMed

Casaregola, Serge; Vasilenko, Alexander; Romano, Paolo; Robert, Vincent; Ozerskaya, Svetlana; Kopf, Anna; Glöckner, Frank O; Smith, David

2016-01-01

Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible to their users. Clearly, the needs of culture collection curators coincide with those of users on the crucial point of database interoperability. In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.

The DoD Gateway Information System: Bibliography, Directory of Resources, Prototype Experience, [and] User Interface Design.

ERIC Educational Resources Information Center

Cotter, Gladys A.; And Others

The Defense Technical Information Center (DTIC), an organization charged with providing information services to the Department of Defense (DoD) scientific and technical community, actively seeks ways to promote access to and utilization of scientific and technical information (STI) databases, online services, and networks relevant to the conduct…

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.

[Selected aspects of computer-assisted literature management].

PubMed

Reiss, M; Reiss, G

1998-01-01

We want to report about our own experiences with a database manager. Bibliography database managers are used to manage information resources: specifically, to maintain a database to references and create bibliographies and reference lists for written works. A database manager allows to enter summary information (record) for articles, book sections, books, dissertations, conference proceedings, and so on. Other features that may be included in a database manager include the ability to import references from different sources, such as MEDLINE. The word processing components allow to generate reference list and bibliographies in a variety of different styles, generates a reference list from a word processor manuscript. The function and the use of the software package EndNote 2 for Windows are described. Its advantages in fulfilling different requirements for the citation style and the sort order of reference lists are emphasized.

Agricultural Safety and Health: A Resource Guide. Rural Information Center Publication Series, No. 40. Revised Edition.

ERIC Educational Resources Information Center

Zimmerman, Joy, Comp.

This guide lists resource materials that address agricultural occupational injuries and diseases and their prevention. Many of the entries were derived from the AGRICOLA database produced by the National Agricultural Library and include journal articles, books, government reports, training materials, and audiovisual materials. The first section…

Mining Hidden Gems Beneath the Surface: A Look At the Invisible Web.

ERIC Educational Resources Information Center

Carlson, Randal D.; Repman, Judi

2002-01-01

Describes resources for researchers called the Invisible Web that are hidden from the usual search engines and other tools and contrasts them with those resources available on the surface Web. Identifies specialized search tools, databases, and strategies that can be used to locate credible in-depth information. (Author/LRW)

The Database Business: Managing Today--Planning for Tomorrow. Optimizing Human Resource Factors.

ERIC Educational Resources Information Center

Clark, Joseph E.; And Others

1988-01-01

The first paper describes the National Technical Information Service productivity improvement system and its emphasis on human resources development. The second addresses the benefits of telecommuting to employers and employees. The third discusses the problems generated by the baby boom work force pressing for advancement at a time when many…

76 FR 12369 - Notice of Lodging of Consent Decree Under the Clean Water Act

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-07

..., creating a database to track information relevant to compliance efforts, conducting regular internal and... notice. Comments should be addressed to the Assistant Attorney General, Environment and Natural Resources..., Environment & Natural Resources Division. [FR Doc. 2011-5017 Filed 3-4-11; 8:45 am] BILLING CODE 4410-15-P ...

May I Recruit through Your Agency? Considerations for Researchers of Spousal Caregivers

ERIC Educational Resources Information Center

Pote, Steven

2016-01-01

Few resources within social science literature provide helpful information related to participant recruitment for research on spousal caregivers of individuals with dementia. Independent researchers with limited resources may not have access to large databases or centers in which access to caregivers is readily available. As a result, these…

Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration

USDA-ARS?s Scientific Manuscript database

Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of scientific data between information resources difficu...

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.

Information Retrieval Strategies of Millennial Undergraduate Students in Web and Library Database Searches

ERIC Educational Resources Information Center

Porter, Brandi

2009-01-01

Millennial students make up a large portion of undergraduate students attending colleges and universities, and they have a variety of online resources available to them to complete academically related information searches, primarily Web based and library-based online information retrieval systems. The content, ease of use, and required search…

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.

Comprehensive, comprehensible, distributed and intelligent databases: current status.

PubMed

Frishman, D; Heumann, K; Lesk, A; Mewes, H W

1998-01-01

It is only a matter of time until a user will see not many but one integrated database of information for molecular biology. Is this true? Is it a good thing? Why will it happen? Where are we now? What developments are fostering and what developments are impeding progress towards this end? A list of WWW resources devoted to database issues in molecular biology is available at http://www.mips.biochem.mpg.de frishman@mips.biochem.mpg.de

Do You Know where Your Data Are?

ERIC Educational Resources Information Center

Bennett, Cedric

2006-01-01

Many of the information security appliances, devices, and techniques currently in use are designed to keep unwanted users and Internet traffic away from important information assets by denying unauthorized access to servers, databases, networks, storage media, and other underlying technology resources. These approaches employ firewalls, intrusion…

34 CFR 361.23 - Requirements related to the statewide workforce investment system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... technology for individuals with disabilities; (ii) The use of information and financial management systems... statistics, job vacancies, career planning, and workforce investment activities; (iii) The use of customer service features such as common intake and referral procedures, customer databases, resource information...

How Community Colleges Can Capitalize on Changes in Information Services.

ERIC Educational Resources Information Center

Nourse, Jimmie Anne; Widman, Rudy

1991-01-01

Urges community college librarians to become leaders in library instruction by developing aggressive teaching programs using high-technology information resources, such as compact disc read-only-memory (CD-ROM), telecommunications, and on-line databases. Discusses training, hardware, software, and funding issues. (DMM)

Text mining for metabolic pathways, signaling cascades, and protein networks.

PubMed

Hoffmann, Robert; Krallinger, Martin; Andres, Eduardo; Tamames, Javier; Blaschke, Christian; Valencia, Alfonso

2005-05-10

The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources. Text-mining methods have started to play a key role in the creation and maintenance of links between the information stored in biological databases and its original sources in the literature. These links will be extremely useful for database updating and curation, especially if a number of technical problems can be solved satisfactorily, including the identification of protein and gene names (entities in general) and the characterization of their types of interactions. The first generation of openly accessible text-mining systems, such as iHOP (Information Hyperlinked over Proteins), provides additional functions to facilitate the reconstruction of protein interaction networks, combine database and text information, and support the scientist in the formulation of novel hypotheses. The next challenge is the generation of comprehensive information regarding the general function of signaling pathways and protein interaction networks.

Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource

PubMed Central

Koike, Asako; Kobayashi, Yoshiyuki; Takagi, Toshihisa

2003-01-01

Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein–protein, protein–gene, and protein–compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP).The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/. PMID:12799355

GEOTHERM Data Set

DOE Data Explorer

DeAngelo, Jacob

1983-01-01

GEOTHERM is a comprehensive system of public databases and software used to store, locate, and evaluate information on the geology, geochemistry, and hydrology of geothermal systems. Three main databases address the general characteristics of geothermal wells and fields, and the chemical properties of geothermal fluids; the last database is currently the most active. System tasks are divided into four areas: (1) data acquisition and entry, involving data entry via word processors and magnetic tape; (2) quality assurance, including the criteria and standards handbook and front-end data-screening programs; (3) operation, involving database backups and information extraction; and (4) user assistance, preparation of such items as application programs, and a quarterly newsletter. The principal task of GEOTHERM is to provide information and research support for the conduct of national geothermal-resource assessments. The principal users of GEOTHERM are those involved with the Geothermal Research Program of the U.S. Geological Survey.

Evaluation of three point-of-care healthcare databases: BMJ Point-of-Care, Clin-eguide and Nursing Reference Centre.

PubMed

Chan, Rachel; Stieda, Vivian

2011-03-01

  Point of care resources make it easier for clinicians to find answers to questions that arise during a clinical encounter. In order to make informed purchase decisions in times of tight budgets, librarians need to have a better understanding of which resources will meet their patrons' clinical information needs.   The goal of this study was to assess the content, interface and usability of three point-of-care tools: BMJ Point-of-Care, Clin-eguide and Nursing Reference Centre.   A questionnaire designed to gather quantitative and qualitative data was created using Survey Monkey. The survey was distributed to healthcare practitioners in Alberta's two largest health regions, and the data were analysed for emergent themes.   The themes that arose--ease of use, validated content, relevancy to practice--generally echoed those stated in the literature. No one database fared significantly better, due to differing features, content and client preference.   Despite the limitations of the survey, the themes that emerged provide a springboard for future research on the efficacy of information resources used at the point of care, and the need for deeper analysis of these recent additions to the medical information market. © 2010 The authors. Health Information and Libraries Journal © 2010 Health Libraries Group.

Database for the degradation risk assessment of groundwater resources (Southern Italy)

NASA Astrophysics Data System (ADS)

Polemio, M.; Dragone, V.; Mitolo, D.

2003-04-01

The risk characterisation of quality degradation and availability lowering of groundwater resources has been pursued for a wide coastal plain (Basilicata region, Southern Italy), an area covering 40 km along the Ionian Sea and 10 km inland. The quality degradation is due two phenomena: pollution due to discharge of waste water (coming from urban areas) and due to salt pollution, related to seawater intrusion but not only. The availability lowering is due to overexploitation but also due to drought effects. To this purpose the historical data of 1,130 wells have been collected. Wells, homogenously distributed in the area, were the source of geological, stratigraphical, hydrogeological, geochemical data. In order to manage space-related information via a GIS, a database system has been devised to encompass all the surveyed wells and the body of information available per well. Geo-databases were designed to comprise the four types of data collected: a database including geometrical, geological and hydrogeological data on wells (WDB), a database devoted to chemical and physical data on groundwater (CDB), a database including the geotechnical parameters (GDB), a database concering piezometric and hydrological (rainfall, air temperature, river discharge) data (HDB). The record pertaining to each well is identified in these databases by the progressive number of the well itself. Every database is designed as follows: a) the HDB contains 1,158 records, 28 of and 31 fields, mainly describing the geometry of the well and of the stratigraphy; b) the CDB encompasses data about 157 wells, based on which the chemical and physical analyses of groundwater have been carried out. More than one record has been associated with these 157 wells, due to periodic monitoring and analysis; c) the GDB covers 61 wells to which the geotechnical parameters obtained by soil samples taken at various depths; the HDB is designed to permit the analysis of long time series (from 1918) of piezometric data, monitored by more than 60 wells, temperature, rainfall and river discharge data. Based on geo-databases, the geostatistical processing of data has permitted to characterise the degradation risk of groundwater resources of a wide coastal aquifer.

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.

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 Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.

PubMed

Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C

2008-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can be accessed in GOLD through pre-computed lists and a search page. As of September 2007, GOLD contains information on more than 2900 sequencing projects, out of which 639 have been completed and their sequence data deposited in the public databases. GOLD continues to expand with the goal of providing metadata information related to the projects and the organisms/environments towards the Minimum Information about a Genome Sequence' (MIGS) guideline. GOLD is available at http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

PubMed Central

Liolios, Konstantinos; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Kyrpides, Nikos C.

2008-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource that provides information on genome and metagenome projects worldwide. Complete and ongoing projects and their associated metadata can be accessed in GOLD through pre-computed lists and a search page. As of September 2007, GOLD contains information on more than 2900 sequencing projects, out of which 639 have been completed and their sequence data deposited in the public databases. GOLD continues to expand with the goal of providing metadata information related to the projects and the organisms/environments towards the Minimum Information about a Genome Sequence’ (MIGS) guideline. GOLD is available at http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/ PMID:17981842

Coastal resource and sensitivity mapping of Vietnam

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

Odin, L.M.

1997-08-01

This paper describes a project to establish a relationship between environmental sensitivity (primarily to oil pollution) and response planning and prevention priorities for Vietnamese coastal regions. An inventory of coastal environmental sensitivity and the creation of index mapping was performed. Satellite and geographical information system data were integrated and used for database creation. The database was used to create a coastal resource map, coastal sensitivity map, and a field inventory base map. The final coastal environment sensitivity classification showed that almost 40 percent of the 7448 km of mapped shoreline has a high to medium high sensitivity to oil pollution.

DDRprot: a database of DNA damage response-related proteins.

PubMed

Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M

2016-01-01

The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.Database URL: http://ddr.cbbio.es. © The Author(s) 2016. Published by Oxford University Press.

EcoCyc: a comprehensive database resource for Escherichia coli

PubMed Central

Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro; Ingraham, John; Paley, Suzanne; Paulsen, Ian T.; Peralta-Gil, Martín; Karp, Peter D.

2005-01-01

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions. PMID:15608210

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

PubMed Central

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

2017-01-01

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

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

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.

Improving wilderness stewardship through searchable databases of U.S. legislative history and legislated special provisions

Treesearch

David R. Craig; Peter Landres; Laurie Yung

2010-01-01

The online resource Wilderness.net currently provides quick access to the text of every public law designating wilderness in the U.S. National Wilderness Preservation System (NWPS). This article describes two new searchable databases recently completed and added to the information available on Wilderness.net to help wilderness managers and others understand and...

[Tumor Data Interacted System Design Based on Grid Platform].

PubMed

Liu, Ying; Cao, Jiaji; Zhang, Haowei; Zhang, Ke

2016-06-01

In order to satisfy demands of massive and heterogeneous tumor clinical data processing and the multi-center collaborative diagnosis and treatment for tumor diseases,a Tumor Data Interacted System(TDIS)was established based on grid platform,so that an implementing virtualization platform of tumor diagnosis service was realized,sharing tumor information in real time and carrying on standardized management.The system adopts Globus Toolkit 4.0tools to build the open grid service framework and encapsulats data resources based on Web Services Resource Framework(WSRF).The system uses the middleware technology to provide unified access interface for heterogeneous data interaction,which could optimize interactive process with virtualized service to query and call tumor information resources flexibly.For massive amounts of heterogeneous tumor data,the federated stored and multiple authorized mode is selected as security services mechanism,real-time monitoring and balancing load.The system can cooperatively manage multi-center heterogeneous tumor data to realize the tumor patient data query,sharing and analysis,and compare and match resources in typical clinical database or clinical information database in other service node,thus it can assist doctors in consulting similar case and making up multidisciplinary treatment plan for tumors.Consequently,the system can improve efficiency of diagnosis and treatment for tumor,and promote the development of collaborative tumor diagnosis model.

The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome

PubMed Central

Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui; Mezheritsky, Yarik; Muller, Robert; Strait, Emily; Huala, Eva

2015-01-01

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR’s biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR’s focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally-based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible. PMID:26201819

NCBI Epigenomics: what's new for 2013.

PubMed

Fingerman, Ian M; Zhang, Xuan; Ratzat, Walter; Husain, Nora; Cohen, Robert F; Schuler, Gregory D

2013-01-01

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements.

NCBI Epigenomics: What’s new for 2013

PubMed Central

Fingerman, Ian M.; Zhang, Xuan; Ratzat, Walter; Husain, Nora; Cohen, Robert F.; Schuler, Gregory D.

2013-01-01

The Epigenomics resource at the National Center for Biotechnology Information (NCBI) has been created to serve as a comprehensive public repository for whole-genome epigenetic data sets (www.ncbi.nlm.nih.gov/epigenomics). We have constructed this resource by selecting the subset of epigenetics-specific data from the Gene Expression Omnibus (GEO) database and then subjecting them to further review and annotation. Associated data tracks can be viewed using popular genome browsers or downloaded for local analysis. We have performed extensive user testing throughout the development of this resource, and new features and improvements are continuously being implemented based on the results. We have made substantial usability improvements to user interfaces, enhanced functionality, made identification of data tracks of interest easier and created new tools for preliminary data analyses. Additionally, we have made efforts to enhance the integration between the Epigenomics resource and other NCBI databases, including the Gene database and PubMed. Data holdings have also increased dramatically since the initial publication describing the NCBI Epigenomics resource and currently consist of >3700 viewable and downloadable data tracks from 955 biological sources encompassing five well-studied species. This updated manuscript highlights these changes and improvements. PMID:23193265

PrimateLit:Using this Site

Science.gov Websites

Contact Information Primate Info Net Related Databases National Center for Research Resources WA Primate Information Center, Washington National Primate Research Center. Using The Search History The History button journal articles, books, theses, and other documents related to their area of research. The advantages of

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.

PubMed

McQuilton, Peter; Gonzalez-Beltran, Alejandra; Rocca-Serra, Philippe; Thurston, Milo; Lister, Allyson; Maguire, Eamonn; Sansone, Susanna-Assunta

2016-01-01

BioSharing (http://www.biosharing.org) is a manually curated, searchable portal of three linked registries. These resources cover standards (terminologies, formats and models, and reporting guidelines), databases, and data policies in the life sciences, broadly encompassing the biological, environmental and biomedical sciences. Launched in 2011 and built by the same core team as the successful MIBBI portal, BioSharing harnesses community curation to collate and cross-reference resources across the life sciences from around the world. BioSharing makes these resources findable and accessible (the core of the FAIR principle). Every record is designed to be interlinked, providing a detailed description not only on the resource itself, but also on its relations with other life science infrastructures. Serving a variety of stakeholders, BioSharing cultivates a growing community, to which it offers diverse benefits. It is a resource for funding bodies and journal publishers to navigate the metadata landscape of the biological sciences; an educational resource for librarians and information advisors; a publicising platform for standard and database developers/curators; and a research tool for bench and computer scientists to plan their work. BioSharing is working with an increasing number of journals and other registries, for example linking standards and databases to training material and tools. Driven by an international Advisory Board, the BioSharing user-base has grown by over 40% (by unique IP address), in the last year thanks to successful engagement with researchers, publishers, librarians, developers and other stakeholders via several routes, including a joint RDA/Force11 working group and a collaboration with the International Society for Biocuration. In this article, we describe BioSharing, with a particular focus on community-led curation.Database URL: https://www.biosharing.org. © The Author(s) 2016. Published by Oxford University Press.

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules—Search Options and Applications in Food Science

PubMed Central

Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

2016-01-01

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs. PMID:27929431

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

PubMed

Minkiewicz, Piotr; Darewicz, Małgorzata; Iwaniak, Anna; Bucholska, Justyna; Starowicz, Piotr; Czyrko, Emilia

2016-12-06

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

Lunar e-Library: Putting Space History to Work

NASA Technical Reports Server (NTRS)

McMahan, Tracy A.; Shea, Charlotte A.; Finckenor, Miria

2006-01-01

As NASA plans and implements the Vision for Space Exploration, managers, engineers, and scientists need historically important information that is readily available and easily accessed. The Lunar e-Library - a searchable collection of 1100 electronic (.PDF) documents - makes it easy to find critical technical data and lessons learned and put space history knowledge in action. The Lunar e-Library, a DVD knowledge database, was developed by NASA to shorten research time and put knowledge at users' fingertips. Funded by NASA's Space Environments and Effects (SEE) Program headquartered at Marshall Space Flight Center (MSFC) and the MSFC Materials and Processes Laboratory, the goal of the Lunar e- Library effort was to identify key lessons learned from Apollo and other lunar programs and missions and to provide technical information from those programs in an easy-to-use format. The SEE Program began distributing the Lunar e-Library knowledge database in 2006. This paper describes the Lunar e-Library development process (including a description of the databases and resources used to acquire the documents) and the contents of the DVD product, demonstrates its usefulness with focused searches, and provides information on how to obtain this free resource.

Design of Knowledge Bases for Plant Gene Regulatory Networks.

PubMed

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

2017-01-01

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

Mycobacterial biomaterials and resources for researchers.

PubMed

Hazbón, Manzour Hernando; Rigouts, Leen; Schito, Marco; Ezewudo, Matthew; Kudo, Takuji; Itoh, Takashi; Ohkuma, Moriya; Kiss, Katalin; Wu, Linhuan; Ma, Juncai; Hamada, Moriyuki; Strong, Michael; Salfinger, Max; Daley, Charles L; Nick, Jerry A; Lee, Jung-Sook; Rastogi, Nalin; Couvin, David; Hurtado-Ortiz, Raquel; Bizet, Chantal; Suresh, Anita; Rodwell, Timothy; Albertini, Audrey; Lacourciere, Karen A; Deheer-Graham, Ana; Alexander, Sarah; Russell, Julie E; Bradford, Rebecca; Riojas, Marco A

2018-06-01

There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.

International Soil Carbon Network (ISCN) Database v3-1

DOE Data Explorer

Nave, Luke [University of Michigan] (ORCID:0000000182588335); Johnson, Kris [USDA-Forest Service; van Ingen, Catharine [Microsoft Research; Agarwal, Deborah [Lawrence Berkeley National Laboratory] (ORCID:0000000150452396); Humphrey, Marty [University of Virginia; Beekwilder, Norman [University of Virginia

2016-01-01

The ISCN is an international scientific community devoted to the advancement of soil carbon research. The ISCN manages an open-access, community-driven soil carbon database. This is version 3-1 of the ISCN Database, released in December 2015. It gathers 38 separate dataset contributions, totalling 67,112 sites with data from 71,198 soil profiles and 431,324 soil layers. For more information about the ISCN, its scientific community and resources, data policies and partner networks visit: http://iscn.fluxdata.org/.

CanisOme--The protein signatures of Canis lupus familiaris diseases.

PubMed

Fernandes, Mónica; Rosa, Nuno; Esteves, Eduardo; Correia, Maria José; Arrais, Joel; Ribeiro, Paulo; Vala, Helena; Barros, Marlene

2016-03-16

Although the applications of Proteomics in Human Biomedicine have been explored for some time now, in animal and veterinary research, the potential of this resource has just started to be explored, especially when companion animal health is considered. In the last years, knowledge on the Canis lupus familiaris proteome has been accumulating in the literature and a resource compiling all this information and critically reviewing it was lacking. This article presents such a resource for the first time. CanisOme is a database of all proteins identified in Canis lupus familiaris tissues, either in health or in disease, annotated with information on the proteins present on the sample and on the donors. This database reunites information on 549 proteins, associated with 63 dog diseases and 33 dog breeds. Examples of how this information may be used to produce new hypothesis on disease mechanisms is presented both through the functional analysis of the proteins quantified in canine cutaneous mast cell tumors and through the study of the interactome of C. lupus familiaris and Leishmania infantum. Therefore, the usefulness of CanisOme for researchers looking for protein biomarkers in dogs and interested in a comprehensive analysis of disease mechanisms is demonstrated. This paper presents CanisOme, a database of proteomic studies with relevant protein annotation, allowing the enlightenment of disease mechanisms and the discovery of novel disease biomarkers for C. lupus familiaris. This knowledge is important not only for the improvement of animal health but also for the use of dogs as models for human health studies. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2011-01-01

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

Searching Across the International Space Station Databases

NASA Technical Reports Server (NTRS)

Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

2007-01-01

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai.

PubMed

Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

2017-03-09

In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai

PubMed Central

Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

2017-01-01

In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone. PMID:28282934

Coordination and standardization of federal sedimentation activities

USGS Publications Warehouse

Glysson, G. Douglas; Gray, John R.

1997-01-01

- precipitation information critical to water resources management. Memorandum M-92-01 covers primarily freshwater bodies and includes activities, such as "development and distribution of consensus standards, field-data collection and laboratory analytical methods, data processing and interpretation, data-base management, quality control and quality assurance, and water- resources appraisals, assessments, and investigations." Research activities are not included.

Marriage and Family Counseling. Searchlight Plus: Relevant Resources in High Interest Areas. 57+.

ERIC Educational Resources Information Center

Okun, Barbara F.

This information analysis paper is based on a computer search of the ERIC database from November 1966 through March 1984, and on pertinent outside resources related to marriage and family counseling. A brief historical perspective of the field of marriage and family counseling is provided, and the differences and overlaps between family,…

Casting the Net: The Development of a Resource Collection for an Internet Database.

ERIC Educational Resources Information Center

McKiernan, Gerry

CyberStacks(sm), a demonstration prototype World Wide Web information service, was established on the home page server at Iowa State University with the intent of facilitating identification and use of significant Internet resources in science and technology. CyberStacks(sm) was created in response to perceived deficiencies in early efforts to…

Investigation of Education Databases in Four States To Support Policy Research on Resource Allocation. Policy Report

ERIC Educational Resources Information Center

Pan, Diane; Smith-Hansen, Lotte; Jones, Debra Hughes; Rudo, Zena H.; Alexander, Celeste; Kahlert, Rahel Kahlert, Rahel

2004-01-01

Information is one of the most important tools education decision makers need to help them effectively spend taxpayer money, allocate qualified staff, and determine the effectiveness of education investments. Decision makers must understand the role and influence of monetary and staff resources on the education system, and they must have…

Electronic Job Search Revolution. Win with the New Technology that's Reshaping Today's Job Market.

ERIC Educational Resources Information Center

Kennedy, Joyce Lain; Morrow, Thomas J.

This book contains information about the resources available to merge new technology and the search for employment. It offers suggestions from human resource specialists, software authors, and database experts. Chapter 1 is an overview of how the computer has become indispensable in a job search. Chapter 2 focuses on external, third-party resume…

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

The MAR databases: development and implementation of databases specific for marine metagenomics

PubMed Central

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen

2018-01-01

Abstract We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. PMID:29106641

HPIDB 2.0: a curated database for host–pathogen interactions

PubMed Central

Ammari, Mais G.; Gresham, Cathy R.; McCarthy, Fiona M.; Nanduri, Bindu

2016-01-01

Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html PMID:27374121

HIVsirDB: a database of HIV inhibiting siRNAs.

PubMed

Tyagi, Atul; Ahmed, Firoz; Thakur, Nishant; Sharma, Arun; Raghava, Gajendra P S; Kumar, Manoj

2011-01-01

Human immunodeficiency virus (HIV) is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi) is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA) for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes. HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i) siRNAmap for mapping siRNAs on target sequence, ii) HIVsirblast for BLAST search against database, iii) siRNAalign for aligning siRNAs. HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

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

Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress.

PubMed

Williams-Devane, ClarLynda R; Wolf, Maritja A; Richard, Ann M

2009-06-01

A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate and aggregate such information by chemical, and broad data coverage within chemical, genomics, and toxicological information domains. This capability also depends on common genomics standards, protocol description, and functional linkages of diverse public Internet data resources. We present a survey of public genomics resources from these vantage points and conclude that, despite progress in many areas, the current state of the majority of public microarray databases is inadequate for supporting these objectives, particularly with regard to chemical indexing. To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus. Automated scripts and extensive manual review were employed to transform free-text experiment descriptions into a standardized, chemically indexed inventory of experiments in both resources. These files, which include top-level summary annotations, allow for identification of current chemical-associated experimental content, as well as chemical-exposure-related (or "Treatment") content of greatest potential value to toxicogenomics investigation. With these chemical-index files, it is possible for the first time to assess the breadth and overlap of chemical study space represented in these databases, and to begin to assess the sufficiency of data with shared protocols for chemical similarity inferences. Chemical indexing of public genomics databases is a first important step toward integrating chemical, toxicological and genomics data into predictive toxicology.

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

Graph-Based Weakly-Supervised Methods for Information Extraction & Integration

ERIC Educational Resources Information Center

Talukdar, Partha Pratim

2010-01-01

The variety and complexity of potentially-related data resources available for querying--webpages, databases, data warehouses--has been growing ever more rapidly. There is a growing need to pose integrative queries "across" multiple such sources, exploiting foreign keys and other means of interlinking data to merge information from diverse…

Research on Higher Education: A U.S. Perspective.

ERIC Educational Resources Information Center

Toombs, William

Characteristics of U.S. higher education are identified, along with the structural features that influence the nature of research, specific research topics, and the locations of research activities. This information was obtained from several sources, including the Educational Resources Information Center database for the years 1981 and 1982, the…

Manual for ERIC Awareness Workshop.

ERIC Educational Resources Information Center

Strohmenger, C. Todd; Lanham, Berma A.

This manual, designed to be used with a video tape, provides information for conducting a workshop to familiarize educators with the Educational Resources Information Center (ERIC). Objectives of the workshop include: (1) to develop an understanding of the contents and structure of the ERIC database; (2) to develop an understanding of ERIC as a…

Evaluation of Point-of-Care Resources for Dietary Supplement Information.

PubMed

Montgomery, Ashley E; Beckett, Robert D; Montagano, Kaitlin J; Kutom, Samah

2018-01-01

To evaluate 6 tertiary, point-of-care drug information resources' dietary supplement content. This was a cross-sectional evaluation of Lexicomp Natural Products Database, Micromedex Alternative Medicine, Clinical Pharmacology, Natural Medicines, The Review of Natural Products, and Handbook of Nonprescription Drugs. Each resource was evaluated for scope, completeness, consistency, and ease of use. For a sample of 66 supplements, scope scores ranged from 69.7% (Micromedex) to 100% (Natural Medicines). Completeness scores were high considering uses, dose, adverse effects, and mechanism (85.7% to 100%). Overall completeness scores ranged from 82.5% ( Handbook of Nonprescription Drugs) to 100% (Clinical Pharmacology, Natural Medicines, The Review of Natural Products). Consistency scores ranged from 0% ( Handbook of Nonprescription Drugs) to 100% (Natural Medicines, The Review of Natural Products). Mean time to locate and gather information was similar among groups. Resources were similar for completeness and ease of use. Scope and consistency varied depending on the resource.

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.

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.

PubMed

Mizutani, Hisashi; Sugawara, Hideaki; Buckle, Ashley M; Sangawa, Takeshi; Miyazono, Ken-Ichi; Ohtsuka, Jun; Nagata, Koji; Shojima, Tomoki; Nosaki, Shohei; Xu, Yuqun; Wang, Delong; Hu, Xiao; Tanokura, Masaru; Yura, Kei

2017-04-24

More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17 th , 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/ . REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

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

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

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

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

NCBI Bookshelf: books and documents in life sciences and health care

PubMed Central

Hoeppner, Marilu A.

2013-01-01

Bookshelf (http://www.ncbi.nlm.nih.gov/books/) is a full-text electronic literature resource of books and documents in life sciences and health care at the National Center for Biotechnology Information (NCBI). Created in 1999 with a single book as an encyclopedic reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 titles. Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, books come in all forms; they are diverse in publication types, formats, sizes and authoring models. The Bookshelf data format is XML tagged in the NCBI Book DTD (Document Type Definition), modeled after the National Library of Medicine journal article DTDs. The book DTD has been used for systematically tagging the diverse data formats of books, a move that has set the foundation for the growth of this resource. Books at NCBI followed the route of journal articles in the PubMed Central project, using the PubMed Central architectural framework, workflows and processes. Through integration with other NCBI molecular databases, books at NCBI can be used to provide reference information for biological data and facilitate its discovery. This article describes Bookshelf at NCBI: its growth, data handling and retrieval and integration with molecular databases. PMID:23203889

NCBI Bookshelf: books and documents in life sciences and health care.

PubMed

Hoeppner, Marilu A

2013-01-01

Bookshelf (http://www.ncbi.nlm.nih.gov/books/) is a full-text electronic literature resource of books and documents in life sciences and health care at the National Center for Biotechnology Information (NCBI). Created in 1999 with a single book as an encyclopedic reference for resources such as PubMed and GenBank, it has grown to its current size of >1300 titles. Unlike other NCBI databases, such as GenBank and Gene, which have a strict data structure, books come in all forms; they are diverse in publication types, formats, sizes and authoring models. The Bookshelf data format is XML tagged in the NCBI Book DTD (Document Type Definition), modeled after the National Library of Medicine journal article DTDs. The book DTD has been used for systematically tagging the diverse data formats of books, a move that has set the foundation for the growth of this resource. Books at NCBI followed the route of journal articles in the PubMed Central project, using the PubMed Central architectural framework, workflows and processes. Through integration with other NCBI molecular databases, books at NCBI can be used to provide reference information for biological data and facilitate its discovery. This article describes Bookshelf at NCBI: its growth, data handling and retrieval and integration with molecular databases.

Integration of environmental simulation models with satellite remote sensing and geographic information systems technologies: case studies

USGS Publications Warehouse

Steyaert, Louis T.; Loveland, Thomas R.; Brown, Jesslyn F.; Reed, Bradley C.

1993-01-01

Environmental modelers are testing and evaluating a prototype land cover characteristics database for the conterminous United States developed by the EROS Data Center of the U.S. Geological Survey and the University of Nebraska Center for Advanced Land Management Information Technologies. This database was developed from multi temporal, 1-kilometer advanced very high resolution radiometer (AVHRR) data for 1990 and various ancillary data sets such as elevation, ecological regions, and selected climatic normals. Several case studies using this database were analyzed to illustrate the integration of satellite remote sensing and geographic information systems technologies with land-atmosphere interactions models at a variety of spatial and temporal scales. The case studies are representative of contemporary environmental simulation modeling at local to regional levels in global change research, land and water resource management, and environmental simulation modeling at local to regional levels in global change research, land and water resource management and environmental risk assessment. The case studies feature land surface parameterizations for atmospheric mesoscale and global climate models; biogenic-hydrocarbons emissions models; distributed parameter watershed and other hydrological models; and various ecological models such as ecosystem, dynamics, biogeochemical cycles, ecotone variability, and equilibrium vegetation models. The case studies demonstrate the important of multi temporal AVHRR data to develop to develop and maintain a flexible, near-realtime land cover characteristics database. Moreover, such a flexible database is needed to derive various vegetation classification schemes, to aggregate data for nested models, to develop remote sensing algorithms, and to provide data on dynamic landscape characteristics. The case studies illustrate how such a database supports research on spatial heterogeneity, land use, sensitivity analysis, and scaling issues involving regional extrapolations and parameterizations of dynamic land processes within simulation models.

Evaluation of the Content and Accessibility of Web Sites for Accredited Orthopaedic Trauma Surgery Fellowships.

PubMed

Shaath, M Kareem; Yeranosian, Michael G; Ippolito, Joseph A; Adams, Mark R; Sirkin, Michael S; Reilly, Mark C

2018-05-02

Orthopaedic trauma fellowship applicants use online-based resources when researching information on potential U.S. fellowship programs. The 2 primary sources for identifying programs are the Orthopaedic Trauma Association (OTA) database and the San Francisco Match (SF Match) database. Previous studies in other orthopaedic subspecialty areas have demonstrated considerable discrepancies among fellowship programs. The purpose of this study was to analyze content and availability of information on orthopaedic trauma surgery fellowship web sites. The online databases of the OTA and SF Match were reviewed to determine the availability of embedded program links or external links for the included programs. Thereafter, a Google search was performed for each program individually by typing the program's name, followed by the term "orthopaedic trauma fellowship." All identified fellowship web sites were analyzed for accessibility and content. Web sites were evaluated for comprehensiveness in mentioning key components of the orthopaedic trauma surgery curriculum. By consensus, we refined the final list of variables utilizing the methodology of previous studies on the topic. We identified 54 OTA-accredited fellowship programs, offering 87 positions. The majority (94%) of programs had web sites accessible through a Google search. Of the 51 web sites found, all (100%) described their program. Most commonly, hospital affiliation (88%), operative experiences (76%), and rotation overview (65%) were listed, and, least commonly, interview dates (6%), selection criteria (16%), on-call requirements (20%), and fellow evaluation criteria (20%) were listed. Programs with ≥2 fellows provided more information with regard to education content (p = 0.0001) and recruitment content (p = 0.013). Programs with Accreditation Council for Graduate Medical Education (ACGME) accreditation status also provided greater information with regard to education content (odds ratio, 4.0; p = 0.0001). Otherwise, no differences were seen by region, residency affiliation, medical school affiliation, or hospital affiliation. The SF Match and OTA databases provide few direct links to fellowship web sites. Individual program web sites do not effectively and completely convey information about the programs. The Internet is an underused resource for fellow recruitment. The lack of information on these sites allows for future opportunity to optimize this resource.

Saccharomyces genome database informs human biology

PubMed Central

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Karra, Kalpana; Binkley, Gail; Simison, Matt; Miyasato, Stuart R

2018-01-01

Abstract The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. PMID:29140510

Explore a Career in Health Sciences Information

MedlinePlus

... tools that range from traditional print journals to electronic databases and the latest mobile devices, health sciences ... an expert search of the literature. connecting licensed electronic resources and decision tools into a patient's electronic ...

UnCover on the Web: search hints and applications in library environments.

PubMed

Galpern, N F; Albert, K M

1997-01-01

Among the huge maze of resources available on the Internet, UnCoverWeb stands out as a valuable tool for medical libraries. This up-to-date, free-access, multidisciplinary database of periodical references is searched through an easy-to-learn graphical user interface that is a welcome improvement over the telnet version. This article reviews the basic and advanced search techniques for UnCoverWeb, as well as providing information on the document delivery functions and table of contents alerting service called Reveal. UnCover's currency is evaluated and compared with other current awareness resources. System deficiencies are discussed, with the conclusion that although UnCoverWeb lacks the sophisticated features of many commercial database search services, it is nonetheless a useful addition to the repertoire of information sources available in a library.

Carbonatites of the World, Explored Deposits of Nb and REE - Database and Grade and Tonnage Models

USGS Publications Warehouse

Berger, Vladimir I.; Singer, Donald A.; Orris, Greta J.

2009-01-01

This report is based on published tonnage and grade data on 58 Nb- and rare-earth-element (REE)-bearing carbonatite deposits that are mostly well explored and are partially mined or contain resources of these elements. The deposits represent only a part of the known 527 carbonatites around the world, but they are characterized by reliable quantitative data on ore tonnages and grades of niobium and REE. Grade and tonnage models are an important component of mineral resource assessments. Carbonatites present one of the main natural sources of niobium and rare-earth elements, the economic importance of which grows consistently. A purpose of this report is to update earlier publications. New information about known deposits, as well as data on new deposits published during the last decade, are incorporated in the present paper. The compiled database (appendix 1; linked to right) contains 60 explored Nb- and REE-bearing carbonatite deposits - resources of 55 of these deposits are taken from publications. In the present updated grade-tonnage model we have added 24 deposits comparing with the previous model of Singer (1998). Resources of most deposits are residuum ores in the upper part of carbonatite bodies. Mineral-deposit models are important in exploration planning and quantitative resource assessments for two reasons: (1) grades and tonnages among deposit types vary significantly, and (2) deposits of different types are present in distinct geologic settings that can be identified from geologic maps. Mineral-deposit models combine the diverse geoscience information on geology, mineral occurrences, geophysics, and geochemistry used in resource assessments and mineral exploration. Globally based deposit models allow recognition of important features and demonstrate how common different features are. Well-designed deposit models allow geologists to deduce possible mineral-deposit types in a given geologic environment, and the grade and tonnage models allow economists to estimate the possible economic viability of these resources. Thus, mineral-deposit models play a central role in presenting geoscience information in a useful form to policy makers. The foundation of mineral-deposit models is information about known deposits. This publication presents the latest geologic information and newly developed grade and tonnage models for Nb- and REE-carbonatite deposits in digital form. The publication contains computer files with information on deposits from around the world. It also contains a text file allowing locations of all deposits to be plotted in geographic information system (GIS) programs. The data are presented in FileMaker Pro as well as in .xls and text files to make the information available to a broadly based audience. The value of this information and any derived analyses depends critically on the consistent manner of data gathering. For this reason, we first discuss the rules used in this compilation. Next, the fields of the database are explained. Finally, we provide new grade and tonnage models and analysis of the information in the file.

Sagace: A web-based search engine for biomedical databases in Japan

PubMed Central

2012-01-01

Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

Hmrbase: a database of hormones and their receptors

PubMed Central

Rashid, Mamoon; Singla, Deepak; Sharma, Arun; Kumar, Manish; Raghava, Gajendra PS

2009-01-01

Background Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors. Description This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information. Conclusion Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from . PMID:19589147

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

Sandia National Laboratories/New Mexico Environmental Information Document - Volume 1

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

BAYLISS, LINDA S.; GUERRERO, JOSEPH V.; JOHNS, WILLIAM H.

This Sandia National Laboratories/New Mexico Environmental Information Document (EID) compiles information on the existing environment, or environmental baseline, for SNUNM. Much of the information is drawn from existing reports and databases supplemented by new research and data. The SNL/NM EID, together with the Sandia National Laboratories/New Mexico Facilities and Safety Information Document, provide a basis for assessing the environment, safety, and health aspects of operating selected facilities at SNL/NM. The environmental baseline provides a record of the existing physical, biological, and socioeconomic environment at SNL/NLM prior to being altered (beneficially or adversely) by proposed programs or projects. More specifically, themore » EID provides information on the following topics: Geology; Land Use; Hydrology and Water Resources; Air Quality and Meteorology; Ecology; Noise and Vibration; Cultural Resources; Visual Resources; Socioeconomic and Community Services; Transportation; Material Management; Waste Management; and Regulatory Requirements.« less

Resource for structure related information on transmembrane proteins

NASA Astrophysics Data System (ADS)

Tusnády, Gábor E.; Simon, István

Transmembrane proteins are involved in a wide variety of vital biological processes including transport of water-soluble molecules, flow of information and energy production. Despite significant efforts to determine the structures of these proteins, only a few thousand solved structures are known so far. Here, we review the various resources for structure-related information on these types of proteins ranging from the 3D structure to the topology and from the up-to-date databases to the various Internet sites and servers dealing with structure prediction and structure analysis. Abbreviations: 3D, three dimensional; PDB, Protein Data Bank; TMP, transmembrane protein.

[Computerization and the importance of information in health system, as in health care resources registry].

PubMed

Troselj, Mario; Fanton, Davor

2005-01-01

The possibilities of creating a health care resources registry and its operating in Croatia as well as the importance of information in health system are described. At the Croatian Institute of Public Health, monitoring of human resources is performed through the national Health Workers Registry. It also covers basic data on all health units, bed capacities of health facilities included. The initiated health care computerization has urged the idea of forming one more database on physical resources, i.e. on registered medical devices and equipment, more complete. Linking these databases on health resources would produce a single Health Care Resources Registry. The concept views Health Care Resources Registry as part of the overall health information system with centralized information on the health system. The planned development of segments of a single health information system is based on the implementation of the accepted international standards and common network services. Network services that are based on verified Internet technologies are used within a safe, reliable and closed health computer network, which makes up the health intranet (WAN--Wide Area Network). The resource registry is a software solution based on the relational database that monitors history, thus permitting the data collected over a longer period to be analyzed. Such a solution assumes the existence of a directory service, which would replace the current independent software for the Health Workers Registry. In the Health Care Resources Registry, the basic data set encompasses data objects and attributes from the directory service. The directory service is compatible with the LDAP protocol (Lightweight Directory Access Protocol), providing services uniformly to the current records on human and physical resources. Through the storage of attributes defined according to the HL7 (Health Level Seven) standard, directory service is accessible to all applications of the health information system. Directory service does not follow the history of attribute changes, and is optimized for a large number of authorizing inquiries. With it, one follows the following objects and attributes: persons, groups of people (patients, physicians, other personnel), roles (right of access and administrator permissions), organizational units, unit locations, devices and services (according to the list of services and procedures). One can add to the Health Care Resource Registry such attributes as are nonessential for inclusion in the directory service, but are of public health value. Authentication, authorization and digital signature are done by means of Smart Cards, which are used as protective elements against access to system functions, and simultaneously as a physical medium for the storage of the official certificate with which documents are signed digitally. As FINA (state financial control agency) has completed a system for certificate issuance and verification, the option of official digital signature is also available as a computer network service. Any changes taking place in the directory service are transferred by XML messages to a separate part of the Registry that reads them and automatically modifies records in the relational database. Because data input and data changes are made in health units, this makes the data updated and directly connected with health working operations. This avoids all one-time data collection campaigns using form filling about the devices and equipment in the future. As it is very difficult to monitor from a central standpoint how accurate and update the information is, it is necessary to delegate the permissions and duties associated with making changes to the directory service. By this organizational setup, the time needed to ensure data quality control is reduced. In the case described, the Health Care Resource Registry becomes an indicator of change, acquiring certain characteristics of an analytical system. An analysis of topical data renders possible proactive action and makes more effective the planning and utilization of available resources. Providing answers on the current data quickly could also be important to solution-seeking in emergencies. The present proposal to establish the Registry is intended to facilitate the future process of planning and striking a balance between investments in human and physical resources. For health expenditure control, having reliable information related to the use and purchase of new medical technology is particularly important. World Health Organization and European Union have also emphasized the need to develop new indicators in this area.

Genealogical databases as a tool for extending follow-up in clinical reviews.

PubMed

Ho, Thuy-Van; Chowdhury, Naweed; Kandl, Christopher; Hoover, Cindy; Robinson, Ann; Hoover, Larry

2016-08-01

Long-term follow-up in clinical reviews often presents significant difficulty with conventional medical records alone. Publicly accessible genealogical databases such as Ancestry.com provide another avenue for obtaining extended follow-up and added outcome information. No previous studies have described the use of genealogical databases in the follow-up of individual patients. Ancestry.com, the largest genealogical database in the United States, houses extensive demographic data on an increasing number of Americans. In a recent retrospective review of esthesioneuroblastoma patients treated at our institution, we used this resource to ascertain the outcomes of patients otherwise lost to follow-up. Additional information such as quality of life and supplemental treatments the patient may have received at home was obtained through direct contact with living relatives. The use of Ancestry.com resulted in a 25% increase (20 months) in follow-up duration as well as incorporation of an additional 7 patients in our study (18%) who would otherwise not have had adequate hospital chart data for inclusion. Many patients within this subset had more advanced disease or were remotely located from our institution. As such, exclusion of these outliers can impact the quality of subsequent outcome analysis. Online genealogical databases provide a unique resource of public information that is acceptable to institutional review boards for patient follow-up in clinical reviews. Utilization of Ancestry.com data led to significant improvement in follow-up duration and increased the number of patients with sufficient data that could be included in our retrospective study. © 2016 ARS-AAOA, LLC.

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database

PubMed Central

Drabkin, Harold J.; Blake, Judith A.

2012-01-01

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as ‘GO’ or ‘homology’ or ‘phenotype’. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as ‘papers selected for GO that refer to genes with NO GO annotation’. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications. PMID:23110975

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.

PubMed

Drabkin, Harold J; Blake, Judith A

2012-01-01

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as 'GO' or 'homology' or 'phenotype'. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as 'papers selected for GO that refer to genes with NO GO annotation'. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications.

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

PubMed

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

2011-10-01

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

ACToR Chemical Structure processing using Open Source ...

EPA Pesticide Factsheets

ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

GPCR & company: databases and servers for GPCRs and interacting partners.

PubMed

Kowalsman, Noga; Niv, Masha Y

2014-01-01

G-protein-coupled receptors (GPCRs) are a large superfamily of membrane receptors that are involved in a wide range of signaling pathways. To fulfill their tasks, GPCRs interact with a variety of partners, including small molecules, lipids and proteins. They are accompanied by different proteins during all phases of their life cycle. Therefore, GPCR interactions with their partners are of great interest in basic cell-signaling research and in drug discovery.Due to the rapid development of computers and internet communication, knowledge and data can be easily shared within the worldwide research community via freely available databases and servers. These provide an abundance of biological, chemical and pharmacological information.This chapter describes the available web resources for investigating GPCR interactions. We review about 40 freely available databases and servers, and provide a few sentences about the essence and the data they supply. For simplification, the databases and servers were grouped under the following topics: general GPCR-ligand interactions; particular families of GPCRs and their ligands; GPCR oligomerization; GPCR interactions with intracellular partners; and structural information on GPCRs. In conclusion, a multitude of useful tools are currently available. Summary tables are provided to ease navigation between the numerous and partially overlapping resources. Suggestions for future enhancements of the online tools include the addition of links from general to specialized databases and enabling usage of user-supplied template for GPCR structural modeling.

Spatial databases of the Humboldt Basin mineral resource assessment, northern Nevada

USGS Publications Warehouse

Mihalasky, Mark J.; Moyer, Lorre A.

2004-01-01

This report describes the origin, generation, and format of tract map databases for deposit types that accompany the metallic mineral resource assessment for the Humboldt River Basin, northern Nevada, (Wallace and others, 2004, Chapter 2). The deposit types include pluton-related polymetallic, sedimentary rock-hosted Au-Ag, and epithermal Au-Ag. The tract maps constitute only part of the assessment, which also includes new research and data for northern Nevada, discussions on land classification, and interpretation of the assessment maps. The purpose of the assessment was to identify areas that may have a greater favorability for undiscovered metallic mineral deposits, provide analysis of the mineral-resource favorability, and present the assessment of the Humboldt River basin and adjacent areas in a digital format using a Geographic Information System (GIS).

Astronaut Demographic Database: Everything You Want to Know About Astronauts and More

NASA Technical Reports Server (NTRS)

Keeton, Kathryn; Patterson, Holly

2011-01-01

A wealth of information regarding the astronaut population is available that could be especially useful to researchers. However, until now, it has been difficult to obtain that information in a systematic way. Therefore, this "astronaut database" began as a way for researchers within the Behavioral Health and Performance Group to keep track of the ever growing astronaut corps population. Before our effort, compilation of such data could be found, but not in a way that was easily acquired or accessible. One would have to use internet search engines, read through lengthy and potentially inaccurate informational sites, or read through astronaut biographies compiled by NASA. Astronauts are a unique class of individuals and, by examining such information, which we dubbed "Demographics," we hoped to find some commonalities that may be useful for other research areas and future research topics. By organizing the information pertaining to astronauts1 in a formal, unified catalog, we believe we have made the information more easily accessible, readily useable, and user friendly. Our end goal is to provide this database to others as a highly functional resource within the research community. Perhaps the database can eventually be an official, published document for researchers to gain full access.

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

Open Access Internet Resources for Nano-Materials Physics Education

NASA Astrophysics Data System (ADS)

Moeck, Peter; Seipel, Bjoern; Upreti, Girish; Harvey, Morgan; Garrick, Will

2006-05-01

Because a great deal of nano-material science and engineering relies on crystalline materials, materials physicists have to provide their own specific contributions to the National Nanotechnology Initiative. Here we briefly review two freely accessible internet-based crystallographic databases, the Nano-Crystallography Database (http://nanocrystallography.research.pdx.edu) and the Crystallography Open Database (http://crystallography.net). Information on over 34,000 full structure determinations are stored in these two databases in the Crystallographic Information File format. The availability of such crystallographic data on the internet in a standardized format allows for all kinds of web-based crystallographic calculations and visualizations. Two examples of which that are dealt with in this paper are: interactive crystal structure visualizations in three dimensions and calculations of lattice-fringe fingerprints for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

The Giardia genome project database.

PubMed

McArthur, A G; Morrison, H G; Nixon, J E; Passamaneck, N Q; Kim, U; Hinkle, G; Crocker, M K; Holder, M E; Farr, R; Reich, C I; Olsen, G E; Aley, S B; Adam, R D; Gillin, F D; Sogin, M L

2000-08-15

The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.

Impact of Local Resources on Hospitalization Patterns of Medicare Beneficiaries and Propensity to Travel outside Local Markets

ERIC Educational Resources Information Center

Basu, Jayasree; Mobley, Lee R.

2010-01-01

Purpose: To examine how local health care resources impact travel patterns of patients age 65 and older across the rural urban continuum. Methods: Information on inpatient hospital discharges was drawn from complete 2004 hospital discharge files from the Healthcare Cost and Utilization Project (HCUP) State Inpatient Databases (SID) for New York,…

Environmental security: a geographic information system analysis approach--the case of Kenya.

PubMed

Bocchi, Stefano; Disperati, Stefano Peppino; Rossi, Simone

2006-02-01

Studies into the relationships between environmental factors and violence or conflicts constitute a very debated research field called environmental security. Several authors think that environmental scarcity, which is scarcity of renewable resources, can contribute to generate violence or social unrest, particularly within states scarcely endowed with technical know-how and social structures, such as developing countries. In this work, we referred to the theoretical model developed by the Environmental Change and Acute Conflict Project. Our goal was to use easily available spatial databases to map the various sources of environmental scarcity through geographic information systems, in order to locate the areas apparently most at risk of suffering negative social effects and their consequences in terms of internal security. The analysis was carried out at a subnational level and applied to the case of Kenya. A first phase of the work included a careful selection of databases relative to renewable resources. Spatial operations among these data allowed us to obtain new information on the availability of renewable resources (cropland, forests, water), on the present and foreseen demographic pressure, as well as on the social and technical ingenuity. The results made it possible to identify areas suffering from scarcity of one or more renewable resources, indicating different levels of gravity. Accounts from Kenya seem to confirm our results, reporting clashes between tribal groups over the access to scarce resources in areas that our work showed to be at high risk.

Knowledge discovery through games and game theory

NASA Astrophysics Data System (ADS)

Smith, James F., III; Rhyne, Robert D.

2001-03-01

A fuzzy logic based expert system has been developed that automatically allocates electronic attack (EA) resources in real-time over many dissimilar platforms. The platforms can be very general, e.g., ships, planes, robots, land based facilities, etc. Potential foes the platforms deal with can also be general. The initial version of the algorithm was optimized using a genetic algorithm employing fitness functions constructed based on expertise. A new approach is being explored that involves embedding the resource manager in a electronic game environment. The game allows a human expert to play against the resource manager in a simulated battlespace with each of the defending platforms being exclusively directed by the fuzzy resource manager and the attacking platforms being controlled by the human expert or operating autonomously under their own logic. This approach automates the data mining problem. The game automatically creates a database reflecting the domain expert's knowledge, it calls a data mining function, a genetic algorithm, for data mining of the database as required. The game allows easy evaluation of the information mined in the second step. The measure of effectiveness (MOE) for re-optimization is discussed. The mined information is extremely valuable as shown through demanding scenarios.

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

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

PubMed

Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

2016-01-04

The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Latin American Social Medicine database

PubMed Central

Eldredge, Jonathan D; Waitzkin, Howard; Buchanan, Holly S; Teal, Janis; Iriart, Celia; Wiley, Kevin; Tregear, Jonathan

2004-01-01

Background Public health practitioners and researchers for many years have been attempting to understand more clearly the links between social conditions and the health of populations. Until recently, most public health professionals in English-speaking countries were unaware that their colleagues in Latin America had developed an entire field of inquiry and practice devoted to making these links more clearly understood. The Latin American Social Medicine (LASM) database finally bridges this previous gap. Description This public health informatics case study describes the key features of a unique information resource intended to improve access to LASM literature and to augment understanding about the social determinants of health. This case study includes both quantitative and qualitative evaluation data. Currently the LASM database at The University of New Mexico brings important information, originally known mostly within professional networks located in Latin American countries to public health professionals worldwide via the Internet. The LASM database uses Spanish, Portuguese, and English language trilingual, structured abstracts to summarize classic and contemporary works. Conclusion This database provides helpful information for public health professionals on the social determinants of health and expands access to LASM. PMID:15627401

Colorado Late Cenozoic Fault and Fold Database and Internet Map Server: User-friendly technology for complex information

USGS Publications Warehouse

Morgan, K.S.; Pattyn, G.J.; Morgan, M.L.

2005-01-01

Internet mapping applications for geologic data allow simultaneous data delivery and collection, enabling quick data modification while efficiently supplying the end user with information. Utilizing Web-based technologies, the Colorado Geological Survey's Colorado Late Cenozoic Fault and Fold Database was transformed from a monothematic, nonspatial Microsoft Access database into a complex information set incorporating multiple data sources. The resulting user-friendly format supports easy analysis and browsing. The core of the application is the Microsoft Access database, which contains information compiled from available literature about faults and folds that are known or suspected to have moved during the late Cenozoic. The database contains nonspatial fields such as structure type, age, and rate of movement. Geographic locations of the fault and fold traces were compiled from previous studies at 1:250,000 scale to form a spatial database containing information such as length and strike. Integration of the two databases allowed both spatial and nonspatial information to be presented on the Internet as a single dataset (http://geosurvey.state.co.us/pubs/ceno/). The user-friendly interface enables users to view and query the data in an integrated manner, thus providing multiple ways to locate desired information. Retaining the digital data format also allows continuous data updating and quick delivery of newly acquired information. This dataset is a valuable resource to anyone interested in earthquake hazards and the activity of faults and folds in Colorado. Additional geologic hazard layers and imagery may aid in decision support and hazard evaluation. The up-to-date and customizable maps are invaluable tools for researchers or the public.

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

Distribution System Upgrade Unit Cost Database

DOE Data Explorer

Horowitz, Kelsey

2017-11-30

This database contains unit cost information for different components that may be used to integrate distributed photovotaic (D-PV) systems onto distribution systems. Some of these upgrades and costs may also apply to integration of other distributed energy resources (DER). Which components are required, and how many of each, is system-specific and should be determined by analyzing the effects of distributed PV at a given penetration level on the circuit of interest in combination with engineering assessments on the efficacy of different solutions to increase the ability of the circuit to host additional PV as desired. The current state of the distribution system should always be considered in these types of analysis. The data in this database was collected from a variety of utilities, PV developers, technology vendors, and published research reports. Where possible, we have included information on the source of each data point and relevant notes. In some cases where data provided is sensitive or proprietary, we were not able to specify the source, but provide other information that may be useful to the user (e.g. year, location where equipment was installed). NREL has carefully reviewed these sources prior to inclusion in this database. Additional information about the database, data sources, and assumptions is included in the "Unit_cost_database_guide.doc" file included in this submission. This guide provides important information on what costs are included in each entry. Please refer to this guide before using the unit cost database for any purpose.

Assessment of COPD-related outcomes via a national electronic medical record database.

PubMed

Asche, Carl; Said, Quayyim; Joish, Vijay; Hall, Charles Oaxaca; Brixner, Diana

2008-01-01

The technology and sophistication of healthcare utilization databases have expanded over the last decade to include results of lab tests, vital signs, and other clinical information. This review provides an assessment of the methodological and analytical challenges of conducting chronic obstructive pulmonary disease (COPD) outcomes research in a national electronic medical records (EMR) dataset and its potential application towards the assessment of national health policy issues, as well as a description of the challenges or limitations. An EMR database and its application to measuring outcomes for COPD are described. The ability to measure adherence to the COPD evidence-based practice guidelines, generated by the NIH and HEDIS quality indicators, in this database was examined. Case studies, before and after their publication, were used to assess the adherence to guidelines and gauge the conformity to quality indicators. EMR was the only source of information for pulmonary function tests, but low frequency in ordering by primary care was an issue. The EMR data can be used to explore impact of variation in healthcare provision on clinical outcomes. The EMR database permits access to specific lab data and biometric information. The richness and depth of information on "real world" use of health services for large population-based analytical studies at relatively low cost render such databases an attractive resource for outcomes research. Various sources of information exist to perform outcomes research. It is important to understand the desired endpoints of such research and choose the appropriate database source.

The Histone Database: an integrated resource for histones and histone fold-containing proteins

PubMed Central

Mariño-Ramírez, Leonardo; Levine, Kevin M.; Morales, Mario; Zhang, Suiyuan; Moreland, R. Travis; Baxevanis, Andreas D.; Landsman, David

2011-01-01

Eukaryotic chromatin is composed of DNA and protein components—core histones—that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins. Database URL: The Histone Sequence Database is freely available and can be accessed at http://research.nhgri.nih.gov/histones/. PMID:22025671

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.

Use of national clinical databases for informing and for evaluating health care policies.

PubMed

Black, Nick; Tan, Stefanie

2013-02-01

Policy-makers and analysts could make use of national clinical databases either to inform or to evaluate meso-level (organisation and delivery of health care) and macro-level (national) policies. Reviewing the use of 15 of the best established databases in England, we identify and describe four published examples of each use. These show that policy-makers can either make use of the data itself or of research based on the database. For evaluating policies, the major advantages are the huge sample sizes available, the generalisability of the data, its immediate availability and historic information. The principal methodological challenges involve the need for risk adjustment and time-series analysis. Given their usefulness in the policy arena, there are several reasons why national clinical databases have not been used more, some due to a lack of 'push' by their custodians and some to the lack of 'pull' by policy-makers. Greater exploitation of these valuable resources would be facilitated by policy-makers' and custodians' increased awareness, minimisation of legal restrictions on data use, improvements in the quality of databases and a library of examples of applications to policy. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Building Information Literacy Using High Technology: A Guide for Schools and Libraries.

ERIC Educational Resources Information Center

Mendrinos, Roxanne

This guide to using the tools of online databases, telecommunications, and CD-ROM technology in the educational environment provides a practical introduction to the concepts and importance of information literacy and high technology resource-based learning. It also describes the drawbacks and advantages of these tools from an educator's viewpoint.…

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.

On the predictability of protein database search complexity and its relevance to optimization of distributed searches.

PubMed

Deciu, Cosmin; Sun, Jun; Wall, Mark A

2007-09-01

We discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as Linux cluster. Load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. The particular case of the Sequest program is considered here, but the general methodology should apply to any similar database search program. We show how the runtimes for Sequest searches of tandem mass spectral data can be predicted from profiles of previous representative searches, and how this information can be used for better load balancing of novel data. A well-known heuristic load balancing method is shown to be applicable to this problem, and its performance is analyzed for a variety of search parameters.

GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

PubMed Central

Samson, Delphine; Legeai, Fabrice; Karsenty, Emmanuelle; Reboux, Sébastien; Veyrieras, Jean-Baptiste; Just, Jeremy; Barillot, Emmanuel

2003-01-01

Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/. PMID:12519976

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.

PatGen--a consolidated resource for searching genetic patent sequences.

PubMed

Rouse, Richard J D; Castagnetto, Jesus; Niedner, Roland H

2005-04-15

Compared to the wealth of online resources covering genomic, proteomic and derived data the Bioinformatics community is rather underserved when it comes to patent information related to biological sequences. The current online resources are either incomplete or rather expensive. This paper describes, PatGen, an integrated database containing data from bioinformatic and patent resources. This effort addresses the inconsistency of publicly available genetic patent data coverage by providing access to a consolidated dataset. PatGen can be searched at http://www.patgendb.com rjdrouse@patentinformatics.com.

The new interactive CESAR

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

Fox, P.B.; Yatabe, M.

1987-01-01

In this report the Nuclear Criticality Safety Analytical Methods Resource Center describes a new interactive version of CESAR, a critical experiments storage and retrieval program available on the Nuclear Criticality Information System (NCIS) database at Lawrence Livermore National Laboratory. The original version of CESAR did not include interactive search capabilities. The CESAR database was developed to provide a convenient, readily accessible means of storing and retrieving code input data for the SCALE Criticality Safety Analytical Sequences and the codes comprising those sequences. The database includes data for both cross section preparation and criticality safety calculations. 3 refs., 1 tab.

SAbDab: the structural antibody database

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terry; Fuchs, Angelika; Georges, Guy; Shi, Jiye; Deane, Charlotte M.

2014-01-01

Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded. PMID:24214988

The MAR databases: development and implementation of databases specific for marine metagenomics.

PubMed

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

2018-01-04

We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

On a High-Performance VLSI Solution to Database Problems.

DTIC Science & Technology

1981-08-01

offer such attractive features as automatic verification and. maintenance of semantic integrity, usage of views as abstraction and authorization...course, is the waste of too much potential resource. The global database may contain information for many different users and applications. In processing...working on, this may cause no damage at all, but some waste of space. Therefore one solution may be perhaps to do nothing to prevent its occurrence

Recent improvements in the NASA technical report server

NASA Technical Reports Server (NTRS)

Maa, Ming-Hokng; Nelson, Michael L.

1995-01-01

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

Considerations of Online Numeric Databases for Social Science Research,

DTIC Science & Technology

1983-09-01

online user groups profit from them has greatly increased the size of the online market . International Resource Development says the revenues of...information services. Carlos Cuadra, however, feels that the customizers have been beneficial to the online market by educating users at a local level...calculations. Online data can sometimes assume a spurious authority due to the medium itself. "The market for numeric databases and systems is still

An open experimental database for exploring inorganic materials

DOE PAGES

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; ...

2018-04-03

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half ofmore » these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.« less

An open experimental database for exploring inorganic materials.

PubMed

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; Perkins, John D; White, Robert; Munch, Kristin; Tumas, William; Phillips, Caleb

2018-04-03

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.

An open experimental database for exploring inorganic materials

PubMed Central

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus; Perkins, John D.; White, Robert; Munch, Kristin; Tumas, William; Phillips, Caleb

2018-01-01

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource. PMID:29611842

An open experimental database for exploring inorganic materials

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

Zakutayev, Andriy; Wunder, Nick; Schwarting, Marcus

The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half ofmore » these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.« less

Literature Review and Database of Relations Between Salinity and Aquatic Biota: Applications to Bowdoin National Wildlife Refuge, Montana

USGS Publications Warehouse

Gleason, Robert A.; Tangen, Brian A.; Laubhan, Murray K.; Finocchiaro, Raymond G.; Stamm, John F.

2009-01-01

Long-term accumulation of salts in wetlands at Bowdoin National Wildlife Refuge (NWR), Mont., has raised concern among wetland managers that increasing salinity may threaten plant and invertebrate communities that provide important habitat and food resources for migratory waterfowl. Currently, the U.S. Fish and Wildlife Service (USFWS) is evaluating various water management strategies to help maintain suitable ranges of salinity to sustain plant and invertebrate resources of importance to wildlife. To support this evaluation, the USFWS requested that the U.S. Geological Survey (USGS) provide information on salinity ranges of water and soil for common plants and invertebrates on Bowdoin NWR lands. To address this need, we conducted a search of the literature on occurrences of plants and invertebrates in relation to salinity and pH of the water and soil. The compiled literature was used to (1) provide a general overview of salinity concepts, (2) document published tolerances and adaptations of biota to salinity, (3) develop databases that the USFWS can use to summarize the range of reported salinity values associated with plant and invertebrate taxa, and (4) perform database summaries that describe reported salinity ranges associated with plants and invertebrates at Bowdoin NWR. The purpose of this report is to synthesize information to facilitate a better understanding of the ecological relations between salinity and flora and fauna when developing wetland management strategies. A primary focus of this report is to provide information to help evaluate and address salinity issues at Bowdoin NWR; however, the accompanying databases, as well as concepts and information discussed, are applicable to other areas or refuges. The accompanying databases include salinity values reported for 411 plant taxa and 330 invertebrate taxa. The databases are available in Microsoft Excel version 2007 (http://pubs.usgs.gov/sir/2009/5098/downloads/databases_21april2009.xls) and contain 27 data fields that include variables such as taxonomic identification, values for salinity and pH, wetland classification, location of study, and source of data. The databases are not exhaustive of the literature and are biased toward wetland habitats located in the glaciated North-Central United States; however, the databases do encompass a diversity of biota commonly found in brackish and freshwater inland wetland habitats.

Putting the Pieces Together: Clinically Relevant Genetic and Genomic Resources for Hospitalists and Neonatologists.

PubMed

Miller, Rebecca; Khromykh, Alina; Babcock, Holly; Jenevein, Callie; Solomon, Benjamin D

2017-02-01

Genetic conditions are individually rare but are common in aggregate, and they often present in the neonatal and early pediatric periods. These conditions are often severe, can be difficult to diagnose and manage, and may heavily affect patients, families, health care systems, and society. Because of recent technological advances, the availability and uptake of genetic and genomic testing are increasing rapidly. However, there is a dearth of trained geneticists and genetic counselors to help guide and explain these conditions and relevant tests. To help hospitalists, neonatologists, and related practitioners navigate this complex and evolving field, we have compiled a list of free (mostly Web-based) resources relevant to the diagnosis and management of genetic conditions and related disorders. These resources, which we describe individually, can be useful for nongeneticist clinicians, and some also include material that can be used to explain concepts and conditions to patients or families. The resources presented are divided into the following categories (which overlap): general information, databases of genetic conditions, resources that can help generate differential diagnoses, databases of genetic testing laboratories (to help with logistics of ordering tests), information on newborn screening, and other resources. We also include a separate list of helpful textbooks and manuals. We conclude with 2 examples describing how some of these resources would be used by a pediatric hospitalist or neonatologist during the inpatient management of a child with a suspected genetic condition. Copyright © 2017 by the American Academy of Pediatrics.

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

PubMed Central

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

2011-01-01

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

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

PubMed

Huang, Weiliang; Brewer, Luke K; Jones, Jace W; Nguyen, Angela T; Marcu, Ana; Wishart, David S; Oglesby-Sherrouse, Amanda G; Kane, Maureen A; Wilks, Angela

2018-01-04

The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

BioMart Central Portal: an open database network for the biological community.

PubMed

Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

Generation and validation of a universal perinatal database and biospecimen repository: PeriBank.

PubMed

Antony, K M; Hemarajata, P; Chen, J; Morris, J; Cook, C; Masalas, D; Gedminas, M; Brown, A; Versalovic, J; Aagaard, K

2016-11-01

There is a dearth of biospecimen repositories available to perinatal researchers. In order to address this need, here we describe the methodology used to establish such a resource. With the collaboration of MedSci.net, we generated an online perinatal database with 847 fields of clinical information. Simultaneously, we established a biospecimen repository of the same clinical participants. The demographic and clinical outcomes data are described for the first 10 000 participants enrolled. The demographic characteristics are consistent with the demographics of the delivery hospitals. Quality analysis of the biospecimens reveals variation in very few analytes. Furthermore, since the creation of PeriBank, we have demonstrated validity of the database and tissue integrity of the biospecimen repository. Here we establish that the creation of a universal perinatal database and biospecimen collection is not only possible, but allows for the performance of state-of-the-science translational perinatal research and is a potentially valuable resource to academic perinatal researchers.

A systematic review of administrative and clinical databases of infants admitted to neonatal units.

PubMed

Statnikov, Yevgeniy; Ibrahim, Buthaina; Modi, Neena

2017-05-01

High quality information, increasingly captured in clinical databases, is a useful resource for evaluating and improving newborn care. We conducted a systematic review to identify neonatal databases, and define their characteristics. We followed a preregistered protocol using MesH terms to search MEDLINE, EMBASE, CINAHL, Web of Science and OVID Maternity and Infant Care Databases for articles identifying patient level databases covering more than one neonatal unit. Full-text articles were reviewed and information extracted on geographical coverage, criteria for inclusion, data source, and maternal and infant characteristics. We identified 82 databases from 2037 publications. Of the country-specific databases there were 39 regional and 39 national. Sixty databases restricted entries to neonatal unit admissions by birth characteristic or insurance cover; 22 had no restrictions. Data were captured specifically for 53 databases; 21 administrative sources; 8 clinical sources. Two clinical databases hold the largest range of data on patient characteristics, USA's Pediatrix BabySteps Clinical Data Warehouse and UK's National Neonatal Research Database. A number of neonatal databases exist that have potential to contribute to evaluating neonatal care. The majority is created by entering data specifically for the database, duplicating information likely already captured in other administrative and clinical patient records. This repetitive data entry represents an unnecessary burden in an environment where electronic patient records are increasingly used. Standardisation of data items is necessary to facilitate linkage within and between countries. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Municipal Emergency Management System: a strategy towards information and managing resources

NASA Astrophysics Data System (ADS)

Pacheco, J.

2009-04-01

The Azores archipelago is located in the North Atlantic Ocean, on a complex geological setting where the North American, Eurasian and African plates meet. Throughout its history the geological and meteorological hazards have been the most significant and had cause thousands of deaths and extensive damages. To prepare and mitigate the impact of catastrophic events there are emergency plans to guide the authorities and to instruct the population. However, a key point on the effectiveness of any emergency plan is the efficiency on getting the relevant information from the existing plans and conveying quality information to the operational teams and to the population. To address this issue the Municipal Emergency Management System was designed as a modular software with a core database and two different applications; one back-office to input and manage data and one front-end to query the database. The database is installed in a server and the system runs over an Intranet or the Internet, allowing its management and query to be done anywhere. The information on the system comprises two sets of data: (a) static data, regarding guidelines from the official Municipal Emergency Plan and a broad characterization of the county that does not need to be updated frequently (geography, geomorphology, climatology and the main hazards to consider) and (b) dynamic information, concerning data that requires regular updating such as available resources, administrative officials, pertinent private organisations etc.. All dynamic data in the core database is organised in three layers: (1) administrative organisations with geographical expression (such as province or district), (2) entities with capability to provide aid on provisions, accommodations, health, infrastructures, construction, transportation and security (public services, non-governmental organisations, enterprises or individual persons) and (3) operative information (applicable laws, tasks of each operative structure of the emergency plan) All entities are indexed to a geographic region, corresponding to an administrative organisation, and all the resources available on the county are indexed to an entity and ultimately to one identified person. The back-office operations are performed through a web browser. In order to ensure the quality of the data, the system requires the operator to register with a valid login and keeps a record of every operation performed by each registered user. The frontend also runs over a web browser and is the key vector towards an efficient communication with the operative teams and the general public. Its menu structure was designed to provide direct answers to the main questions raised on emergency situations, such as where dislodged population will be accommodate? How to transport them? How to provide provisions? Who has the provisions? How to contact the pertinent persons? The front-end, however, has two distinct access levels. The general public access level allows browsing through the structure of the emergency plan the identification of the public officials involved in the plan and their respective roles, and to get logistic information regarding meeting points, resources available, etc... The unlimited access is restricted to authorized personnel with a valid login and grants the access to report forms to be used during the emergency situations as well as information considered confidential such as providers of the available resources and their contacts. The outcome of the Municipal Emergency Management System is a light structure, accessible from anywhere and managed at municipal level, but with the potential to develop a network of emergency management nodes that can work cooperatively since each county can provide the surrounding counties with access to its database.

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.

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.

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.

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

Autophagic compound database: A resource connecting autophagy-modulating compounds, their potential targets and relevant diseases.

PubMed

Deng, Yiqi; Zhu, Lingjuan; Cai, Haoyang; Wang, Guan; Liu, Bo

2018-06-01

Autophagy, a highly conserved lysosomal degradation process in eukaryotic cells, can digest long-lived proteins and damaged organelles through vesicular trafficking pathways. Nowadays, mechanisms of autophagy have been gradually elucidated and thus the discovery of small-molecule drugs targeting autophagy has always been drawing much attention. So far, some autophagy-related web servers have been available online to facilitate scientists to obtain the information relevant to autophagy conveniently, such as HADb, CTLPScanner, iLIR server and ncRDeathDB. However, to the best of our knowledge, there is not any web server available about the autophagy-modulating compounds. According to published articles, all the compounds and their relations with autophagy were anatomized. Subsequently, an online Autophagic Compound Database (ACDB) (http://www.acdbliulab.com/) was constructed, which contained information of 357 compounds with 164 corresponding signalling pathways and potential targets in different diseases. We achieved a great deal of information of autophagy-modulating compounds, including compounds, targets/pathways and diseases. ACDB is a valuable resource for users to access to more than 300 curated small-molecule compounds correlated with autophagy. Autophagic compound database will facilitate to the discovery of more novel therapeutic drugs in the near future. © 2017 John Wiley & Sons Ltd.

UKPMC: a full text article resource for the life sciences.

PubMed

McEntyre, Johanna R; Ananiadou, Sophia; Andrews, Stephen; Black, William J; Boulderstone, Richard; Buttery, Paula; Chaplin, David; Chevuru, Sandeepreddy; Cobley, Norman; Coleman, Lee-Ann; Davey, Paul; Gupta, Bharti; Haji-Gholam, Lesley; Hawkins, Craig; Horne, Alan; Hubbard, Simon J; Kim, Jee-Hyub; Lewin, Ian; Lyte, Vic; MacIntyre, Ross; Mansoor, Sami; Mason, Linda; McNaught, John; Newbold, Elizabeth; Nobata, Chikashi; Ong, Ernest; Pillai, Sharmila; Rebholz-Schuhmann, Dietrich; Rosie, Heather; Rowbotham, Rob; Rupp, C J; Stoehr, Peter; Vaughan, Philip

2011-01-01

UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched as the first 'mirror' site to PMC, which in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide international preservation of the open and free-access biomedical literature. UKPMC (http://ukpmc.ac.uk) has undergone considerable development since its inception in 2007 and now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. Here we describe UKPMC and clarify the relationship between PMC and UKPMC, providing historical context and future directions, 10 years on from when PMC was first launched.

Data collection and compilation for a geodatabase of groundwater, surface-water, water-quality, geophysical, and geologic data, Pecos County Region, Texas, 1930-2011

USGS Publications Warehouse

Pearson, Daniel K.; Bumgarner, Johnathan R.; Houston, Natalie A.; Stanton, Gregory P.; Teeple, Andrew; Thomas, Jonathan V.

2012-01-01

The U.S. Geological Survey, in cooperation with Middle Pecos Groundwater Conservation District, Pecos County, City of Fort Stockton, Brewster County, and Pecos County Water Control and Improvement District No. 1, compiled groundwater, surface-water, water-quality, geophysical, and geologic data for site locations in the Pecos County region, Texas, and developed a geodatabase to facilitate use of this information. Data were compiled for an approximately 4,700 square mile area of the Pecos County region, Texas. The geodatabase contains data from 8,242 sampling locations; it was designed to organize and store field-collected geochemical and geophysical data, as well as digital database resources from the U.S. Geological Survey, Middle Pecos Groundwater Conservation District, Texas Water Development Board, Texas Commission on Environmental Quality,and numerous other State and local databases. The geodatabase combines these disparate database resources into a simple data model. Site locations are geospatially enabled and stored in a geodatabase feature class for cartographic visualization and spatial analysis within a Geographic Information System. The sampling locations are related to hydrogeologic information through the use of geodatabase relationship classes. The geodatabase relationship classes provide the ability to perform complex spatial and data-driven queries to explore data stored in the geodatabase.

UKPMC: a full text article resource for the life sciences

PubMed Central

McEntyre, Johanna R.; Ananiadou, Sophia; Andrews, Stephen; Black, William J.; Boulderstone, Richard; Buttery, Paula; Chaplin, David; Chevuru, Sandeepreddy; Cobley, Norman; Coleman, Lee-Ann; Davey, Paul; Gupta, Bharti; Haji-Gholam, Lesley; Hawkins, Craig; Horne, Alan; Hubbard, Simon J.; Kim, Jee-Hyub; Lewin, Ian; Lyte, Vic; MacIntyre, Ross; Mansoor, Sami; Mason, Linda; McNaught, John; Newbold, Elizabeth; Nobata, Chikashi; Ong, Ernest; Pillai, Sharmila; Rebholz-Schuhmann, Dietrich; Rosie, Heather; Rowbotham, Rob; Rupp, C. J.; Stoehr, Peter; Vaughan, Philip

2011-01-01

UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched as the first ‘mirror’ site to PMC, which in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide international preservation of the open and free-access biomedical literature. UKPMC (http://ukpmc.ac.uk) has undergone considerable development since its inception in 2007 and now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. UKPMC also differs from PubMed/PMC in that the full text and abstract information can be searched in an integrated manner from one input box. Furthermore, UKPMC contains ‘Cited By’ information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources. Finally, UKPMC also offers added-value services (UKPMC+) that enable grantees to deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. Here we describe UKPMC and clarify the relationship between PMC and UKPMC, providing historical context and future directions, 10 years on from when PMC was first launched. PMID:21062818

Using the TIGR gene index databases for biological discovery.

PubMed

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

Decision Support for Emergency Operations Centers

NASA Technical Reports Server (NTRS)

Harvey, Craig; Lawhead, Joel; Watts, Zack

2005-01-01

The Flood Disaster Mitigation Decision Support System (DSS) is a computerized information system that allows regional emergency-operations government officials to make decisions regarding the dispatch of resources in response to flooding. The DSS implements a real-time model of inundation utilizing recently acquired lidar elevation data as well as real-time data from flood gauges, and other instruments within and upstream of an area that is or could become flooded. The DSS information is updated as new data become available. The model generates realtime maps of flooded areas and predicts flood crests at specified locations. The inundation maps are overlaid with information on population densities, property values, hazardous materials, evacuation routes, official contact information, and other information needed for emergency response. The program maintains a database and a Web portal through which real-time data from instrumentation are gathered into the database. Also included in the database is a geographic information system, from which the program obtains the overlay data for areas of interest as needed. The portal makes some portions of the database accessible to the public. Access to other portions of the database is restricted to government officials according to various levels of authorization. The Flood Disaster Mitigation DSS has been integrated into a larger DSS named REACT (Real-time Emergency Action Coordination Tool), which also provides emergency operations managers with data for any type of impact area such as floods, fires, bomb

Determining the level of awareness of the physicians in using the variety of electronic information resources and the effecting factors.

PubMed

Papi, Ahmad; Ghazavi, Roghayeh; Moradi, Salimeh

2015-01-01

Understanding of the medical society's from the types of information resources for quick and easy access to information is an imperative task in medical researches and management of the treatment. The present study was aimed to determine the level of awareness of the physicians in using various electronic information resources and the factors affecting it. This study was a descriptive survey. The data collection tool was a researcher-made questionnaire. The study population included all the physicians and specialty physicians of the teaching hospitals affiliated to Isfahan University of Medical Sciences and numbered 350. The sample size based on Morgan's formula was set at 180. The content validity of the tool was confirmed by the library and information professionals and the reliability was 95%. Descriptive statistics were used including the SPSS software version 19. On reviewing the need of the physicians to obtain the information on several occasions, the need for information in conducting the researches was reported by the maximum number of physicians (91.9%) and the usage of information resources, especially the electronic resources, formed 65.4% as the highest rate with regard to meeting the information needs of the physicians. Among the electronic information databases, the maximum awareness was related to Medline with 86.5%. Among the various electronic information resources, the highest awareness (43.3%) was related to the E-journals. The highest usage (36%) was also from the same source. The studied physicians considered the most effective deterrent in the use of electronic information resources as being too busy and lack of time. Despite the importance of electronic information resources for the physician's community, there was no comprehensive knowledge of these resources. This can lead to less usage of these resources. Therefore, careful planning is necessary in the hospital libraries in order to introduce the facilities and full capabilities of the mentioned resources and methods of information retrieval.

The STEP (Safety and Toxicity of Excipients for Paediatrics) database: part 2 - the pilot version.

PubMed

Salunke, Smita; Brandys, Barbara; Giacoia, George; Tuleu, Catherine

2013-11-30

The screening and careful selection of excipients is a critical step in paediatric formulation development as certain excipients acceptable in adult formulations, may not be appropriate for paediatric use. While there is extensive toxicity data that could help in better understanding and highlighting the gaps in toxicity studies, the data are often scattered around the information sources and saddled with incompatible data types and formats. This paper is the second in a series that presents the update on the Safety and Toxicity of Excipients for Paediatrics ("STEP") database being developed by Eu-US PFIs, and describes the architecture data fields and functions of the database. The STEP database is a user designed resource that compiles the safety and toxicity data of excipients that is scattered over various sources and presents it in one freely accessible source. Currently, in the pilot database data from over 2000 references/10 excipients presenting preclinical, clinical, regulatory information and toxicological reviews, with references and source links. The STEP database allows searching "FOR" excipients and "BY" excipients. This dual nature of the STEP database, in which toxicity and safety information can be searched in both directions, makes it unique from existing sources. If the pilot is successful, the aim is to increase the number of excipients in the existing database so that a database large enough to be of practical research use will be available. It is anticipated that this source will prove to be a useful platform for data management and data exchange of excipient safety information. Copyright © 2013 Elsevier B.V. All rights reserved.

National parks. (Latest citations from the NTIS database). Published Search

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

Not Available

The bibliography contains citations concerning U.S. and foreign national parks. Citations discuss terrestrial biology, botany, coastal biology, fire ecology, endangered and exotic species, and resource analysis. Topics also include the impact of park visitors on natural resources in the parks, resource management, planning, and mapping. Information about specific parks including Rocky Mountain, Great Smoky Mountains, Redwood, Grand Canyon, Sequoia, Glacier Bay, and others is presented. (Contains a minimum of 55 citations and includes a subject term index and title list.)

Information-seeking behavior of health sciences faculty: the impact of new information technologies.

PubMed

Curtis, K L; Weller, A C; Hurd, J M

1997-10-01

This paper reports on an ongoing investigation into health sciences faculty's information-seeking behavior, including their use of new information technologies. A survey was administered to all faculty in medicine, nursing, and pharmacy at the University of Illinois at Chicago. It was similar to one administered to the same population in 1991. The survey asked about faculty's use of electronic resources, documented any shift from the use of print to electronic formats, and measured the utilization of library training. The response rate was 48.5% for medicine faculty, 45.0% for nursing, and 62.5% for pharmacy. The study found that use of the print Index Medicus among faculty was in transition: While 30.5% continued to use the print resources, 68.0% of faculty accessed MEDLINE through electronic means. Faculty preferred accessing electronic databases from their offices to doing so from the library. Health sciences faculty used a wide variety of databases, in addition to MEDLINE, to fill their information needs. Most faculty did not take advantage of either in-house or electronic training sessions offered by librarians. The study concluded that the training preferences of faculty need to be further explored.

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

PubMed Central

Mochida, Keiichi; Uehara-Yamaguchi, Yukiko; Takahashi, Fuminori; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo

2013-01-01

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops. PMID:24130698

A lake-centric geospatial database to guide research and inform management decisions in an Arctic watershed in northern Alaska experiencing climate and land-use changes

USGS Publications Warehouse

Jones, Benjamin M.; Arp, Christopher D.; Whitman, Matthew S.; Nigro, Debora A.; Nitze, Ingmar; Beaver, John; Gadeke, Anne; Zuck, Callie; Liljedahl, Anna K.; Daanen, Ronald; Torvinen, Eric; Fritz, Stacey; Grosse, Guido

2017-01-01

Lakes are dominant and diverse landscape features in the Arctic, but conventional land cover classification schemes typically map them as a single uniform class. Here, we present a detailed lake-centric geospatial database for an Arctic watershed in northern Alaska. We developed a GIS dataset consisting of 4362 lakes that provides information on lake morphometry, hydrologic connectivity, surface area dynamics, surrounding terrestrial ecotypes, and other important conditions describing Arctic lakes. Analyzing the geospatial database relative to fish and bird survey data shows relations to lake depth and hydrologic connectivity, which are being used to guide research and aid in the management of aquatic resources in the National Petroleum Reserve in Alaska. Further development of similar geospatial databases is needed to better understand and plan for the impacts of ongoing climate and land-use changes occurring across lake-rich landscapes in the Arctic.

The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data

PubMed Central

Wang, Norman; Sherwood, Alison R; Kurihara, Akira; Conklin, Kimberly Y; Sauvage, Thomas; Presting, Gernot G

2009-01-01

Background Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS). The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. Description We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. Conclusion The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at . PMID:19728892

CSPMS supported by information technology

NASA Astrophysics Data System (ADS)

Zhang, Hudan; Wu, Heng

This paper will propose a whole new viewpoint about building a CSPMS(Coal-mine Safety Production Management System) by means of information technology. This system whose core part is a four-grade automatic triggered warning system achieves the goal that information transmission will be smooth, nondestructive and in time. At the same time, the system provides a comprehensive and collective technology platform for various Public Management Organizations and coal-mine production units to deal with safety management, advance warning, unexpected incidents, preplan implementation, and resource deployment at different levels. The database of this system will support national related industry's resource control, plan, statistics, tax and the construction of laws and regulations effectively.

FARME DB: a functional antibiotic resistance element database

PubMed Central

Wallace, James C.; Port, Jesse A.; Smith, Marissa N.; Faustman, Elaine M.

2017-01-01

Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates. Database URL: http://staff.washington.edu/jwallace/farme PMID:28077567

Bundled payment reimbursement for anterior and posterior approaches for cervical spondylotic myelopathy: an analysis of private payer and Medicare databases.

PubMed

Virk, Sohrab S; Phillips, Frank M; Khan, Safdar N

2018-03-01

OBJECTIVE Cervical spondylotic myelopathy (CSM) is a progressive spinal condition that often requires surgery. Studies have shown the clinical equivalency of anterior versus posterior approaches for CSM surgery. The purpose of this study was to determine the amount and type of resources used for anterior and posterior surgical treatment of CSM by using large national databases of clinical and financial information from patients. METHODS This study consists of 2 large cohorts of patients who underwent either an anterior or posterior approach for treatment of CSM. These patients were selected from the Medicare 5% National Sample Administrative Database (SAF5) and the Humana orthopedic database (HORTHO), which is a database of patients with private payer health insurance. The outcome measures were the cost of a 90-day episode of care, as well as a breakdown of the cost components for each surgical procedure between 2005 and 2014. RESULTS A total of 16,444 patients were included in this analysis. In HORTHO, there were 10,332 and 1556 patients treated with an anterior or posterior approach for CSM, respectively. In SAF5, there were 3851 and 705 patients who were treated by an anterior or posterior approach for CSM, respectively. The mean ± SD reimbursements for anterior and posterior approaches in the HORTHO database were $20,863 ± $2014 and $23,813 ± $4258, respectively (p = 0.048). The mean ± SD reimbursements for anterior and posterior approaches in the SAF5 database were $18,219 ± $1053 and $25,598 ± $1686, respectively (p < 0.0001). There were also significantly higher reimbursements for a rehabilitation/skilled nursing facility and hospital/inpatient care for patients who underwent a posterior approach in both the private payer and Medicare databases. In all cohorts in this study, the hospital-related reimbursement was more than double the surgeon-related reimbursement. CONCLUSIONS This study provides resource utilization information for a 90-day episode of care for both anterior and posterior approaches for CSM surgery. There is a statistically significant higher resource utilization for patients undergoing the posterior approach for CSM, which is consistent with the literature. Understanding the reimbursement patterns for anterior versus posterior approaches for CSM will help providers design a bundled payment for patients requiring surgery for CSM, and this study suggests that a subset of patients who require the posterior approach for treatment also require greater resources. The data also suggest that hospital-related reimbursement is the major driver of payments.

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

PubMed Central

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

2015-01-01

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

Establishing a library of resources to help people understand key concepts in assessing treatment claims-The "Critical thinking and Appraisal Resource Library" (CARL).

PubMed

Castle, John C; Chalmers, Iain; Atkinson, Patricia; Badenoch, Douglas; Oxman, Andrew D; Austvoll-Dahlgren, Astrid; Nordheim, Lena; Krause, L Kendall; Schwartz, Lisa M; Woloshin, Steven; Burls, Amanda; Mosconi, Paola; Hoffmann, Tammy; Cusack, Leila; Albarqouni, Loai; Glasziou, Paul

2017-01-01

People are frequently confronted with untrustworthy claims about the effects of treatments. Uncritical acceptance of these claims can lead to poor, and sometimes dangerous, treatment decisions, and wasted time and money. Resources to help people learn to think critically about treatment claims are scarce, and they are widely scattered. Furthermore, very few learning-resources have been assessed to see if they improve knowledge and behavior. Our objectives were to develop the Critical thinking and Appraisal Resource Library (CARL). This library was to be in the form of a database containing learning resources for those who are responsible for encouraging critical thinking about treatment claims, and was to be made available online. We wished to include resources for groups we identified as 'intermediaries' of knowledge, i.e. teachers of schoolchildren, undergraduates and graduates, for example those teaching evidence-based medicine, or those communicating treatment claims to the public. In selecting resources, we wished to draw particular attention to those resources that had been formally evaluated, for example, by the creators of the resource or independent research groups. CARL was populated with learning-resources identified from a variety of sources-two previously developed but unmaintained inventories; systematic reviews of learning-interventions; online and database searches; and recommendations by members of the project group and its advisors. The learning-resources in CARL were organised by 'Key Concepts' needed to judge the trustworthiness of treatment claims, and were made available online by the James Lind Initiative in Testing Treatments interactive (TTi) English (www.testingtreatments.org/category/learning-resources).TTi English also incorporated the database of Key Concepts and the Claim Evaluation Tools developed through the Informed Healthcare Choices (IHC) project (informedhealthchoices.org). We have created a database of resources called CARL, which currently contains over 500 open-access learning-resources in a variety of formats: text, audio, video, webpages, cartoons, and lesson materials. These are aimed primarily at 'Intermediaries', that is, 'teachers', 'communicators', 'advisors', 'researchers', as well as for independent 'learners'. The resources included in CARL are currently accessible at www.testingtreatments.org/category/learning-resources. We hope that ready access to CARL will help to promote the critical thinking about treatment claims, needed to help improve healthcare choices.

Establishing a library of resources to help people understand key concepts in assessing treatment claims—The “Critical thinking and Appraisal Resource Library” (CARL)

PubMed Central

Chalmers, Iain; Atkinson, Patricia; Badenoch, Douglas; Oxman, Andrew D.; Austvoll-Dahlgren, Astrid; Nordheim, Lena; Krause, L. Kendall; Schwartz, Lisa M.; Woloshin, Steven; Burls, Amanda; Mosconi, Paola; Hoffmann, Tammy; Cusack, Leila; Albarqouni, Loai; Glasziou, Paul

2017-01-01

Background People are frequently confronted with untrustworthy claims about the effects of treatments. Uncritical acceptance of these claims can lead to poor, and sometimes dangerous, treatment decisions, and wasted time and money. Resources to help people learn to think critically about treatment claims are scarce, and they are widely scattered. Furthermore, very few learning-resources have been assessed to see if they improve knowledge and behavior. Objectives Our objectives were to develop the Critical thinking and Appraisal Resource Library (CARL). This library was to be in the form of a database containing learning resources for those who are responsible for encouraging critical thinking about treatment claims, and was to be made available online. We wished to include resources for groups we identified as ‘intermediaries’ of knowledge, i.e. teachers of schoolchildren, undergraduates and graduates, for example those teaching evidence-based medicine, or those communicating treatment claims to the public. In selecting resources, we wished to draw particular attention to those resources that had been formally evaluated, for example, by the creators of the resource or independent research groups. Methods CARL was populated with learning-resources identified from a variety of sources—two previously developed but unmaintained inventories; systematic reviews of learning-interventions; online and database searches; and recommendations by members of the project group and its advisors. The learning-resources in CARL were organised by ‘Key Concepts’ needed to judge the trustworthiness of treatment claims, and were made available online by the James Lind Initiative in Testing Treatments interactive (TTi) English (www.testingtreatments.org/category/learning-resources).TTi English also incorporated the database of Key Concepts and the Claim Evaluation Tools developed through the Informed Healthcare Choices (IHC) project (informedhealthchoices.org). Results We have created a database of resources called CARL, which currently contains over 500 open-access learning-resources in a variety of formats: text, audio, video, webpages, cartoons, and lesson materials. These are aimed primarily at ‘Intermediaries’, that is, ‘teachers’, ‘communicators’, ‘advisors’, ‘researchers’, as well as for independent ‘learners’. The resources included in CARL are currently accessible at www.testingtreatments.org/category/learning-resources Conclusions We hope that ready access to CARL will help to promote the critical thinking about treatment claims, needed to help improve healthcare choices. PMID:28738058

RatMap--rat genome tools and data.

PubMed

Petersen, Greta; Johnson, Per; Andersson, Lars; Klinga-Levan, Karin; Gómez-Fabre, Pedro M; Ståhl, Fredrik

2005-01-01

The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB-Genetics at Goteborg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. The database is under the supervision of the Rat Gene and Nomenclature Committee (RGNC); thus much attention is paid to rat gene nomenclature. RatMap presents information on rat idiograms, karyotypes and provides a unified presentation of the rat genome sequence and integrated rat linkage maps. A set of tools is also available to facilitate the identification and characterization of rat QTLs, as well as the estimation of exon/intron number and sizes in individual rat genes. Furthermore, comparative gene maps of rat in regard to mouse and human are provided.

RatMap—rat genome tools and data

PubMed Central

Petersen, Greta; Johnson, Per; Andersson, Lars; Klinga-Levan, Karin; Gómez-Fabre, Pedro M.; Ståhl, Fredrik

2005-01-01

The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB–Genetics at Göteborg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. The database is under the supervision of the Rat Gene and Nomenclature Committee (RGNC); thus much attention is paid to rat gene nomenclature. RatMap presents information on rat idiograms, karyotypes and provides a unified presentation of the rat genome sequence and integrated rat linkage maps. A set of tools is also available to facilitate the identification and characterization of rat QTLs, as well as the estimation of exon/intron number and sizes in individual rat genes. Furthermore, comparative gene maps of rat in regard to mouse and human are provided. PMID:15608244

PGMapper: a web-based tool linking phenotype to genes.

PubMed

Xiong, Qing; Qiu, Yuhui; Gu, Weikuan

2008-04-01

With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species. Available online at http://www.genediscovery.org/pgmapper/index.jsp.

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 ...

Development of a geotechnical information database.

DOT National Transportation Integrated Search

2009-08-01

The purpose of this project was to create a user-friendly geotechnical Web site, so the LADOTD Headquarters Geotechnical Design Section and other LADOTD sections will have access to the appropriate and necessary resources to make the best design d...

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.

NON-COMMUNITY WATER SYSTEMS DATABASE

EPA Science Inventory

Resource Purpose:Virtually every SIC code has some establishments which are classified as public water supplies under the SDWA. The survey (entering its design phase) will provide information on drinking water utilization and production at these establishments. With such...

Toxico-Cheminformatics: A New Frontier for Predictive Toxicology

EPA Science Inventory

The DSSTox database network and efforts to improve public access to chemical toxicity information resources, coupled with high-throughput screening (HTS) data and efforts to systematize legacy toxicity studies, have the potential to significantly improve predictive capabilities i...

The history of the CATH structural classification of protein domains.

PubMed

Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

2015-12-01

This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

ERIC Annual Report, 2002: Summarizing the Recent Accomplishments of the Educational Resources Information Center.

ERIC Educational Resources Information Center

Smarte, Lynn; Starcher, Heather

This ERIC Annual Report presents both accomplishments and historical perspectives, as 2001 marks 35 years of ERIC service in delivering educational research and information to the public. This annual report describes the developments in the database of educational literature, the growing variety of ERIC Web-based products and user services, and…

ISAAC: An Introduction to IBM's Information System for Advanced Academic Computing at the University of Washington-Seattle.

ERIC Educational Resources Information Center

Hernandez, Nicolas, Jr.

1988-01-01

Traces the origin of ISAAC (Information System for Advanced Academic Computing) and the development of a languages and linguistics "room" at the University of Washington-Seattle. ISAAC, a free, valuable resource, consists of two databases and an electronic bulletin board spanning broad areas of pedagogical and research fields. (Author/CB)

Indexing and Retrieval in ERIC: The 20th Year.

ERIC Educational Resources Information Center

Barnett, Lynn

This brief review of the Educational Resources Information Center (ERIC) system is intended to make users more aware of (1) the system as a whole, (2) the process of indexing educational literature for the database, and (3) the role of the Thesaurus of ERIC Descriptors in the overall information dissemination process. An overview of the ERIC…

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

Record linkage for pharmacoepidemiological studies in cancer patients.

PubMed

Herk-Sukel, Myrthe P P van; Lemmens, Valery E P P; Poll-Franse, Lonneke V van de; Herings, Ron M C; Coebergh, Jan Willem W

2012-01-01

An increasing need has developed for the post-approval surveillance of (new) anti-cancer drugs by means of pharmacoepidemiology and outcomes research in the area of oncology. To create an overview that makes researchers aware of the available database linkages in Northern America and Europe which facilitate pharmacoepidemiology and outcomes research in cancer patients. In addition to our own database, i.e. the Eindhoven Cancer Registry (ECR) linked to the PHARMO Record Linkage System, we considered database linkages between a population-based cancer registry and an administrative healthcare database that at least contains information on drug use and offers a longitudinal perspective on healthcare utilization. Eligible database linkages were limited to those that had been used in multiple published articles in English language included in Pubmed. The HMO Cancer Research Network (CRN) in the US was excluded from this review, as an overview of the linked databases participating in the CRN is already provided elsewhere. Researchers who had worked with the data resources included in our review were contacted for additional information and verification of the data presented in the overview. The following database linkages were included: the Surveillance, Epidemiology, and End-Results-Medicare; cancer registry data linked to Medicaid; Canadian cancer registries linked to population-based drug databases; the Scottish cancer registry linked to the Tayside drug dispensing data; linked databases in the Nordic Countries of Europe: Norway, Sweden, Finland and Denmark; and the ECR-PHARMO linkage in the Netherlands. Descriptives of the included database linkages comprise population size, generalizability of the population, year of first data availability, contents of the cancer registry, contents of the administrative healthcare database, the possibility to select a cancer-free control cohort, and linkage to other healthcare databases. The linked databases offer a longitudinal perspective, allowing for observations of health care utilization before, during, and after cancer diagnosis. They create new powerful data resources for the monitoring of post-approval drug utilization, as well as a framework to explore the (cost-)effectiveness of new, often expensive, anti-cancer drugs as used in everyday practice. Copyright © 2011 John Wiley & Sons, Ltd.

Medical Optimization Network for Space Telemedicine Resources

NASA Technical Reports Server (NTRS)

Rubin, D.; Shah, R. V.; Kerstman, E. L.; Reyes, D.; Mulcahy, R.; Antonsen, E.

2017-01-01

INTRODUCTION: Long-duration missions beyond low Earth orbit introduce new constraints to the space medical system. Beyond the traditional limitations in mass, power, and volume, consideration must be given to other factors such as the inability to evacuate to Earth, communication delays, and limitations in clinical skillsets. As NASA develops the medical system for an exploration mission, it must have an ability to evaluate the trade space of what resources will be most important. The Medical Optimization Network for Space Telemedicine Resources (MONSTR) was developed over the past year for this reason, and is now a system for managing data pertaining to medical resources and their relative importance when addressing medical conditions. METHODS: The MONSTR web application with a Microsoft SQL database backend was developed and made accessible to Tableau v9.3 for analysis and visualization. The database was initially populated with a list of medical conditions of concern for an exploration mission taken from the Integrated Medical Model (IMM), a probabilistic model designed to quantify in-flight medical risk. A team of physicians working within the Exploration Medical Capability Element of NASA's Human Research Program compiled a list diagnostic and treatment medical resources required to address best- and worst-case scenarios of each medical condition using a terrestrial standard of care and entered this data into the system. This list included both tangible resources (e.g. medical equipment, medications) and intangible resources (e.g. clinical skills required to perform a procedure). The physician team then assigned criticality values to each instance of a resource, representing the importance of that resource to diagnosing or treating its associated condition(s). Medical condition probabilities of occurrence during a Mars mission were pulled from the IMM and imported into the MONSTR database for use within a resource criticality-weighting algorithm. DISCUSSION: The MONSTR tool is a novel approach to assess the relative value of individual resources needed for the diagnosis and treatment of medical conditions. Future work will add resources for prevention and long term care of these conditions. Once data collection is complete, MONSTR will provide the operational and research communities at NASA with information to support informed decisions regarding areas of research investment, future crew training, and medical supplies manifested as part of any exploration medical system.

EPA Facility Registry Service (FRS): Facility Interests Dataset - Intranet

EPA Pesticide Factsheets

This web feature service consists of location and facility identification information from EPA's Facility Registry Service (FRS) for all sites that are available in the FRS individual feature layers. The layers comprise the FRS major program databases, including:Assessment Cleanup and Redevelopment Exchange System (ACRES) : brownfields sites ; Air Facility System (AFS) : stationary sources of air pollution ; Air Quality System (AQS) : ambient air pollution data from monitoring stations; Bureau of Indian Affairs (BIA) : schools data on Indian land; Base Realignment and Closure (BRAC) facilities; Clean Air Markets Division Business System (CAMDBS) : market-based air pollution control programs; Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) : hazardous waste sites; Integrated Compliance Information System (ICIS) : integrated enforcement and compliance information; National Compliance Database (NCDB) : Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Toxic Substances Control Act (TSCA); National Pollutant Discharge Elimination System (NPDES) module of ICIS : NPDES surface water permits; Radiation Information Database (RADINFO) : radiation and radioactivity facilities; RACT/BACT/LAER Clearinghouse (RBLC) : best available air pollution technology requirements; Resource Conservation and Recovery Act Information System (RCRAInfo) : tracks generators, transporters, treaters, storers, and disposers of haz

EPA Facility Registry Service (FRS): Facility Interests Dataset - Intranet Download

EPA Pesticide Factsheets

This downloadable data package consists of location and facility identification information from EPA's Facility Registry Service (FRS) for all sites that are available in the FRS individual feature layers. The layers comprise the FRS major program databases, including:Assessment Cleanup and Redevelopment Exchange System (ACRES) : brownfields sites ; Air Facility System (AFS) : stationary sources of air pollution ; Air Quality System (AQS) : ambient air pollution data from monitoring stations; Bureau of Indian Affairs (BIA) : schools data on Indian land; Base Realignment and Closure (BRAC) facilities; Clean Air Markets Division Business System (CAMDBS) : market-based air pollution control programs; Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) : hazardous waste sites; Integrated Compliance Information System (ICIS) : integrated enforcement and compliance information; National Compliance Database (NCDB) : Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Toxic Substances Control Act (TSCA); National Pollutant Discharge Elimination System (NPDES) module of ICIS : NPDES surface water permits; Radiation Information Database (RADINFO) : radiation and radioactivity facilities; RACT/BACT/LAER Clearinghouse (RBLC) : best available air pollution technology requirements; Resource Conservation and Recovery Act Information System (RCRAInfo) : tracks generators, transporters, treaters, storers, and disposers

EPA Facility Registry Service (FRS): Facility Interests Dataset Download

EPA Pesticide Factsheets

This downloadable data package consists of location and facility identification information from EPA's Facility Registry Service (FRS) for all sites that are available in the FRS individual feature layers. The layers comprise the FRS major program databases, including:Assessment Cleanup and Redevelopment Exchange System (ACRES) : brownfields sites ; Air Facility System (AFS) : stationary sources of air pollution ; Air Quality System (AQS) : ambient air pollution data from monitoring stations; Bureau of Indian Affairs (BIA) : schools data on Indian land; Base Realignment and Closure (BRAC) facilities; Clean Air Markets Division Business System (CAMDBS) : market-based air pollution control programs; Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) : hazardous waste sites; Integrated Compliance Information System (ICIS) : integrated enforcement and compliance information; National Compliance Database (NCDB) : Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Toxic Substances Control Act (TSCA); National Pollutant Discharge Elimination System (NPDES) module of ICIS : NPDES surface water permits; Radiation Information Database (RADINFO) : radiation and radioactivity facilities; RACT/BACT/LAER Clearinghouse (RBLC) : best available air pollution technology requirements; Resource Conservation and Recovery Act Information System (RCRAInfo) : tracks generators, transporters, treaters, storers, and disposers

EPA Facility Registry Service (FRS): Facility Interests Dataset

EPA Pesticide Factsheets

This web feature service consists of location and facility identification information from EPA's Facility Registry Service (FRS) for all sites that are available in the FRS individual feature layers. The layers comprise the FRS major program databases, including:Assessment Cleanup and Redevelopment Exchange System (ACRES) : brownfields sites ; Air Facility System (AFS) : stationary sources of air pollution ; Air Quality System (AQS) : ambient air pollution data from monitoring stations; Bureau of Indian Affairs (BIA) : schools data on Indian land; Base Realignment and Closure (BRAC) facilities; Clean Air Markets Division Business System (CAMDBS) : market-based air pollution control programs; Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) : hazardous waste sites; Integrated Compliance Information System (ICIS) : integrated enforcement and compliance information; National Compliance Database (NCDB) : Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Toxic Substances Control Act (TSCA); National Pollutant Discharge Elimination System (NPDES) module of ICIS : NPDES surface water permits; Radiation Information Database (RADINFO) : radiation and radioactivity facilities; RACT/BACT/LAER Clearinghouse (RBLC) : best available air pollution technology requirements; Resource Conservation and Recovery Act Information System (RCRAInfo) : tracks generators, transporters, treaters, storers, and disposers of haz

Evaluation of Online Information Sources on Alien Species in Europe: The Need of Harmonization and Integration

NASA Astrophysics Data System (ADS)

Gatto, Francesca; Katsanevakis, Stelios; Vandekerkhove, Jochen; Zenetos, Argyro; Cardoso, Ana Cristina

2013-06-01

Europe is severely affected by alien invasions, which impact biodiversity, ecosystem services, economy, and human health. A large number of national, regional, and global online databases provide information on the distribution, pathways of introduction, and impacts of alien species. The sufficiency and efficiency of the current online information systems to assist the European policy on alien species was investigated by a comparative analysis of occurrence data across 43 online databases. Large differences among databases were found which are partially explained by variations in their taxonomical, environmental, and geographical scopes but also by the variable efforts for continuous updates and by inconsistencies on the definition of "alien" or "invasive" species. No single database covered all European environments, countries, and taxonomic groups. In many European countries national databases do not exist, which greatly affects the quality of reported information. To be operational and useful to scientists, managers, and policy makers, online information systems need to be regularly updated through continuous monitoring on a country or regional level. We propose the creation of a network of online interoperable web services through which information in distributed resources can be accessed, aggregated and then used for reporting and further analysis at different geographical and political scales, as an efficient approach to increase the accessibility of information. Harmonization, standardization, conformity on international standards for nomenclature, and agreement on common definitions of alien and invasive species are among the necessary prerequisites.

Identification of contaminant trends and data gaps for terrestrial vertebrates residing in northeastern estuaries of the United States

USGS Publications Warehouse

Rattner, B.A.; Pearson, J.L.; Golden, N.H.; Erwin, R.M.; Ottinger, M.A.

1998-01-01

The Biomonitoring of Environmental Status and Trends (BEST) program of the Department of the Interior is focused to identify and understand effects of contaminant stressors on biological resources under their stewardship. One BEST program activity involves evaluation of retrospective data to assess and predict the condition of biota in Atlantic coast estuaries. A 'Contaminant Exposure and Effects--Terrestrial Vertebrates' database (CEE-TV) has been compiled through computerized literature searches of Fish and Wildlife Reviews, BIOSIS, AGRICOLA, and TOXLINE, review of existing databases (e.g., US EPA Ecological Incident Information System, USGS Diagnostic and Epizootic Databases), and solicitation of unpublished reports from conservation agencies, private groups, and universities. Summary information has been entered into the CEE-TV database, including species, collection date (1965-present), site coordinates, sample matrix, contaminant concentrations, biomarker and bioindicator responses, and reference source, utilizing a 96-field dBase format. Currently, the CEE-TV database contains 3500 georeferenced records representing >200 vertebrate species and > 100,000 individuals residing in estuaries from Maine through Florida. This relational database can be directly queried, imported into the ARC/INFO geographic information system (GIS) to examine spatial tendencies, and used to identify 'hot-spots', generate hypotheses, and focus ecotoxicological assessments. An overview of temporal, phylogenetic, and geographic contaminant exposure and effects information, trends, and data gaps will be presented for terrestrial vertebrates residing in estuaries in the northeast United States.

Fifteen hundred guidelines and growing: the UK database of clinical guidelines.

PubMed

van Loo, John; Leonard, Niamh

2006-06-01

The National Library for Health offers a comprehensive searchable database of nationally approved clinical guidelines, called the Guidelines Finder. This resource, commissioned in 2002, is managed and developed by the University of Sheffield Health Sciences Library. The authors introduce the historical and political dimension of guidelines and the nature of guidelines as a mechanism to ensure clinical effectiveness in practice. The article then outlines the maintenance and organisation of the Guidelines Finder database itself, the criteria for selection, who publishes guidelines and guideline formats, usage of the Guidelines Finder service and finally looks at some lessons learnt from a local library offering a national service. Clinical guidelines are central to effective clinical practice at the national, organisational and individual level. The Guidelines Finder is one of the most visited resources within the National Library for Health and is successful in answering information needs related to specific patient care, clinical research, guideline development and education.

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

America's Changing Energy Landscape - USGS National Coal Resources Data System Changes to National Energy Resources Data System.

NASA Astrophysics Data System (ADS)

East, J. A., II

2016-12-01

The U.S. Geological Survey's (USGS) Eastern Energy Resources Science Center (EERSC) has an ongoing project which has mapped coal chemistry and stratigraphy since 1977. Over the years, the USGS has collected various forms of coal data and archived that data into the National Coal Resources Data System (NCRDS) database. NCRDS is a repository that houses data from the major coal basins in the United States and includes information on location, seam thickness, coal rank, geologic age, geographic region, geologic province, coalfield, and characteristics of the coal or lithology for that data point. These data points can be linked to the US Coal Quality Database (COALQUAL) to include ultimate, proximate, major, minor and trace-element data. Although coal is an inexpensive energy provider, the United States has shifted away from coal usage recently and branched out into other forms of non-renewable and renewable energy because of environmental concerns. NCRDS's primary method of data capture has been USGS field work coupled with cooperative agreements with state geological agencies and universities doing coal-related research. These agreements are on competitive five-year cycles that have evolved into larger scope research efforts including solid fuel resources such as coal-bed methane, shale gas and oil. Recently these efforts have expanded to include environmental impacts of the use of fossil fuels, which has allowed the USGS to enter into agreements with states for the Geologic CO2 Storage Resources Assessment as required by the Energy Independence and Security Act. In 2016 they expanded into research areas to include geothermal, conventional and unconventional oil and gas. The NCRDS and COALQUAL databases are now online for the public to use, and are in the process of being updated to include new data for other energy resources. Along with this expansion of scope, the database name will change to the National Energy Resources Data System (NERDS) in FY 2017.

Saccharomyces genome database informs human biology.

PubMed

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

2018-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The data operation centre tool. Architecture and population strategies

NASA Astrophysics Data System (ADS)

Dal Pra, Stefano; Crescente, Alberto

2012-12-01

Keeping track of the layout of the informatic resources in a big datacenter is a complex task. DOCET is a database-based webtool designed and implemented at INFN. It aims at providing a uniform interface to manage and retrieve needed information about one or more datacenter, such as available hardware, software and their status. Having a suitable application is however useless until most of the information about the centre are not inserted in the DOCET'S database. Manually inserting all the information from scratch is an unfeasible task. After describing DOCET'S high level architecture, its main features and current development track, we present and discuss the work done to populate the DOCET database for the INFN-T1 site by retrieving information from a heterogenous variety of authoritative sources, such as DNS, DHCP, Quattor host profiles, etc. We then describe the work being done to integrate DOCET with some common management operation, such as adding a newly installed host to DHCP and DNS, or creating a suitable Quattor profile template for it.

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.

Water-Related Power Plant Curtailments: An Overview of Incidents and Contributing Factors

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

McCall, James; Macknick, Jordan; Macknick, Jordan

Water temperatures and water availability can affect the reliable operations of power plants in the United States. Data on water-related impacts on the energy sector are not consolidated and are reported by multiple agencies. This study provides an overview of historical incidents where water resources have affected power plant operations, discusses the various data sources providing information, and creates a publicly available and open access database that contains consolidated information about water-related power plant curtailment and shut-down incidents. Power plants can be affected by water resources if incoming water temperatures are too high, water discharge temperatures are too high, ormore » if there is not enough water available to operate. Changes in climate have the potential to exacerbate uncertainty over water resource availability and temperature. Power plant impacts from water resources include curtailment of generation, plant shut-downs, and requests for regulatory variances. In addition, many power plants have developed adaptation approaches to reducing the potential risks of water-related issues by investing in new technologies or developing and implementing plans to undertake during droughts or heatwaves. This study identifies 42 incidents of water-related power plant issues from 2000-2015, drawing from a variety of different datasets. These incidents occur throughout the U.S., and affect coal and nuclear plants that use once-through, recirculating, and pond cooling systems. In addition, water temperature violations reported to the Environmental Protection Agency are also considered, with 35 temperature violations noted from 2012-2015. In addition to providing some background information on incidents, this effort has also created an open access database on the Open Energy Information platform that contains information about water-related power plant issues that can be updated by users.« less

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

Abbott, Jennifer; Sandberg, Tami

The Wind-Wildlife Impacts Literature Database (WILD), formerly known as the Avian Literature Database, was created in 1997. The goal of the database was to begin tracking the research that detailed the potential impact of wind energy development on birds. The Avian Literature Database was originally housed on a proprietary platform called Livelink ECM from Open- Text and maintained by in-house technical staff. The initial set of records was added by library staff. A vital part of the newly launched Drupal-based WILD database is the Bibliography module. Many of the resources included in the database have digital object identifiers (DOI). Themore » bibliographic information for any item that has a DOI can be imported into the database using this module. This greatly reduces the amount of manual data entry required to add records to the database. The content available in WILD is international in scope, which can be easily discerned by looking at the tags available in the browse menu.« less

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

PubMed Central

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S.

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome PMID:26980518

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. 'Fish Karyome' database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome. © The Author(s) 2016. Published by Oxford University Press.

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.

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.

Online access to international aerospace science and technology

NASA Technical Reports Server (NTRS)

Lahr, Thomas F.; Harrison, Laurie K.

1993-01-01

The NASA Aerospace Database contains over 625,000 foreign R&D documents from 1962 to the present from over 60 countries worldwide. In 1991 over 26,000 new non-U.S. entries were added from a variety of innovative exchange programs. An active international acquisitions effort by the NASA STI Program seeks to increase the percentage of foreign data in the coming years, focusing on Japan, the Commonwealth of Independent States, Western Europe, Australia, and Canada. It also has plans to target China, India, Brazil, and Eastern Europe in the future. The authors detail the resources the NASA Aerospace Database offers in the international arena, the methods used to gather this information, and the STI Program's initiatives for maintaining and expanding the percentage of international information in this database.

[Design and implementation of mobile terminal data acquisition for Chinese materia medica resources survey].

PubMed

Qi, Yuan-Hua; Wang, Hui; Zhang, Xiao-Bo; Jin, Yan; Ge, Xiao-Guang; Jing, Zhi-Xian; Wang, Ling; Zhao, Yu-Ping; Guo, Lan-Ping; Huang, Lu-Qi

2017-11-01

In this paper, a data acquisition system based on mobile terminal combining GPS, offset correction, automatic speech recognition and database networking technology was designed implemented with the function of locating the latitude and elevation information fast, taking conveniently various types of Chinese herbal plant photos, photos, samples habitat photos and so on. The mobile system realizes automatic association with Chinese medicine source information, through the voice recognition function it records the information of plant characteristics and environmental characteristics, and record relevant plant specimen information. The data processing platform based on Chinese medicine resources survey data reporting client can effectively assists in indoor data processing, derives the mobile terminal data to computer terminal. The established data acquisition system provides strong technical support for the fourth national survey of the Chinese materia medica resources (CMMR). Copyright© by the Chinese Pharmaceutical Association.

CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

PubMed

Paananen, Jussi; Storvik, Markus; Wong, Garry

2006-09-22

Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies. We have developed a web-based software resource, called CROPPER that uses the latest genomic information concerning different data identifiers and orthologous genes from the Ensembl database. CROPPER can be used to combine genomic data from different heterogeneous sources, allowing researchers to perform cross-platform/cross-species compendium studies without the need for complex computational tools or the requirement of setting up one's own in-house database. We also present an example of a simple cross-platform/cross-species compendium study based on publicly available Parkinson's disease data derived from different sources. CROPPER is a user-friendly and freely available web-based software resource that can be successfully used for cross-species/cross-platform compendium studies.

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.

Basic Concepts, Current Practices and Available Resources for Forensic Investigations on Pavements

DOT National Transportation Integrated Search

1997-09-01

The purpose of the project, entitled Development of a Methodology for Identifying Pavement Design and Construction Data Needed to Support a Forensic Investigation," is to develop a database containing information useful in identifying the premature f...

Mapping Indigenous Depth of Place

ERIC Educational Resources Information Center

Pearce, Margaret Wickens; Louis, Renee Pualani

2008-01-01

Indigenous communities have successfully used Western geospatial technologies (GT) (for example, digital maps, satellite images, geographic information systems (GIS), and global positioning systems (GPS)) since the 1970s to protect tribal resources, document territorial sovereignty, create tribal utility databases, and manage watersheds. The use…

Information needs of health technology assessment units and agencies in Spain.

PubMed

Galnares-Cordero, Lorea; Gutiérrez-Ibarluzea, Iñaki

2010-10-01

The aim of this study was to analyze the information needs of Spanish health technology assessment (HTA) agencies and units to facilitate access to the resources they require to substantiate their reports. A questionnaire was designed and distributed among HTA bodies to ascertain the actual situation of subscriptions to information resources and what information specialists from these bodies considered would be the ideal subscription situation. Their information needs were then studied, and the resources that best met these needs were put forward. Following this definition, a subscriptions policy was adopted with suppliers and publishers. The survey showed that HTA bodies share a minimum of core subscriptions that includes open sources (MEDLINE, DARE) and sources that the government subscribes to for the health community (ISI Web of Science, Cochrane Library Plus). There was no common approach to determining which databases to subscribe to (UpToDate, EMBASE, Ovid EBMR, CINAHL, or ECRI). After identifying the information needs, a list of resources was proposed that would best cover these needs and, of these, subscription to the following was proposed: Scopus, Ovid EBMR, Clinical Evidence, DynaMed, ECRI, and Hayes. There are differences in the way that HTA agencies and units access the different resources of biomedical information. Combined subscription to several resources for documentation services was suggested as a way of resolving these differences.

Nevada low-temperaure geothermal resource assessment: 1994. Final report

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

Garside, L.J.

Data compilation for the low-temperature program is being done by State Teams in two western states. Final products of the study include: a geothermal database, in hardcopy and as digital data (diskette) listing information on all known low- and moderate- temperature springs and wells in Nevada; a 1:1,000,000-scale map displaying these geothermal localities, and a bibliography of references on Nevada geothermal resources.