Searching fee and non-fee toxicology information resources: an overview of selected databases.

PubMed

Wright, L L

2001-01-12

Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.

Database Resources of the BIG Data Center in 2018

PubMed Central

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

2018-01-01

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

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

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

Mexican Art and Architecture Databases: Needs, Achievements, Problems.

ERIC Educational Resources Information Center

Barberena, Elsa

At the international level, a lack of diffusion of Mexican art and architecture in indexes and abstracts has been detected. Reasons for this could be lack of continuity in publications, the use of the Spanish language, lack of interest in Mexican art and architecture, and sporadic financial resources. Nevertheless, even though conditions are not…

Increasing access to Latin American social medicine resources: a preliminary report.

PubMed

Buchanan, Holly Shipp; Waitzkin, Howard; Eldredge, Jonathan; Davidson, Russ; Iriart, Celia; Teal, Janis

2003-10-01

This preliminary report describes the development and implementation of a project to improve access to literature in Latin American social medicine (LASM). The University of New Mexico project team collaborated with participants from Argentina, Brazil, Chile, and Ecuador to identify approximately 400 articles and books in Latin American social medicine. Structured abstracts were prepared, translated into English, Spanish, and Portuguese, assigned Medical Subject Headings (MeSH), and loaded into a Web-based database for public searching. The project has initiated Web-based publication for two LASM journals. Evaluation included measures of use and content. The LASM Website (http://hsc.unm.edu/lasm) and database create access to formerly little-known literature that addresses problems relevant to current medicine and public health. This Website offers a unique resource for researchers, practitioners, and teachers who seek to understand the links between socioeconomic conditions and health. The project provides a model for collaboration between librarians and health care providers. Challenges included procurement of primary material; preparation of concise abstracts; working with trilingual translations of abstracts, metadata, and indexing; and the work processes of the multidisciplinary team. The literature of Latin American social medicine has become more readily available to researchers worldwide. The LASM project serves as a collaborative model for the creation of sustainable solutions for disseminating information that is difficult to access through traditional methods.

Increasing access to Latin American social medicine resources: a preliminary report*

PubMed Central

Buchanan, Holly Shipp; Waitzkin, Howard; Eldredge, Jonathan; Davidson, Russ; Iriart, Celia; Teal, Janis

2003-01-01

Purpose: This preliminary report describes the development and implementation of a project to improve access to literature in Latin American social medicine (LASM). Methods: The University of New Mexico project team collaborated with participants from Argentina, Brazil, Chile, and Ecuador to identify approximately 400 articles and books in Latin American social medicine. Structured abstracts were prepared, translated into English, Spanish, and Portuguese, assigned Medical Subject Headings (MeSH), and loaded into a Web-based database for public searching. The project has initiated Web-based publication for two LASM journals. Evaluation included measures of use and content. Results: The LASM Website (http://hsc.unm.edu/lasm) and database create access to formerly little-known literature that addresses problems relevant to current medicine and public health. This Website offers a unique resource for researchers, practitioners, and teachers who seek to understand the links between socioeconomic conditions and health. The project provides a model for collaboration between librarians and health care providers. Challenges included procurement of primary material; preparation of concise abstracts; working with trilingual translations of abstracts, metadata, and indexing; and the work processes of the multidisciplinary team. Conclusions: The literature of Latin American social medicine has become more readily available to researchers worldwide. The LASM project serves as a collaborative model for the creation of sustainable solutions for disseminating information that is difficult to access through traditional methods. PMID:14566372

U.S. Geological Survey national computer technology meeting; program and abstracts, New Orleans, Louisiana, April 10-15, 1994

USGS Publications Warehouse

Balthrop, B. H.; Baker, E.G.

1994-01-01

This report contains some of the abstracts of papers that were presented at the National Computer Technology Meeting that was held in April 1994. This meeting was sponsored by the Water Resources Division of the U.S. Geological Survey, and was attended by more than 200 technical and managerial personnel representing all the Divisions of the U.S. Geological Survey. Computer-related information from all Divisions of the U.S. Geological Survey are discussed in this compilation of abstracts. Some of the topics addressed are data transfer, data-base management, hydrologic applications, national water information systems, and geographic information systems applications and techniques.

MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

PubMed Central

Guignon, V.; Sempere, G.; Sardos, J.; Hueber, Y.; Duvergey, H.; Andrieu, A.; Chase, R.; Jenny, C.; Hazekamp, T.; Irish, B.; Jelali, K.; Adeka, J.; Ayala-Silva, T.; Chao, C.P.; Daniells, J.; Dowiya, B.; Effa effa, B.; Gueco, L.; Herradura, L.; Ibobondji, L.; Kempenaers, E.; Kilangi, J.; Muhangi, S.; Ngo Xuan, P.; Paofa, J.; Pavis, C.; Thiemele, D.; Tossou, C.; Sandoval, J.; Sutanto, A.; Vangu Paka, G.; Yi, G.; Van den houwe, I.; Roux, N.

2017-01-01

Abstract Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL: https://www.crop-diversity.org/mgis/ PMID:29220435

A Novel Concept for the Search and Retrieval of the Derwent Markush Resource Database.

PubMed

Barth, Andreas; Stengel, Thomas; Litterst, Edwin; Kraut, Hans; Matuszczyk, Henry; Ailer, Franz; Hajkowski, Steve

2016-05-23

The representation of and search for generic chemical structures (Markush) remains a continuing challenge. Several research groups have addressed this problem, and over time a limited number of practical solutions have been proposed. Today there are two large commercial providers of Markush databases: Chemical Abstracts Service (CAS) and Thomson Reuters. The Thomson Reuters "Derwent" Markush database is currently offered via the online services Questel and STN and as a data feed for in-house use. The aim of this paper is to briefly review the existing Markush systems (databases plus search engines) and to describe our new approach for the implementation of the Derwent Markush Resource on STN. Our new approach demonstrates the integration of the Derwent Markush Resource database into the existing chemistry-focused STN platform without loss of detail. This provides compatibility with other structure and Markush databases on STN and at the same time makes it possible to deploy the specific features and functions of the Derwent approach. It is shown that the different Markush languages developed by CAS and Derwent can be combined into a single general Markush description. In this concept the generic nodes are grouped together in a unique hierarchy where all chemical elements and fragments can be integrated. As a consequence, both systems are searchable using a single structure query. Moreover, the presented concept could serve as a promising starting point for a common generalized description of Markush structures.

STCRDab: the structural T-cell receptor database

PubMed Central

de Oliveira, Saulo H P; Krawczyk, Konrad

2018-01-01

Abstract The Structural T–cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, the database provides annotations, such as the α/β or γ/δ chain pairings, major histocompatibility complex details, and where available, antigen binding affinities. In addition, the orientation between the variable domains and the canonical forms of the complementarity-determining region loops are also provided. Users can select, view, and download individual or bulk sets of structures based on these criteria. Where available, STCRDab also finds antibody structures that are similar to TCRs, helping users explore the relationship between TCRs and antibodies. PMID:29087479

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

ERIC Educational Resources Information Center

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

1999-01-01

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

A bibliography of IRIS-related publications, 2000-2011

NASA Astrophysics Data System (ADS)

Muco, B.

2012-12-01

Citations and acknowledgements in scientific journals can be an indicator of the role an organization has on the research of that field. Since its formation and incorporation in May 1984, the IRIS Consortium (Incorporated Research Institutions for Seismology) is mentioned more and more as a valuable source of data, instruments and programs in the literature of earth sciences. As a large organization with more than 100 member domestic institutes and about 40 international affiliates, obviously IRIS has a direct impact on the earth sciences through all its programs, projects, workshops, symposia, and news¬letters and as a lively forum for exchanging ideas. In order to maintain support from National Science Foundation (NSF) and the research community, it is important to document the continued use of IRIS facilities in basic research programs. IRIS maintains a database of articles that are based on the use of IRIS facilities or which reference use of IRIS data and resources. Articles in this database have been either been provided to IRIS by the authors or selected through an annual search of a number of prominent journals. A text version of the full bibliographic database is available on the IRIS website and a version in EndNote format is also provided. To provide a more complete bibliography and a consistent evaluation of temporal tends in publications, a special annual search began in 2000 which focused on a subset of key seismology and Earth science journals: Bulletin of Seismological Society of America, Journal of Geophysical Research, Seismological Research Letters, Geophysical Research Letters, Earth and Planetary Science Letters, Physics of the Earth and Planetary Interiors, Tectonophysics, Geophysical Journal International, Nature, Science, Geology and EOS. Using different search engines as Scirus, ScienceDirect, GeoRef, OCLC First Search, EASI Search, NASA Abstract Service etc. for online journals and publishers' databases, we searched for key words (IRIS, GSN, DMS, PASSCAL, USArray etc) in titles, abstracts and text. Most of the selections found by this method were confirmed by reading through online texts or original journals. This bibliography of peer-reviewed articles (excluding abstracts) identified in these key journals for 2000-2011 includes approximately 1800 entries. As for American Geophysical Union (AGU) transaction, the bibliography of IRIS-related abstracts for the abovementioned period includes approximately 1400 abstracts. This study is a clear indicator of making intensive use by the seismological community of the resources that IRIS provides and of the paramount importance this organization has in advancement of seismological research worldwide.

The prescribable drugs with efficacy in experimental epilepsies (PDE3) database for drug repurposing research in epilepsy.

PubMed

Sivapalarajah, Shayeeshan; Krishnakumar, Mathangi; Bickerstaffe, Harry; Chan, YikYing; Clarkson, Joseph; Hampden-Martin, Alistair; Mirza, Ahmad; Tanti, Matthew; Marson, Anthony; Pirmohamed, Munir; Mirza, Nasir

2018-02-01

Current antiepileptic drugs (AEDs) have several shortcomings. For example, they fail to control seizures in 30% of patients. Hence, there is a need to identify new AEDs. Drug repurposing is the discovery of new indications for approved drugs. This drug "recycling" offers the potential of significant savings in the time and cost of drug development. Many drugs licensed for other indications exhibit antiepileptic efficacy in animal models. Our aim was to create a database of "prescribable" drugs, approved for other conditions, with published evidence of efficacy in animal models of epilepsy, and to collate data that would assist in choosing the most promising candidates for drug repurposing. The database was created by the following: (1) computational literature-mining using novel software that identifies Medline abstracts containing the name of a prescribable drug, a rodent model of epilepsy, and a phrase indicating seizure reduction; then (2) crowdsourced manual curation of the identified abstracts. The final database includes 173 drugs and 500 abstracts. It is made freely available at www.liverpool.ac.uk/D3RE/PDE3. The database is reliable: 94% of the included drugs have corroborative evidence of efficacy in animal models (for example, evidence from multiple independent studies). The database includes many drugs that are appealing candidates for repurposing, as they are widely accepted by prescribers and patients-the database includes half of the 20 most commonly prescribed drugs in England-and they target many proteins involved in epilepsy but not targeted by current AEDs. It is important to note that the drugs are of potential relevance to human epilepsy-the database is highly enriched with drugs that target proteins of known causal human epilepsy genes (Fisher's exact test P-value < 3 × 10 -5 ). We present data to help prioritize the most promising candidates for repurposing from the database. The PDE3 database is an important new resource for drug repurposing research in epilepsy. Wiley Periodicals, Inc. © 2018 International League Against Epilepsy.

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.

Choosing a Database for Social Work: A Comparison of Social Work Abstracts and Social Service Abstracts

ERIC Educational Resources Information Center

Flatley, Robert K.; Lilla, Rick; Widner, Jack

2007-01-01

This study compared Social Work Abstracts and Social Services Abstracts databases in terms of indexing, journal coverage, and searches. The authors interviewed editors, analyzed journal coverage, and compared searches. It was determined that the databases complement one another more than compete. The authors conclude with some considerations.

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

PubMed Central

2013-01-01

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

Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis.

PubMed

Taboada, María; Martínez, Diego; Pilo, Belén; Jiménez-Escrig, Adriano; Robinson, Peter N; Sobrido, María J

2012-07-31

Semantic Web technology can considerably catalyze translational genetics and genomics research in medicine, where the interchange of information between basic research and clinical levels becomes crucial. This exchange involves mapping abstract phenotype descriptions from research resources, such as knowledge databases and catalogs, to unstructured datasets produced through experimental methods and clinical practice. This is especially true for the construction of mutation databases. This paper presents a way of harmonizing abstract phenotype descriptions with patient data from clinical practice, and querying this dataset about relationships between phenotypes and genetic variants, at different levels of abstraction. Due to the current availability of ontological and terminological resources that have already reached some consensus in biomedicine, a reuse-based ontology engineering approach was followed. The proposed approach uses the Ontology Web Language (OWL) to represent the phenotype ontology and the patient model, the Semantic Web Rule Language (SWRL) to bridge the gap between phenotype descriptions and clinical data, and the Semantic Query Web Rule Language (SQWRL) to query relevant phenotype-genotype bidirectional relationships. The work tests the use of semantic web technology in the biomedical research domain named cerebrotendinous xanthomatosis (CTX), using a real dataset and ontologies. A framework to query relevant phenotype-genotype bidirectional relationships is provided. Phenotype descriptions and patient data were harmonized by defining 28 Horn-like rules in terms of the OWL concepts. In total, 24 patterns of SWQRL queries were designed following the initial list of competency questions. As the approach is based on OWL, the semantic of the framework adapts the standard logical model of an open world assumption. This work demonstrates how semantic web technologies can be used to support flexible representation and computational inference mechanisms required to query patient datasets at different levels of abstraction. The open world assumption is especially good for describing only partially known phenotype-genotype relationships, in a way that is easily extensible. In future, this type of approach could offer researchers a valuable resource to infer new data from patient data for statistical analysis in translational research. In conclusion, phenotype description formalization and mapping to clinical data are two key elements for interchanging knowledge between basic and clinical research.

Plant genome and transcriptome annotations: from misconceptions to simple solutions

PubMed Central

Bolger, Marie E; Arsova, Borjana; Usadel, Björn

2018-01-01

Abstract Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources. PMID:28062412

Economic evidence for the prevention and treatment of atopic eczema: a protocol for a systematic review.

PubMed

Sach, Tracey Helen; McManus, Emma; Mcmonagle, Christopher; Levell, Nick

2016-05-27

Eczema, synonymous with atopic eczema or atopic dermatitis, is a chronic skin disease that has a similar impact on health-related quality of life as other chronic diseases. The proposed research aims to provide a comprehensive systematic assessment of the economic evidence base available to inform economic modelling and decision making on interventions to prevent and treat eczema at any stage of the life course. Whilst the Global Resource of Eczema Trials (GREAT) database collects together the effectiveness evidence for eczema, there is currently no such systematic resource on the economics of eczema. It is important to gain an overview of the current state of the art of economic methods in the field of eczema in order to strengthen the economic evidence base further. The proposed study is a systematic review of the economic evidence surrounding interventions for the prevention and treatment of eczema. Relevant search terms will be used to search MEDLINE, EMBASE, Database of Abstracts of Reviews of Effects, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, National Health Service (NHS) Economic Evaluation Database, Health Technology Assessment, Cumulative Index to Nursing and Allied Health Literature, EconLit, Scopus, Cost-Effectiveness Analysis Registry and Web of Science in order to identify relevant evidence. To be eligible for inclusion studies will be primary empirical studies evaluating the cost, utility or full economic evaluation of interventions for preventing or treating eczema. Two reviewers will independently assess studies for eligibility and perform data abstraction. Evidence tables will be produced presenting details of study characteristics, costing methods, outcome methods and quality assessment. The methodological quality of studies will be assessed using accepted checklists. The systematic review is being undertaken to identify the type of economic evidence available, summarise the results of the available economic evidence and critically appraise the quality of economic evidence currently available to inform future economic modelling and resource allocation decisions about interventions to prevent or treat eczema. We aim to use the review to offer guidance about how to gather economic evidence in studies of eczema and/or what further research is necessary in order to inform this. PROSPERO CRD42015024633.

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

Environmentally conscious alternative energy production

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

Kutz, M.

This fourth volume of the series describes and compares the environmental and economic impacts of renewable and conventional power generation technologies. Chapter heading are: Economic comparisons of power generation technologies (Todd Nemec); Solar energy applications (Jan F. Kreider); Fuel cells (Matthew W. Mench); Geothermal resources and technology: an introduction (Peter D. Blair); Wind power generation (Todd Nemec); Cogeneration (Jerald Caton); Hydrogen energy (Elias K. Stefanakos, Yogi Goswami, S.S. Srinivasan, and J.T. Wolan); Clean power generation from coal (Prabir Basu and James Butler); and Using waste heat from power plants (Herbert A. Ingley). The chapter on clean coal power generation frommore » coal has been abstracted separately on the Coal Abstracts database. 2 apps.« less

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

PubMed

Jiang, Xiangying; Ringwald, Martin; Blake, Judith; Shatkay, Hagit

2017-01-01

The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area. www.informatics.jax.org. © The Author(s) 2017. Published by Oxford University Press.

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

PubMed Central

Fox, Naomi K.; Brenner, Steven E.

2015-01-01

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

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

PubMed Central

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

2014-01-01

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

Seventy Years of RN Effectiveness: A Database Development Project to Inform Best Practice.

PubMed

Lulat, Zainab; Blain-McLeod, Julie; Grinspun, Doris; Penney, Tasha; Harripaul-Yhap, Anastasia; Rey, Michelle

2018-03-23

The appropriate nursing staff mix is imperative to the provision of quality care. Nurse staffing levels and staff mix vary from country to country, as well as between care settings. Understanding how staffing skill mix impacts patient, organizational, and financial outcomes is critical in order to allow policymakers and clinicians to make evidence-informed staffing decisions. This paper reports on the methodology for creation of an electronic database of studies exploring the effectiveness of Registered Nurses (RNs) on clinical and patient outcomes, organizational and nurse outcomes, and financial outcomes. Comprehensive literature searches were conducted in four electronic databases. Inclusion criteria for the database included studies published from 1946 to 2016, peer-reviewed international literature, and studies focused on RNs in all health-care disciplines, settings, and sectors. Masters-prepared nurse researchers conducted title and abstract screening and relevance review to determine eligibility of studies for the database. High-level analysis was conducted to determine key outcomes and the frequency at which they appeared within the database. Of the initial 90,352 records, a total of 626 abstracts were included within the database. Studies were organized into three groups corresponding to clinical and patient outcomes, organizational and nurse-related outcomes, and financial outcomes. Organizational and nurse-related outcomes represented the largest category in the database with 282 studies, followed by clinical and patient outcomes with 244 studies, and lastly financial outcomes, which included 124 studies. The comprehensive database of evidence for RN effectiveness is freely available at https://rnao.ca/bpg/initiatives/RNEffectiveness. The database will serve as a resource for the Registered Nurses' Association of Ontario, as well as a tool for researchers, clinicians, and policymakers for making evidence-informed staffing decisions. © 2018 The Authors. Worldviews on Evidence-Based Nursing published by Wiley Periodicals, Inc. on behalf of Sigma Theta Tau International The Honor Society of Nursing.

User assumptions about information retrieval systems: Ethical concerns

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

Froehlich, T.J.

Information professionals, whether designers, intermediaries, database producers or vendors, bear some responsibility for the information that they make available to users of information systems. The users of such systems may tend to make many assumptions about the information that a system provides, such as believing: that the data are comprehensive, current and accurate, that the information resources or databases have same degree of quality and consistency of indexing; that the abstracts, if they exist, correctly and adequate reflect the content of the article; that there is consistency informs of author names or journal titles or indexing within and across databases;more » that there is standardization in and across databases; that once errors are detected, they are corrected; that appropriate choices of databases or information resources are a relatively easy matter, etc. The truth is that few of these assumptions are valid in commercia or corporate or organizational databases. However, given these beliefs and assumptions by many users, often promoted by information providers, information professionals, impossible, should intervene to warn users about the limitations and constraints of the databases they are using. With the growth of the Internet and end-user products (e.g., CD-ROMs), such interventions have significantly declined. In such cases, information should be provided on start-up or through interface screens, indicating to users, the constraints and orientation of the system they are using. The principle of {open_quotes}caveat emptor{close_quotes} is naive and socially irresponsible: information professionals or systems have an obligation to provide some framework or context for the information that users are accessing.« less

Bibliographic Resources for the Historian of Astronomy

NASA Astrophysics Data System (ADS)

Corbin, B. G.

1999-12-01

Many large library collections now have online bibliographic catalogs on the web. These provide many hidden resources for the historian of astronomy. Special searching techniques will allow the historian to scan bibliographic records of hundreds of entries relating to biographies of astronomers, collected works of astronomers, ancient and medieval astronomy and many other historical subjects. Abstract databases such as the Astrophysics Data System and ARIBIB are also adding much historical bibliographic information. ARIBIB will eventually contain scanned images of the Astronomischer Jahresbericht containing bibliographic entries for all literature of astronomy from 1899 to 1968 and Astronomy and Astrophysics Abstracts from 1969 to present. Commercial services such as UnCover and FirstSearch provide a means of reaching bibliographic entries for journal and book literature in the history of astronomy which were not easily located in the past. A broad overview of these collections and services will be given, and searching techniques for finding ``hidden" bibliographic data will be presented. Web page addresses will be given for all sources covered.

The travesty of choosing after positive prenatal diagnosis.

PubMed

Sandelowski, Margarete; Barroso, Julie

2005-01-01

To integrate the findings of qualitative studies of expectant parents receiving positive prenatal diagnosis. Seventeen published and unpublished reports appearing between 1984 and 2001 and retrieved between December of 2002 and March of 2003. The electronic databases searched include Academic Search Elite, AIDS Information Online (AIDSLINE), Anthropological Index Online, Anthropological Literature, Black Studies, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Digital Dissertations, Dissertation Abstracts Index (DAI), Educational Resource Information Center (ERIC), MEDLINE, PsycInfo, Public Affairs Information Service (PAIS), PubMed, Social Science Abstracts (SocSci Abstracts), Social Science Citation Index, Social Work Abstracts, Sociological Abstracts (Sociofile), Women's Resources International, and Women's Studies. Qualitative studies involving expectant parents living in the United States of any race, ethnicity, nationality, or class who learned during any time in pregnancy of any fetal impairment by any means of diagnosis were eligible for inclusion. Metasummary techniques, including the calculation of frequency effect sizes, were used to aggregate the findings. Metasynthesis techniques, including constant comparison analysis and the reciprocal translation of concepts, were used to interpret the findings. The topical emphasis in the findings is on the termination of pregnancy following positive diagnosis. The thematic emphasis is on the dilemmas of choice and decision making. Positive prenatal diagnosis was for couples an experience of chosen losses and lost choices. Couples managed information to minimize stigmatization and cognitive dissonance. Existing guidelines for caring for couples after perinatal losses must accommodate the chosen loss experientially defining positive prenatal diagnosis.

Database Management: Building, Changing and Using Databases. Collected Papers and Abstracts of the Mid-Year Meeting of the American Society for Information Science (15th, Portland, Oregon, May 1986).

ERIC Educational Resources Information Center

American Society for Information Science, Washington, DC.

This document contains abstracts of papers on database design and management which were presented at the 1986 mid-year meeting of the American Society for Information Science (ASIS). Topics considered include: knowledge representation in a bilingual art history database; proprietary database design; relational database design; in-house databases;…

miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal

PubMed Central

Chen, Liang; Heikkinen, Liisa; Wang, ChangLiang; Yang, Yang; Knott, K Emily

2018-01-01

Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and rankable. The ranking feature is vital to quickly identify and prioritize the more useful from the obscure tools. Tools are ranked via different criteria including the PageRank algorithm, date of publication, number of citations, average of votes and number of publications. miRToolsGallery provides links and data for the comprehensive collection of currently available miRNA tools with a ranking function which can be adjusted using different criteria according to specific requirements. Database URL: http://www.mirtoolsgallery.org PMID:29688355

TISSUES 2.0: an integrative web resource on mammalian tissue expression

PubMed Central

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

2018-01-01

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

NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods.

PubMed

Jensen, Kasper; Panagiotou, Gianni; Kouskoumvekaki, Irene

2015-01-01

There is rising evidence of an inverse association between chronic diseases and diets characterized by rich fruit and vegetable consumption. Dietary components may act directly or indirectly on the human genome and modulate multiple processes involved in disease risk and disease progression. However, there is currently no exhaustive resource on the health benefits associated to specific dietary interventions, or a resource covering the broad molecular content of food. Here we present the first release of NutriChem, available at http://cbs.dtu.dk/services/NutriChem-1.0, a database generated by text mining of 21 million MEDLINE abstracts for information that links plant-based foods with their small molecule components and human disease phenotypes. NutriChem contains text-mined data for 18478 pairs of 1772 plant-based foods and 7898 phytochemicals, and 6242 pairs of 1066 plant-based foods and 751 diseases. In addition, it includes predicted associations for 548 phytochemicals and 252 diseases. To the best of our knowledge this database is the only resource linking the chemical space of plant-based foods with human disease phenotypes and provides a foundation for understanding mechanistically the consequences of eating behaviors on health. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

PubMed

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The economic impact of Clostridium difficile infection: a systematic review.

PubMed

Nanwa, Natasha; Kendzerska, Tetyana; Krahn, Murray; Kwong, Jeffrey C; Daneman, Nick; Witteman, William; Mittmann, Nicole; Cadarette, Suzanne M; Rosella, Laura; Sander, Beate

2015-04-01

With Clostridium difficile infection (CDI) on the rise, knowledge of the current economic burden of CDI can inform decisions on interventions related to CDI. We systematically reviewed CDI cost-of-illness (COI) studies. We performed literature searches in six databases: MEDLINE, Embase, the Health Technology Assessment Database, the National Health Service Economic Evaluation Database, the Cost-Effectiveness Analysis Registry, and EconLit. We also searched gray literature and conducted reference list searches. Two reviewers screened articles independently. One reviewer abstracted data and assessed quality using a modified guideline for economic evaluations. The second reviewer validated the abstraction and assessment. We identified 45 COI studies between 1988 and June 2014. Most (84%) of the studies were from the United States, calculating costs of hospital stays (87%), and focusing on direct costs (100%). Attributable mean CDI costs ranged from $8,911 to $30,049 for hospitalized patients. Few studies stated resource quantification methods (0%), an epidemiological approach (0%), or a justified study perspective (16%) in their cost analyses. In addition, few studies conducted sensitivity analyses (7%). Forty-five COI studies quantified and confirmed the economic impact of CDI. Costing methods across studies were heterogeneous. Future studies should follow standard COI methodology, expand study perspectives (e.g., patient), and explore populations least studied (e.g., community-acquired CDI).

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species

PubMed Central

Kumar, Sujai; Stevens, Lewis; Blaxter, Mark

2017-01-01

Abstract As the generation and use of genomic datasets is becoming increasingly common in all areas of biology, the need for resources to collate, analyse and present data from one or more genome projects is becoming more pressing. The Ensembl platform is a powerful tool to make genome data and cross-species analyses easily accessible through a web interface and a comprehensive application programming interface. Here we introduce GenomeHubs, which provide a containerized environment to facilitate the setup and hosting of custom Ensembl genome browsers. This simplifies mirroring of existing content and import of new genomic data into the Ensembl database schema. GenomeHubs also provide a set of analysis containers to decorate imported genomes with results of standard analyses and functional annotations and support export to flat files, including EMBL format for submission of assemblies and annotations to International Nucleotide Sequence Database Collaboration. Database URL: http://GenomeHubs.org PMID:28605774

BioCIDER: a Contextualisation InDEx for biological Resources discovery

PubMed Central

Horro, Carlos; Cook, Martin; Attwood, Teresa K.; Brazas, Michelle D.; Hancock, John M.; Palagi, Patricia; Corpas, Manuel; Jimenez, Rafael

2017-01-01

Abstract Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence. Contact carlos.horro@earlham.ac.uk or rafael.jimenez@elixir-europe.org or manuel@repositive.io PMID:28407033

MSDB: A Comprehensive Database of Simple Sequence Repeats

PubMed Central

Avvaru, Akshay Kumar; Saxena, Saketh; Mishra, Rakesh Kumar

2017-01-01

Abstract Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. PMID:28854643

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

Digital database architecture and delineation methodology for deriving drainage basins, and a comparison of digitally and non-digitally derived numeric drainage areas

USGS Publications Warehouse

Dupree, Jean A.; Crowfoot, Richard M.

2012-01-01

The drainage basin is a fundamental hydrologic entity used for studies of surface-water resources and during planning of water-related projects. Numeric drainage areas published by the U.S. Geological Survey water science centers in Annual Water Data Reports and on the National Water Information Systems (NWIS) Web site are still primarily derived from hard-copy sources and by manual delineation of polygonal basin areas on paper topographic map sheets. To expedite numeric drainage area determinations, the Colorado Water Science Center developed a digital database structure and a delineation methodology based on the hydrologic unit boundaries in the National Watershed Boundary Dataset. This report describes the digital database architecture and delineation methodology and also presents the results of a comparison of the numeric drainage areas derived using this digital methodology with those derived using traditional, non-digital methods. (Please see report for full Abstract)

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

Helicobacter pylori eradication: gastric cancer prevention.

PubMed

Leontiadis, Grigorios I; Ford, Alexander Charles

2015-12-01

The principal effect of Helicobacter pylori infection is lifelong chronic gastritis, affecting up to 20% of younger adults but 50% to 80% of adults born in resource-rich countries before 1950. We conducted a systematic overview, aiming to answer the following clinical question: What are the effects of H pylori eradication treatment on the risk of developing gastric cancer? We searched: Medline, Embase, The Cochrane Library, and other important databases up to July 2014 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). At this update, searching of electronic databases retrieved 208 studies. After deduplication and removal of conference abstracts, 166 records were screened for inclusion in the overview. Appraisal of titles and abstracts led to the exclusion of 124 studies and the further review of 42 full publications. Of the 42 full articles evaluated, one systematic review was added at this update. We performed a GRADE evaluation for two PICO combinations. In this systematic overview, we categorised the efficacy for one intervention based on information about the effectiveness and safety of H pylori eradication treatment for the prevention of gastric cancer.

Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of cerebrotendinous xanthomatosis

PubMed Central

2012-01-01

Background Semantic Web technology can considerably catalyze translational genetics and genomics research in medicine, where the interchange of information between basic research and clinical levels becomes crucial. This exchange involves mapping abstract phenotype descriptions from research resources, such as knowledge databases and catalogs, to unstructured datasets produced through experimental methods and clinical practice. This is especially true for the construction of mutation databases. This paper presents a way of harmonizing abstract phenotype descriptions with patient data from clinical practice, and querying this dataset about relationships between phenotypes and genetic variants, at different levels of abstraction. Methods Due to the current availability of ontological and terminological resources that have already reached some consensus in biomedicine, a reuse-based ontology engineering approach was followed. The proposed approach uses the Ontology Web Language (OWL) to represent the phenotype ontology and the patient model, the Semantic Web Rule Language (SWRL) to bridge the gap between phenotype descriptions and clinical data, and the Semantic Query Web Rule Language (SQWRL) to query relevant phenotype-genotype bidirectional relationships. The work tests the use of semantic web technology in the biomedical research domain named cerebrotendinous xanthomatosis (CTX), using a real dataset and ontologies. Results A framework to query relevant phenotype-genotype bidirectional relationships is provided. Phenotype descriptions and patient data were harmonized by defining 28 Horn-like rules in terms of the OWL concepts. In total, 24 patterns of SWQRL queries were designed following the initial list of competency questions. As the approach is based on OWL, the semantic of the framework adapts the standard logical model of an open world assumption. Conclusions This work demonstrates how semantic web technologies can be used to support flexible representation and computational inference mechanisms required to query patient datasets at different levels of abstraction. The open world assumption is especially good for describing only partially known phenotype-genotype relationships, in a way that is easily extensible. In future, this type of approach could offer researchers a valuable resource to infer new data from patient data for statistical analysis in translational research. In conclusion, phenotype description formalization and mapping to clinical data are two key elements for interchanging knowledge between basic and clinical research. PMID:22849591

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

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

Toward designing for trust in database automation

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

Duez, P. P.; Jamieson, G. A.

Appropriate reliance on system automation is imperative for safe and productive work, especially in safety-critical systems. It is unsafe to rely on automation beyond its designed use; conversely, it can be both unproductive and unsafe to manually perform tasks that are better relegated to automated tools. Operator trust in automated tools mediates reliance, and trust appears to affect how operators use technology. As automated agents become more complex, the question of trust in automation is increasingly important. In order to achieve proper use of automation, we must engender an appropriate degree of trust that is sensitive to changes in operatingmore » functions and context. In this paper, we present research concerning trust in automation in the domain of automated tools for relational databases. Lee and See have provided models of trust in automation. One model developed by Lee and See identifies three key categories of information about the automation that lie along a continuum of attributional abstraction. Purpose-, process-and performance-related information serve, both individually and through inferences between them, to describe automation in such a way as to engender r properly-calibrated trust. Thus, one can look at information from different levels of attributional abstraction as a general requirements analysis for information key to appropriate trust in automation. The model of information necessary to engender appropriate trust in automation [1] is a general one. Although it describes categories of information, it does not provide insight on how to determine the specific information elements required for a given automated tool. We have applied the Abstraction Hierarchy (AH) to this problem in the domain of relational databases. The AH serves as a formal description of the automation at several levels of abstraction, ranging from a very abstract purpose-oriented description to a more concrete description of the resources involved in the automated process. The connection between an AH for an automated tool and a list of information elements at the three levels of attributional abstraction is then direct, providing a method for satisfying information requirements for appropriate trust in automation. In this paper, we will present our method for developing specific information requirements for an automated tool, based on a formal analysis of that tool and the models presented by Lee and See. We will show an example of the application of the AH to automation, in the domain of relational database automation, and the resulting set of specific information elements for appropriate trust in the automated tool. Finally, we will comment on the applicability of this approach to the domain of nuclear plant instrumentation. (authors)« less

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

PubMed Central

Rigden, Daniel J

2017-01-01

Abstract This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/. PMID:28053160

Multi-Database Searching in the Behavioral Sciences--Part I: Basic Techniques and Core Databases.

ERIC Educational Resources Information Center

Angier, Jennifer J.; Epstein, Barbara A.

1980-01-01

Outlines practical searching techniques in seven core behavioral science databases accessing psychological literature: Psychological Abstracts, Social Science Citation Index, Biosis, Medline, Excerpta Medica, Sociological Abstracts, ERIC. Use of individual files is discussed and their relative strengths/weaknesses are compared. Appended is a list…

Where Full-Text Is Viable.

ERIC Educational Resources Information Center

Cotton, P. L.

1987-01-01

Defines two types of online databases: source, referring to those intended to be complete in themselves, whether full-text or abstracts; and bibliographic, meaning those that are not complete. Predictions are made about the future growth rate of these two types of databases, as well as full-text versus abstract databases. (EM)

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.

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

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2004

2004-01-01

This annotated bibliography provides abstracts for 14 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Educational Research Abstract; Abstract number; Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; and Issue (journal…

A high level interface to SCOP and ASTRAL implemented in python.

PubMed

Casbon, James A; Crooks, Gavin E; Saqi, Mansoor A S

2006-01-10

Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources. We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL. The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

Legal Agreements and the Governance of Research Commons: Lessons from Materials Sharing in Mouse Genomics

PubMed Central

Mishra, Amrita

2014-01-01

Abstract Omics research infrastructure such as databases and bio-repositories requires effective governance to support pre-competitive research. Governance includes the use of legal agreements, such as Material Transfer Agreements (MTAs). We analyze the use of such agreements in the mouse research commons, including by two large-scale resource development projects: the International Knockout Mouse Consortium (IKMC) and International Mouse Phenotyping Consortium (IMPC). We combine an analysis of legal agreements and semi-structured interviews with 87 members of the mouse model research community to examine legal agreements in four contexts: (1) between researchers; (2) deposit into repositories; (3) distribution by repositories; and (4) exchanges between repositories, especially those that are consortium members of the IKMC and IMPC. We conclude that legal agreements for the deposit and distribution of research reagents should be kept as simple and standard as possible, especially when minimal enforcement capacity and resources exist. Simple and standardized legal agreements reduce transactional bottlenecks and facilitate the creation of a vibrant and sustainable research commons, supported by repositories and databases. PMID:24552652

Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens

PubMed Central

Sosa, Ezequiel J; Burguener, Germán; Lanzarotti, Esteban; Radusky, Leandro; Pardo, Agustín M; Marti, Marcelo

2018-01-01

Abstract Available genomic data for pathogens has created new opportunities for drug discovery and development to fight them, including new resistant and multiresistant strains. In particular structural data must be integrated with both, gene information and experimental results. In this sense, there is a lack of an online resource that allows genome wide-based data consolidation from diverse sources together with thorough bioinformatic analysis that allows easy filtering and scoring for fast target selection for drug discovery. Here, we present Target-Pathogen database (http://target.sbg.qb.fcen.uba.ar/patho), designed and developed as an online resource that allows the integration and weighting of protein information such as: function, metabolic role, off-targeting, structural properties including druggability, essentiality and omic experiments, to facilitate the identification and prioritization of candidate drug targets in pathogens. We include in the database 10 genomes of some of the most relevant microorganisms for human health (Mycobacterium tuberculosis, Mycobacterium leprae, Klebsiella pneumoniae, Plasmodium vivax, Toxoplasma gondii, Leishmania major, Wolbachia bancrofti, Trypanosoma brucei, Shigella dysenteriae and Schistosoma Smanosoni) and show its applicability. New genomes can be uploaded upon request. PMID:29106651

MGDB: a comprehensive database of genes involved in melanoma.

PubMed

Zhang, Di; Zhu, Rongrong; Zhang, Hanqian; Zheng, Chun-Hou; Xia, Junfeng

2015-01-01

The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL: http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp. © The Author(s) 2015. Published by Oxford University Press.

Textpresso site-specific recombinases: A text-mining server for the recombinase literature including Cre mice and conditional alleles.

PubMed

Urbanski, William M; Condie, Brian G

2009-12-01

Textpresso Site Specific Recombinases (http://ssrc.genetics.uga.edu/) is a text-mining web server for searching a database of more than 9,000 full-text publications. The papers and abstracts in this database represent a wide range of topics related to site-specific recombinase (SSR) research tools. Included in the database are most of the papers that report the characterization or use of mouse strains that express Cre recombinase as well as papers that describe or analyze mouse lines that carry conditional (floxed) alleles or SSR-activated transgenes/knockins. The database also includes reports describing SSR-based cloning methods such as the Gateway or the Creator systems, papers reporting the development or use of SSR-based tools in systems such as Drosophila, bacteria, parasites, stem cells, yeast, plants, zebrafish, and Xenopus as well as publications that describe the biochemistry, genetics, or molecular structure of the SSRs themselves. Textpresso Site Specific Recombinases is the only comprehensive text-mining resource available for the literature describing the biology and technical applications of SSRs. (c) 2009 Wiley-Liss, Inc.

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.

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases

PubMed Central

Xu, Yanjun; Yang, Haixiu; Wu, Tan; Dong, Qun; Sun, Zeguo; Shang, Desi; Li, Feng; Xu, Yingqi; Su, Fei; Liu, Siyao

2017-01-01

Abstract BioM2MetDisease is a manually curated database that aims to provide a comprehensive and experimentally supported resource of associations between metabolic diseases and various biomolecules. Recently, metabolic diseases such as diabetes have become one of the leading threats to people’s health. Metabolic disease associated with alterations of multiple types of biomolecules such as miRNAs and metabolites. An integrated and high-quality data source that collection of metabolic disease associated biomolecules is essential for exploring the underlying molecular mechanisms and discovering novel therapeutics. Here, we developed the BioM2MetDisease database, which currently documents 2681 entries of relationships between 1147 biomolecules (miRNAs, metabolites and small molecules/drugs) and 78 metabolic diseases across 14 species. Each entry includes biomolecule category, species, biomolecule name, disease name, dysregulation pattern, experimental technique, a brief description of metabolic disease-biomolecule relationships, the reference, additional annotation information etc. BioM2MetDisease provides a user-friendly interface to explore and retrieve all data conveniently. A submission page was also offered for researchers to submit new associations between biomolecules and metabolic diseases. BioM2MetDisease provides a comprehensive resource for studying biology molecules act in metabolic diseases, and it is helpful for understanding the molecular mechanisms and developing novel therapeutics for metabolic diseases. Database URL: http://www.bio-bigdata.com/BioM2MetDisease/ PMID:28605773

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

2017-01-01

Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

Impact of cancer anorexia-cachexia syndrome on health-related quality of life and resource utilisation: A systematic review.

PubMed

Tarricone, Rosanna; Ricca, Giada; Nyanzi-Wakholi, Barbara; Medina-Lara, Antonieta

2016-03-01

Cancer anorexia-cachexia syndrome (CACS) negatively impacts patients' quality of life (QoL) and increases the burden on healthcare resources. To review published CACS data regarding health-related QOL (HRQoL) and its economic impact on the healthcare system. Searches were conducted in MEDLINE, EMBASE, DARE, and NHS EED databases. A total of 458 HRQoL and 189 healthcare resources utilisation abstracts were screened, and 42 and 2 full-text articles were included, respectively. The EORTC QLQ-C30 and FAACT instruments were most favoured for assessing HRQOL but none of the current tools cover all domains affected by CACS. Economic estimates for managing CACS are scarce, with studies lacking a breakdown of healthcare resource utilisation items. HRQoL instruments that can better assess and incorporate all the domains affected by CACS are required. Rigorous assessment of costs and benefits of treatment are needed to understand the magnitude of the impact of CACS. Copyright © 2016. Published by Elsevier Ireland Ltd.

Nuclear science abstracts (NSA) database 1948--1974 (on the Internet)

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

NONE

Nuclear Science Abstracts (NSA) is a comprehensive abstract and index collection of the International Nuclear Science and Technology literature for the period 1948 through 1976. Included are scientific and technical reports of the US Atomic Energy Commission, US Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Coverage of the literature since 1976 is provided by Energy Science and Technology Database. Approximately 25% of the records in the file contain abstracts. These are from the following volumes of the print Nuclear Science Abstracts: Volumes 12--18, Volume 29, and Volume 33. The database containsmore » over 900,000 bibliographic records. All aspects of nuclear science and technology are covered, including: Biomedical Sciences; Metals, Ceramics, and Other Materials; Chemistry; Nuclear Materials and Waste Management; Environmental and Earth Sciences; Particle Accelerators; Engineering; Physics; Fusion Energy; Radiation Effects; Instrumentation; Reactor Technology; Isotope and Radiation Source Technology. The database includes all records contained in Volume 1 (1948) through Volume 33 (1976) of the printed version of Nuclear Science Abstracts (NSA). This worldwide coverage includes books, conference proceedings, papers, patents, dissertations, engineering drawings, and journal literature. This database is now available for searching through the GOV. Research Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

Finding Qualitative Research Evidence for Health Technology Assessment.

PubMed

DeJean, Deirdre; Giacomini, Mita; Simeonov, Dorina; Smith, Andrea

2016-08-01

Health technology assessment (HTA) agencies increasingly use reviews of qualitative research as evidence for evaluating social, experiential, and ethical aspects of health technologies. We systematically searched three bibliographic databases (MEDLINE, CINAHL, and Social Science Citation Index [SSCI]) using published search filters or "hedges" and our hybrid filter to identify qualitative research studies pertaining to chronic obstructive pulmonary disease and early breast cancer. The search filters were compared in terms of sensitivity, specificity, and precision. Our screening by title and abstract revealed that qualitative research constituted only slightly more than 1% of all published research on each health topic. The performance of the published search filters varied greatly across topics and databases. Compared with existing search filters, our hybrid filter demonstrated a consistently high sensitivity across databases and topics, and minimized the resource-intensive process of sifting through false positives. We identify opportunities for qualitative health researchers to improve the uptake of qualitative research into evidence-informed policy making. © The Author(s) 2016.

Database Overlap vs. Complementary Coverage in Forestry and Forest Products: Factors in Database Acquisition.

ERIC Educational Resources Information Center

Hoover, Ryan E.

This study examines (1) subject content, (2) file size, (3) types of documents indexed, (4) range of years spanned, and (5) level of indexing and abstracting in five databases which collectively provide extensive coverage of the forestry and forest products industries: AGRICOLA, CAB ABSTRACTS, FOREST PRODUCTS (AIDS), PAPERCHEM, and PIRA. The…

Optimization of infobutton design and Implementation: A systematic review.

PubMed

Teixeira, Miguel; Cook, David A; Heale, Bret S E; Del Fiol, Guilherme

2017-10-01

Infobuttons are clinical decision tools embedded in the electronic health record that attempt to link clinical data with context sensitive knowledge resources. We systematically reviewed technical approaches that contribute to improved infobutton design, implementation and functionality. We searched databases including MEDLINE, EMBASE, and the Cochrane Library database from inception to March 1, 2016 for studies describing the use of infobuttons. We selected full review comparative studies, usability studies, and qualitative studies examining infobutton design and implementation. We abstracted usability measures such as user satisfaction, impact, and efficiency, as well as prediction accuracy of infobutton content retrieval algorithms and infobutton adoption/interoperability. We found 82 original research studies on infobuttons. Twelve studies met criteria for detailed abstraction. These studies investigated infobutton interoperability (1 study); tools to help tailor infobutton functionality (1 study); interventions to improve user experience (7 studies); and interventions to improve content retrieval by improving prediction of relevant knowledge resources and information needs (3 studies). In-depth interviews with implementers showed the Health Level Seven (HL7) Infobutton standard to be simple and easy to implement. A usability study demonstrated the feasibility of a tool to help medical librarians tailor infobutton functionality. User experience studies showed that access to resources with which users are familiar increased user satisfaction ratings; and that links to specific subsections of drug monographs increased information seeking efficiency. However, none of the user experience improvements led to increased usage uptake. Recommender systems based on machine learning algorithms outperformed hand-crafted rules in the prediction of relevant resources and clinicians' information needs in a laboratory setting, but no studies were found using these techniques in clinical settings. Improved content indexing in one study led to improved content retrieval across three health care organizations. Best practice technical approaches to ensure optimal infobutton functionality, design and implementation remain understudied. The HL7 Infobutton standard has supported wide adoption of infobutton functionality among clinical information systems and knowledge resources. Limited evidence supports infobutton enhancements such as links to specific subtopics, configuration of optimal resources for specific tasks and users, and improved indexing and content coverage. Further research is needed to investigate user experience improvements to increase infobutton use and effectiveness. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Enhancements to the NASA Astrophysics Science Information and Abstract Service

NASA Astrophysics Data System (ADS)

Kurtz, M. J.; Eichhorn, G.; Accomazzi, A.; Grant, C. S.; Murray, S. S.

1995-05-01

The NASA Astrophysics Data System Astrophysics Science Information and Abstract Service, the extension of the ADS Abstract Service continues rapidly to expand in both use and capabilities. Each month the service is used by about 4,000 different people, and returns about 1,000,000 pieces of bibliographic information. Among the recent additions to the system are: 1. Whole Text Access. In addition to the ApJ Letters we now have whole text for the ApJ on-line, soon we will have AJ and Rev. Mexicana. Discussions with other publishers are in progress. 2. Space Instrumentation Database. We now provide a second abstract service, covering papers related to space instruments. This is larger than the astronomy and astrophysics database in terms of total abstracts. 3. Reference Books and Historical Journals. We have begun putting the SAO Annals and the HCO Annals on-line. We have put the Handbook of Space Astronomy and Astrophysics by M.V. Zombeck (Cambridge U.P.) on-line. 4. Author Abstracts. We can now include original abstracts in addition to those we get from the NASA STI Abstracts Database. We have included abstracts for A&A in collaboration with the CDS in Strasbourg, and are collaborating with the AAS and the ASP on others. We invite publishers and editors of journals and conference proceedings to include their original abstracts in our service; send inquiries via e-mail to ads@cfa.harvard.edu. 5. Author Notes. We now accept notes and comments from authors of articles in our database. These are arbitrary html files and may contain pointers to other WWW documents, they are listed along with the abstracts, whole text, and data available in the index listing for every reference. The ASIAS is available at: http://adswww.harvard.edu/

Energy science and technology database (on the internet). Online data

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

NONE

The Energy Science and Technology Database (EDB) is a multidisciplinary file containing worldwide references to basic and applied scientific and technical research literature. The information is collected for use by government managers, researchers at the national laboratories, and other research efforts sponsored by the U.S. Department of Energy, and the results of this research are transferred to the public. Abstracts are included for records from 1976 to the present. The EDB also contains the Nuclear Science Abstracts which is a comprehensive abstract and index collection to the international nuclear science and technology literature for the period 1948 through 1976. Includedmore » are scientific and technical reports of the U.S. Atomic Energy Commission, U.S. Energy Research and Development Administration and its contractors, other agencies, universities, and industrial and research organizations. Approximately 25% of the records in the file contain abstracts. Nuclear Science Abstracts contains over 900,000 bibliographic records. The entire Energy Science and Technology Database contains over 3 million bibliographic records. This database is now available for searching through the GOV. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

Process improvement: a multi-registry database abstraction success story.

PubMed

Abrich, Victor; Rokey, Roxann; Devadas, Christopher; Uebel, Julie

2014-01-01

The St. Joseph Hospital/Marshfield Clinic Cardiac Database Registry submits data to the National Cardiovascular Data Registry (NCDR) and to the Society of Thoracic Surgeons (STS) National Database. Delayed chart abstraction is problematic, since hospital policy prohibits patient care clarifications made to the medical record more than 1 month after hospital discharge. This can also lead to late identification of missed care opportunities and untimely notification to providers. Our institution was 3.5 months behind in retrospective postdischarge case abstraction. A process improvement plan was implemented to shorten this delay to 1 month postdischarge. Daily demand of incoming cases and abstraction capacity were determined for 4 employees. Demand was matched to capacity, with the remaining time allocated to reducing backlog. Daily demand of new cases was 17.1 hours. Daily abstraction capacity was 24 hours, assuming 6 hours of effective daily abstraction time per employee, leaving 7 hours per day for backlogged case abstraction. The predicted time to reach abstraction target was 10 weeks. This was accomplished after 10 weeks, as predicted, leading to a 60% reduction of backlogged cases. The delay of postdischarge chart abstraction was successfully shortened from 3.5 months to 1 month. We intend to maintain same-day abstraction efficiency without reaccumulating substantial backlog.

Abstraction of the Relational Model from a Department of Veterans Affairs DHCP Database: Bridging Theory and Working Application

PubMed Central

Levy, C.; Beauchamp, C.

1996-01-01

This poster describes the methods used and working prototype that was developed from an abstraction of the relational model from the VA's hierarchical DHCP database. Overlaying the relational model on DHCP permits multiple user views of the physical data structure, enhances access to the database by providing a link to commercial (SQL based) software, and supports a conceptual managed care data model based on primary and longitudinal patient care. The goal of this work was to create a relational abstraction of the existing hierarchical database; to construct, using SQL data definition language, user views of the database which reflect the clinical conceptual view of DHCP, and to allow the user to work directly with the logical view of the data using GUI based commercial software of their choosing. The workstation is intended to serve as a platform from which a managed care information model could be implemented and evaluated.

Publication trend, resource utilization, and impact of the US National Cancer Database

PubMed Central

Su, Chang; Peng, Cuiying; Agbodza, Ena; Bai, Harrison X.; Huang, Yuqian; Karakousis, Giorgos; Zhang, Paul J.; Zhang, Zishu

2018-01-01

Abstract Background: The utilization and impact of the studies published using the National Cancer Database (NCDB) is currently unclear. In this study, we aim to characterize the published studies, and identify relatively unexplored areas for future investigations. Methods: A literature search was performed using PubMed in January 2017 to identify all papers published using NCDB data. Characteristics of the publications were extracted. Citation frequencies were obtained through the Web of Science. Results: Three hundred 2 articles written by 230 first authors met the inclusion criteria. The number of publications grew exponentially since 2013, with 108 articles published in 2016. Articles were published in 86 journals. The majority of the published papers focused on digestive system cancer, while bone and joints, eye and orbit, myeloma, mesothelioma, and Kaposi Sarcoma were never studied. Thirteen institutions in the United States were associated with more than 5 publications. The papers have been cited for a total of 9858 times since the publication of the first paper in 1992. Frequently appearing keywords congregated into 3 clusters: “demographics,” “treatments and survival,” and “statistical analysis method.” Even though the main focuses of the articles captured a extremely wide range, they can be classified into 2 main categories: survival analysis and characterization. Other focuses include database(s) analysis and/or comparison, and hospital reporting. Conclusion: The surging interest in the use of NCDB is accompanied by unequal utilization of resources by individuals and institutions. Certain areas were relatively understudied and should be further explored. PMID:29489679

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

PubMed Central

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

2018-01-01

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

Fire-induced water-repellent soils, an annotated bibliography

USGS Publications Warehouse

Kalendovsky, M.A.; Cannon, S.H.

1997-01-01

The development and nature of water-repellent, or hydrophobic, soils are important issues in evaluating hillslope response to fire. The following annotated bibliography was compiled to consolidate existing published research on the topic. Emphasis was placed on the types, causes, effects and measurement techniques of water repellency, particularly with respect to wildfires and prescribed burns. Each annotation includes a general summary of the respective publication, as well as highlights of interest to this focus. Although some references on the development of water repellency without fires, the chemistry of hydrophobic substances, and remediation of water-repellent conditions are included, coverage of these topics is not intended to be comprehensive. To develop this database, the GeoRef, Agricola, and Water Resources Abstracts databases were searched for appropriate references, and the bibliographies of each reference were then reviewed for additional entries. Additional references will be added to this bibliography as they become available. The annotated bibliography can be accessed on the Web at http://geohazards.cr.usgs.gov/html_files/landslides/ofr97-720/biblio.html. A database consisting of the references and keywords is available through a link at the above address. This database was compiled using EndNote2 plus software by Niles and Associates, and is necessary to search the database.

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

PubMed Central

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

2018-01-01

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

Structure Identification Using High Resolution Mass ...

EPA Pesticide Factsheets

The iCSS CompTox Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. This poster reviews the benefits of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. Standard approaches for both mass and formula lookup are available but the dashboard delivers a novel approach for hit ranking based on functional use of the chemicals. The focus on high-quality data, novel ranking approaches and integration to other resources of value to mass spectrometrists makes the CompTox Dashboard a valuable resource for the identification of environmental chemicals. This abstract does not reflect U.S. EPA policy poster presented at the Eastern Analytical Symposium (EAS) held in Somerset, NJ

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

PubMed Central

Wei, Chih-Hsuan; Hakala, Kai; Pyysalo, Sampo; Ananiadou, Sophia; Kao, Hung-Yu; Lu, Zhiyong; Salakoski, Tapio; Van de Peer, Yves; Ginter, Filip

2013-01-01

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license. PMID:23613707

HopBase: a unified resource for Humulus genomics

PubMed Central

Hill, Steven T.; Sudarsanam, Ramcharan

2017-01-01

Abstract Hop (Humulus lupulus L. var lupulus) is a dioecious plant of worldwide significance, used primarily for bittering and flavoring in brewing beer. Studies on the medicinal properties of several unique compounds produced by hop have led to additional interest from pharmacy and healthcare industries as well as livestock production as a natural antibiotic. Genomic research in hop has resulted a published draft genome and transcriptome assemblies. As research into the genomics of hop has gained interest, there is a critical need for centralized online genomic resources. To support the growing research community, we report the development of an online resource "HopBase.org." In addition to providing a gene annotation to the existing Shinsuwase draft genome, HopBase makes available genome assemblies and annotations for both the cultivar “Teamaker” and male hop accession number USDA 21422M. These genome assemblies, gene annotations, along with other common data, coupled with a genome browser and BLAST database enable the hop community to enter the genomic age. The HopBase genomic resource is accessible at http://hopbase.org and http://hopbase.cgrb.oregonstate.edu. PMID:28415075

Psychopharmacological and Other Treatments in Preschool Children with Attention-Deficit/Hyperactivity Disorder: Current Evidence and Practice

PubMed Central

Arnold, L. Eugene; Anthony, Bruno J.

2008-01-01

Abstract Objective This article reviews rational approaches to treating attention-deficit/hyperactivity disorder (ADHD) in preschool children, including pharmacological and nonpharmacological treatments. Implications for clinical practice are discussed. Data Sources We searched MEDLINE, PsychINFO, Cumulative Index to Nursing & Allied Health, Educational Resources Information Center, Cochrane Database of Systematic Reviews and Database of Abstracts of Reviews of Effects for relevant literature published in English from 1967 to 2007 on preschool ADHD. We also reviewed the references cited in identified reports. Study Selection Studies were reviewed if the sample included at least some children younger than 6 years of age or attending kindergarten, the study participants had a diagnosis of ADHD or equivalent symptoms, received intervention aimed at ADHD symptoms, and included a relevant outcome measure. Data Extraction Studies were reviewed for type of intervention and outcome relevant to ADHD and were rated for the level of evidence for adequacy of the data to inform clinical practice. Conclusions The current level of evidence for adequacy of empirical data to inform clinical practice for short-term treatment of ADHD in preschool children is Level A for methylphenidate and Level B for parent behavior training, child training, and additive-free elimination diet. PMID:18844482

The Efficacy of Multidimensional Constraint Keys in Database Query Performance

ERIC Educational Resources Information Center

Cardwell, Leslie K.

2012-01-01

This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

Development, dissemination, and applications of a new terminological resource, the Q-Code taxonomy for professional aspects of general practice/family medicine.

PubMed

Jamoulle, Marc; Resnick, Melissa; Grosjean, Julien; Ittoo, Ashwin; Cardillo, Elena; Vander Stichele, Robert; Darmoni, Stefan; Vanmeerbeek, Marc

2018-12-01

While documentation of clinical aspects of General Practice/Family Medicine (GP/FM) is assured by the International Classification of Primary Care (ICPC), there is no taxonomy for the professional aspects (context and management) of GP/FM. To present the development, dissemination, applications, and resulting face validity of the Q-Codes taxonomy specifically designed to describe contextual features of GP/FM, proposed as an extension to the ICPC. The Q-Codes taxonomy was developed from Lamberts' seminal idea for indexing contextual content (1987) by a multi-disciplinary team of knowledge engineers, linguists and general practitioners, through a qualitative and iterative analysis of 1702 abstracts from six GP/FM conferences using Atlas.ti software. A total of 182 concepts, called Q-Codes, representing professional aspects of GP/FM were identified and organized in a taxonomy. Dissemination: The taxonomy is published as an online terminological resource, using semantic web techniques and web ontology language (OWL) ( http://www.hetop.eu/Q ). Each Q-Code is identified with a unique resource identifier (URI), and provided with preferred terms, and scope notes in ten languages (Portuguese, Spanish, English, French, Dutch, Korean, Vietnamese, Turkish, Georgian, German) and search filters for MEDLINE and web searches. This taxonomy has already been used to support queries in bibliographic databases (e.g., MEDLINE), to facilitate indexing of grey literature in GP/FM as congress abstracts, master theses, websites and as an educational tool in vocational teaching, Conclusions: The rapidly growing list of practical applications provides face-validity for the usefulness of this freely available new terminological resource.

Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes

PubMed Central

Pierneef, Rian; Cronje, Louis; Bezuidt, Oliver; Reva, Oleg N.

2015-01-01

Abstract The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php . Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries. Database URL: http://pregi.bi.up.ac.za/index.php , Version 2015 PMID:26200753

Constructing a Geology Ontology Using a Relational Database

NASA Astrophysics Data System (ADS)

Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

2013-12-01

In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances relationship. Based on a Quaternary database of downtown of Foshan city, Guangdong Province, in Southern China, a geological ontology was constructed using the proposed method. To measure the maintenance of semantics in the conversation process and the results, an inverse mapping from the ontology to a relational database was tested based on a proposed conversation rule. The comparison of schema and entities and the reduction of tables between the inverse database and the original database illustrated that the proposed method retains the semantic information well during the conversation process. An application for abstracting sandstone information showed that semantic relationships among concepts in the geological database were successfully reorganized in the constructed ontology. Key words: geological ontology; geological spatial database; multiple inheritance; OWL Acknowledgement: This research is jointly funded by the Specialized Research Fund for the Doctoral Program of Higher Education of China (RFDP) (20100171120001), NSFC (41102207) and the Fundamental Research Funds for the Central Universities (12lgpy19).

The CTSA Consortium's Catalog of Assets for Translational and Clinical Health Research (CATCHR)

PubMed Central

Mapes, Brandy; Basford, Melissa; Zufelt, Anneliese; Wehbe, Firas; Harris, Paul; Alcorn, Michael; Allen, David; Arnim, Margaret; Autry, Susan; Briggs, Michael S.; Carnegie, Andrea; Chavis‐Keeling, Deborah; De La Pena, Carlos; Dworschak, Doris; Earnest, Julie; Grieb, Terri; Guess, Marilyn; Hafer, Nathaniel; Johnson, Tesheia; Kasper, Amanda; Kopp, Janice; Lockie, Timothy; Lombardo, Vincetta; McHale, Leslie; Minogue, Andrea; Nunnally, Beth; O'Quinn, Deanna; Peck, Kelly; Pemberton, Kieran; Perry, Cheryl; Petrie, Ginny; Pontello, Andria; Posner, Rachel; Rehman, Bushra; Roth, Deborah; Sacksteder, Paulette; Scahill, Samantha; Schieri, Lorri; Simpson, Rosemary; Skinner, Anne; Toussant, Kim; Turner, Alicia; Van der Put, Elaine; Wasser, June; Webb, Chris D.; Williams, Maija; Wiseman, Lori; Yasko, Laurel; Pulley, Jill

2014-01-01

Abstract The 61 CTSA Consortium sites are home to valuable programs and infrastructure supporting translational science and all are charged with ensuring that such investments translate quickly to improved clinical care. Catalog of Assets for Translational and Clinical Health Research (CATCHR) is the Consortium's effort to collect and make available information on programs and resources to maximize efficiency and facilitate collaborations. By capturing information on a broad range of assets supporting the entire clinical and translational research spectrum, CATCHR aims to provide the necessary infrastructure and processes to establish and maintain an open‐access, searchable database of consortium resources to support multisite clinical and translational research studies. Data are collected using rigorous, defined methods, with the resulting information made visible through an integrated, searchable Web‐based tool. Additional easy‐to‐use Web tools assist resource owners in validating and updating resource information over time. In this paper, we discuss the design and scope of the project, data collection methods, current results, and future plans for development and sustainability. With increasing pressure on research programs to avoid redundancy, CATCHR aims to make available information on programs and core facilities to maximize efficient use of resources. PMID:24456567

Prairie Resources

Science.gov Websites

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

A Brief Review of RNA–Protein Interaction Database Resources

PubMed Central

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

2017-01-01

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

Inventory of U.S. Health Care Data Bases, 1976-1987.

ERIC Educational Resources Information Center

Kralovec, Peter D.; Andes, Steven M.

This inventory contains summary abstracts of 305 current (1976-1987) non-bibliographic machine-readable databases and national health care data that have been created by public and private organizations throughout the United States. Each of the abstracts contains pertinent information on the sponsor or database, a description of the purpose and…

AbDb: antibody structure database—a database of PDB-derived antibody structures

PubMed Central

Ferdous, Saba

2018-01-01

Abstract In order to analyse structures of proteins of a particular class, these need to be extracted from Protein Data Bank (PDB) files. In the case of antibodies, there are a number of special considerations: (i) identifying antibodies in the PDB is not trivial, (ii) they may be crystallized with or without antigen, (iii) for analysis purposes, one is normally only interested in the Fv region of the antibody, (iv) structural analysis of epitopes, in particular, requires individual antibody–antigen complexes from a PDB file which may contain multiple copies of the same, or different, antibodies and (v) standard numbering schemes should be applied. Consequently, there is a need for a specialist resource containing pre-numbered non-redundant antibody Fv structures with their cognate antigens. We have created an automatically updated resource, AbDb, which collects the Fv regions from antibody structures using information from our SACS database which summarizes antibody structures from the PDB. PDB files containing multiple structures are split and numbered and each antibody structure is associated with its antigen where available. Antibody structures with only light or heavy chains have also been processed and sequences of antibodies are compared to identify multiple structures of the same antibody. The data may be queried on the basis of PDB code, or the name or species of the antibody or antigen, and the complete datasets may be downloaded. Database URL: www.bioinf.org.uk/abs/abdb/ PMID:29718130

SeedStor: A Germplasm Information Management System and Public Database

PubMed Central

Horler, RSP; Turner, AS; Fretter, P; Ambrose, M

2018-01-01

Abstract SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK’s plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks. PMID:29228298

Diagnostic imaging learning resources evaluated by students and recent graduates.

PubMed

Alexander, Kate; Bélisle, Marilou; Dallaire, Sébastien; Fernandez, Nicolas; Doucet, Michèle

2013-01-01

Many learning resources can help students develop the problem-solving abilities and clinical skills required for diagnostic imaging. This study explored veterinary students' perceptions of the usefulness of a variety of learning resources. Perceived resource usefulness was measured for different levels of students and for academic versus clinical preparation. Third-year (n=139) and final (fifth) year (n=105) students and recent graduates (n=56) completed questionnaires on perceived usefulness of each resource. Resources were grouped for comparison: abstract/low complexity (e.g., notes, multimedia presentations), abstract/high complexity (e.g., Web-based and film case repositories), concrete/low complexity (e.g., large-group "clicker" workshops), and concrete/high complexity (e.g., small-group interpretation workshops). Lower-level students considered abstract/low-complexity resources more useful for academic preparation and concrete resources more useful for clinical preparation. Higher-level students/recent graduates also considered abstract/low-complexity resources more useful for academic preparation. For all levels, lecture notes were considered highly useful. Multimedia slideshows were an interactive complement to notes. The usefulness of a Web-based case repository was limited by accessibility problems and difficulty. Traditional abstract/low-complexity resources were considered useful for more levels and contexts than expected. Concrete/high-complexity resources need to better represent clinical practice to be considered more useful for clinical preparation.

NREL: Renewable Resource Data Center - Biomass Resource Publications

Science.gov Websites

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

Hawaii bibliographic database

USGS Publications Warehouse

Wright, T.L.; Takahashi, T.J.

1998-01-01

The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

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

USGS Publications Warehouse

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

2016-07-13

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

High-Level Data-Abstraction System

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1986-01-01

Communication with data-base processor flexible and efficient. High Level Data Abstraction (HILDA) system is three-layer system supporting data-abstraction features of Intel data-base processor (DBP). Purpose of HILDA establishment of flexible method of efficiently communicating with DBP. Power of HILDA lies in its extensibility with regard to syntax and semantic changes. HILDA's high-level query language readily modified. Offers powerful potential to computer sites where DBP attached to DEC VAX-series computer. HILDA system written in Pascal and FORTRAN 77 for interactive execution.

A RESTful application programming interface for the PubMLST molecular typing and genome databases

PubMed Central

Bray, James E.; Maiden, Martin C. J.

2017-01-01

Abstract Molecular typing is used to differentiate microorganisms at the subspecies or strain level for epidemiological investigations, infection control, public health and environmental sampling. DNA sequence-based typing methods require authoritative databases that link sequence variants to nomenclature in order to facilitate communication and comparison of identified types in national or global settings. The PubMLST website (https://pubmlst.org/) fulfils this role for over a hundred microorganisms for which it hosts curated molecular sequence typing data, providing sequence and allelic profile definitions for multi-locus sequence typing (MLST) and single-gene typing approaches. In recent years, these have expanded to cover the whole genome with schemes such as core genome MLST (cgMLST) and whole genome MLST (wgMLST) which catalogue the allelic diversity found in hundreds to thousands of genes. These approaches provide a common nomenclature for high-resolution strain characterization and comparison. Molecular typing information is linked to isolate provenance, phenotype, and increasingly genome assemblies, providing a resource for outbreak investigation and research in to population structure, gene association, global epidemiology and vaccine coverage. A Representational State Transfer (REST) Application Programming Interface (API) has been developed for the PubMLST website to make these large quantities of structured molecular typing and whole genome sequence data available for programmatic access by any third party application. The API is an integral component of the Bacterial Isolate Genome Sequence Database (BIGSdb) platform that is used to host PubMLST resources, and exposes all public data within the site. In addition to data browsing, searching and download, the API supports authentication and submission of new data to curator queues. Database URL: http://rest.pubmlst.org/ PMID:29220452

An Integrated Molecular Database on Indian Insects.

PubMed

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

2018-01-01

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

Abstract - Cooperative Research and Development Agreement between Environmental Defense Fund and National Energy Technology Laboratory

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

Rose, Kelly K.; Zavala-Zraiza, Daniel

Here, we summarize an effort to develop a global oil and gas infrastructure (GOGI) taxonomy and geodatabase, using a combination of big data computing, custom search and data integration algorithms, and expert driven spatio-temporal analytics to identify, access, and evaluate open oil and gas data resources and uncertainty trends worldwide. This approach leveraged custom National Energy Technology Laboratory (NETL) tools and capabilities in collaboration with Environmental Defense Fund (EDF) and Carbon Limits subject matter expertise, to identify over 380 datasets and integrate more than 4.8 million features into the GOGI database. In addition to acquisition of open oil and gasmore » infrastructure data, information was collected and analyzed to assess the spatial, temporal, and source quality of these resources, and estimate their completeness relative to the top 40 hydrocarbon producing and consuming countries.« less

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

PubMed Central

2010-01-01

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

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

PubMed Central

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

2016-01-01

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

Definitions of database files and fields of the Personal Computer-Based Water Data Sources Directory

USGS Publications Warehouse

Green, J. Wayne

1991-01-01

This report describes the data-base files and fields of the personal computer-based Water Data Sources Directory (WDSD). The personal computer-based WDSD was derived from the U.S. Geological Survey (USGS) mainframe computer version. The mainframe version of the WDSD is a hierarchical data-base design. The personal computer-based WDSD is a relational data- base design. This report describes the data-base files and fields of the relational data-base design in dBASE IV (the use of brand names in this abstract is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey) for the personal computer. The WDSD contains information on (1) the type of organization, (2) the major orientation of water-data activities conducted by each organization, (3) the names, addresses, and telephone numbers of offices within each organization from which water data may be obtained, (4) the types of data held by each organization and the geographic locations within which these data have been collected, (5) alternative sources of an organization's data, (6) the designation of liaison personnel in matters related to water-data acquisition and indexing, (7) the volume of water data indexed for the organization, and (8) information about other types of data and services available from the organization that are pertinent to water-resources activities.

A literature review of quantitative indicators to measure the quality of labor and delivery care.

PubMed

Tripathi, Vandana

2016-02-01

Strengthening measurement of the quality of labor and delivery (L&D) care in low-resource countries requires an understanding of existing approaches. To identify quantitative indicators of L&D care quality and assess gaps in indicators. PubMed, CINAHL Plus, and Embase databases were searched for research published in English between January 1, 1990, and October 31, 2013, using structured terms. Studies describing indicators for L&D care quality assessment were included. Those whose abstracts contained inclusion criteria underwent full-text review. Study characteristics, including indicator selection and data sources, were extracted via a standard spreadsheet. The structured search identified 1224 studies. After abstract and full-text review, 477 were included in the analysis. Most studies selected indicators by using literature review, clinical guidelines, or expert panels. Few indicators were empirically validated; most studies relied on medical record review to measure indicators. Many quantitative indicators have been used to measure L&D care quality, but few have been validated beyond expert opinion. There has been limited use of clinical observation in quality assessment of care processes. The findings suggest the need for validated, efficient consensus indicators of the quality of L&D care processes, particularly in low-resource countries. Copyright © 2015 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

SERS internship fall 1995 abstracts and research papers

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

Davis, Beverly

1996-05-01

This report is a compilation of twenty abstracts and their corresponding full papers of research projects done under the US Department of Energy Science and Engineering Research Semester (SERS) program. Papers cover a broad range of topics, for example, environmental transport, supercomputers, databases, biology. Selected papers were indexed separately for inclusion the the Energy Science and Technology Database.

Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease

PubMed Central

Zhi, Hui; Li, Xin; Wang, Peng; Gao, Yue; Gao, Baoqing; Zhou, Dianshuang; Zhang, Yan; Guo, Maoni; Yue, Ming; Shen, Weitao

2018-01-01

Abstract Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. The resource provides: (i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types; (ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs; (iii) the prognostic values for each hit transcript calculated from the patients clinical data; (iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease; (v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets; (vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers. Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases. PMID:29069510

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2007

2007-01-01

This annotated bibliography provides abstracts for 12 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; Issue (journal citation information for the resource within the…

International Early Childhood Resources from Educational Research Abstracts (ERA) Online

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2011

2011-01-01

This annotated bibliography provides abstracts for 17 resources relating to early childhood around the world. Each annotation contains: title; author name(s); source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; and issue (journal citation information for the resource within the…

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2006

2006-01-01

This annotated bibliography provides abstracts for 18 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; Issue (journal citation information for the resource within the…

Ioss IO Subsystem

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

Sjaardema, Gregory; Bauer, David; Erik, & Illescas

2017-01-06

The Ioss is a database-independent package for providing an object-oriented, abstract interface to IO capabilities for a finite element application; and concrete database interfaces which provided input and/or output to exodusII, xdmf, generated, and heartbeat database formats. The Ioss provides an object-oriented C++-based IO interface for a finite element application code. The application code can perform all IO operations through the Ioss interface which is typically at a higher abstraction level than the concrete database formats. The Ioss then performs the needed operations to translate the finite element data to the specific format required by the concrete database implementations. Themore » Ioss currently supports interfaces to exodusII, xdmf, generated, and heartbeat formats, but additional formats can be easily added.« less

A bibliometric analysis of systematic reviews on vaccines and immunisation.

PubMed

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

2018-04-19

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

Online access to journal abstracts and articles.

PubMed

Giedd, J N; Smith, K G

1997-01-01

Advances in information technology now offer several options for child and adolescent psychopharmacologists to navigate the increasingly complex terrain of scientific literature and keep abreast of the rapidly changing advances in our field. MEDLINE, the world's largest database of medical literature, can be accessed and searched by a variety of free or fee-based services. In addition to efficient retrieval of citations and abstracts based on subject, author, or title, many of these services now provide, for a fee, the entire text and graphics of articles (displayed on computer screen, faxed, or mailed). There are also current awareness services to alert the user when new requested literature become available as well as services to send via e-mail the tables of contents of requested journals (sometimes prior to paper publication). For online citation and abstract retrieval, we found that free services, such as PubMed, performed as good or better than fee-based services. Physicians' Online, sponsored by the pharmaceutical industry, offered the lowest price for full-text manuscript delivery. In this article, we review literature search, delivery, and update services and offer some tips on how to most effectively use these resources.

Trends in the Scholarship on Teachers of Color for Diverse Populations: Implications for Multicultural Education.

ERIC Educational Resources Information Center

Sheets, Rosa Hernandez

This paper reviews patterns in the literature on minority teachers and teacher preparation. The study involved an extensive literature search using the following database selections: Books in Print A-Z; ERIC Database 1966-2000; Education Abstracts FTX 6/83-12/99; PsycINFO 1984-2000/02; Sociological Abstracts 1963-1999/12; and Social Sciences Abst…

Abstracting/Annotating. ERIC Processing Manual, Section VI.

ERIC Educational Resources Information Center

Brandhorst, Ted, Ed.

Rules and guidelines are provided for the preparation of abstracts and annotations for documents and journal articles entering the ERIC database. Various types of abstracts are defined, including the Informative, Indicative, and mixed Informative-Indicative. Advice is given on how to select the abstract type appropriate for the particular…

Measurement tools of resource use and quality of life in clinical trials for dementia or cognitive impairment interventions: protocol for a scoping review.

PubMed

Yang, Fan; Dawes, Piers; Leroi, Iracema; Gannon, Brenda

2017-01-26

Dementia and cognitive impairment could severely impact patients' life and bring heavy burden to patients, caregivers and societies. Some interventions are suggested for the older patients with these conditions to help them live well, but economic evaluation is needed to assess the cost-effectiveness of these interventions. Trial-based economic evaluation is an ideal method; however, little is known about the tools used to collect data of resource use and quality of life alongside the trials. Therefore, the aim of this review is to identify and describe the resource use and quality of life instruments in clinical trials of interventions for older patients with dementia or cognitive impairment. We will perform a search in main electronic databases (Ovid MEDLINE, PsycINFO, EMBASE, CINAHL, Cochrane Databases of Systematic Reviews, Web of Science and Scopus) using the key terms or their synonyms: older, dementia, cognitive impairment, cost, quality of life, intervention and tools. After removing duplicates, two independent reviewers will screen each entry for eligibility, initially by title and abstract, then by full-text. A hand search of the references of included articles and general search, e.g. Google Scholar, will also be conducted to identify potential relevant studies. All disagreements will be resolved by discussion or consultation with a third reviewer if necessary. Data analysis will be completed and reported in a narrative review. This review will identify the instruments used in clinical trials to collect resource use and quality of life data for dementia or cognitive impairment interventions. This will help to guide the study design of future trial-based economic evaluation of these interventions. PROSPERO CRD42016038495.

Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods

PubMed Central

Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

2016-01-01

Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

Full Text Searching and Customization in the NASA ADS Abstract Service

NASA Technical Reports Server (NTRS)

Eichhorn, G.; Accomazzi, A.; Grant, C. S.; Kurtz, M. J.; Henneken, E. A.; Thompson, D. M.; Murray, S. S.

2004-01-01

The NASA-ADS Abstract Service provides a sophisticated search capability for the literature in Astronomy, Planetary Sciences, Physics/Geophysics, and Space Instrumentation. The ADS is funded by NASA and access to the ADS services is free to anybody worldwide without restrictions. It allows the user to search the literature by author, title, and abstract text. The ADS database contains over 3.6 million references, with 965,000 in the Astronomy/Planetary Sciences database, and 1.6 million in the Physics/Geophysics database. 2/3 of the records have full abstracts, the rest are table of contents entries (titles and author lists only). The coverage for the Astronomy literature is better than 95% from 1975. Before that we cover all major journals and many smaller ones. Most of the journal literature is covered back to volume 1. We now get abstracts on a regular basis from most journals. Over the last year we have entered basically all conference proceedings tables of contents that are available at the Harvard Smithsonian Center for Astrophysics library. This has greatly increased the coverage of conference proceedings in the ADS. The ADS also covers the ArXiv Preprints. We download these preprints every night and index all the preprints. They can be searched either together with the other abstracts or separately. There are currently about 260,000 preprints in that database. In January 2004 we have introduced two new services, full text searching and a personal notification service called "myADS". As all other ADS services, these are free to use for anybody.

Characteristics of Resources Represented in the OCLC CORC Database.

ERIC Educational Resources Information Center

Connell, Tschera Harkness; Prabha, Chandra

2002-01-01

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

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge

PubMed Central

Wei, Wei; Ji, Zhanglong; He, Yupeng; Zhang, Kai; Ha, Yuanchi; Li, Qi; Ohno-Machado, Lucila

2018-01-01

Abstract The number and diversity of biomedical datasets grew rapidly in the last decade. A large number of datasets are stored in various repositories, with different formats. Existing dataset retrieval systems lack the capability of cross-repository search. As a result, users spend time searching datasets in known repositories, and they typically do not find new repositories. The biomedical and healthcare data discovery index ecosystem (bioCADDIE) team organized a challenge to solicit new indexing and searching strategies for retrieving biomedical datasets across repositories. We describe the work of one team that built a retrieval pipeline and examined its performance. The pipeline used online resources to supplement dataset metadata, automatically generated queries from users’ free-text questions, produced high-quality retrieval results and achieved the highest inferred Normalized Discounted Cumulative Gain among competitors. The results showed that it is a promising solution for cross-database, cross-domain and cross-repository biomedical dataset retrieval. Database URL: https://github.com/w2wei/dataset_retrieval_pipeline PMID:29688374

The method of abstraction in the design of databases and the interoperability

NASA Astrophysics Data System (ADS)

Yakovlev, Nikolay

2018-03-01

When designing the database structure oriented to the contents of indicators presented in the documents and communications subject area. First, the method of abstraction is applied by expansion of the indices of new, artificially constructed abstract concepts. The use of abstract concepts allows to avoid registration of relations many-to-many. For this reason, when built using abstract concepts, demonstrate greater stability in the processes. The example abstract concepts to address structure - a unique house number. Second, the method of abstraction can be used in the transformation of concepts by omitting some attributes that are unnecessary for solving certain classes of problems. Data processing associated with the amended concepts is more simple without losing the possibility of solving the considered classes of problems. For example, the concept "street" loses the binding to the land. The content of the modified concept of "street" are only the relations of the houses to the declared name. For most accounting tasks and ensure communication is enough.

A neotropical Miocene pollen database employing image-based search and semantic modeling.

PubMed

Han, Jing Ginger; Cao, Hongfei; Barb, Adrian; Punyasena, Surangi W; Jaramillo, Carlos; Shyu, Chi-Ren

2014-08-01

Digital microscopic pollen images are being generated with increasing speed and volume, producing opportunities to develop new computational methods that increase the consistency and efficiency of pollen analysis and provide the palynological community a computational framework for information sharing and knowledge transfer. • Mathematical methods were used to assign trait semantics (abstract morphological representations) of the images of neotropical Miocene pollen and spores. Advanced database-indexing structures were built to compare and retrieve similar images based on their visual content. A Web-based system was developed to provide novel tools for automatic trait semantic annotation and image retrieval by trait semantics and visual content. • Mathematical models that map visual features to trait semantics can be used to annotate images with morphology semantics and to search image databases with improved reliability and productivity. Images can also be searched by visual content, providing users with customized emphases on traits such as color, shape, and texture. • Content- and semantic-based image searches provide a powerful computational platform for pollen and spore identification. The infrastructure outlined provides a framework for building a community-wide palynological resource, streamlining the process of manual identification, analysis, and species discovery.

PedAM: a database for Pediatric Disease Annotation and Medicine.

PubMed

Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Li, Xin; Liang, Yunxiang; Guo, Dongming; Tai, Jun; Chen, Geng; Jin, Yaqiong; Liu, Zhimei; Ni, Xin; Shi, Tieliu

2018-01-04

There is a significant number of children around the world suffering from the consequence of the misdiagnosis and ineffective treatment for various diseases. To facilitate the precision medicine in pediatrics, a database namely the Pediatric Disease Annotations & Medicines (PedAM) has been built to standardize and classify pediatric diseases. The PedAM integrates both biomedical resources and clinical data from Electronic Medical Records to support the development of computational tools, by which enables robust data analysis and integration. It also uses disease-manifestation (D-M) integrated from existing biomedical ontologies as prior knowledge to automatically recognize text-mined, D-M-specific syntactic patterns from 774 514 full-text articles and 8 848 796 abstracts in MEDLINE. Additionally, disease connections based on phenotypes or genes can be visualized on the web page of PedAM. Currently, the PedAM contains standardized 8528 pediatric disease terms (4542 unique disease concepts and 3986 synonyms) with eight annotation fields for each disease, including definition synonyms, gene, symptom, cross-reference (Xref), human phenotypes and its corresponding phenotypes in the mouse. The database PedAM is freely accessible at http://www.unimd.org/pedam/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

CardioTF, a database of deconstructing transcriptional circuits in the heart system

PubMed Central

2016-01-01

Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html. PMID:27635320

CardioTF, a database of deconstructing transcriptional circuits in the heart system.

PubMed

Zhen, Yisong

2016-01-01

Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method. The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results. Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype. The CardioTF database can be used as a portal to construct transcriptional network of cardiac development. Database URL: http://www.cardiosignal.org/database/cardiotf.html.

CANCER PREVENTION AND CONTROL (CP) DATABASE

EPA Science Inventory

This database focuses on breast, cervical, skin, and colorectal cancer emphasizing the application of early detection and control program activities and risk reduction efforts. The database provides bibliographic citations and abstracts of various types of materials including jou...

Reasoning abstractly about resources

NASA Technical Reports Server (NTRS)

Clement, B.; Barrett, A.

2001-01-01

r describes a way to schedule high level activities before distributing them across multiple rovers in order to coordinate the resultant use of shared resources regardless of how each rover decides how to perform its activities. We present an algorithm for summarizing the metric resource requirements of an abstract activity based n the resource usages of its potential refinements.

Drowning in Data: Sorting through CD ROM and Computer Databases.

ERIC Educational Resources Information Center

Cates, Carl M.; Kaye, Barbara K.

This paper identifies the bibliographic and numeric databases on CD-ROM and computer diskette that should be most useful for investigators in communication, marketing, and communication education. Bibliographic databases are usually found in three formats: citations only, citations and abstracts, and full-text articles. Numeric databases are…

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

PubMed Central

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

2002-01-01

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

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 30, 1987.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

The Environmental Quality Instructional Resources Center acquires, reviews, indexes, and announces both print (books, modules, units, etc.) and non-print (films, slides, video tapes, etc.) materials related to water quality and water resources education and instruction. This publication contains abstracts and indexes to selected materials related…

[Bio-Resources and Database for Preemptive Medicine.

PubMed

Saito, Kuniaki

2016-05-01

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

Teaching-skills training programs for family medicine residents

PubMed Central

Lacasse, Miriam; Ratnapalan, Savithiri

2009-01-01

ABSTRACT OBJECTIVE To review the literature on teaching-skills training programs for family medicine residents and to identify formats and content of these programs and their effects. DATA SOURCES Ovid MEDLINE (1950 to mid-July 2008) and the Education Resources Information Center database (pre-1966 to mid-July 2008) were searched using and combining the MeSH terms teaching, internship and residency, and family practice; and teaching, graduate medical education, and family practice. STUDY SELECTION The initial MEDLINE and Education Resources Information Center database searches identified 362 and 33 references, respectively. Titles and abstracts were reviewed and studies were included if they described the format or content of a teaching-skills program or if they were primary studies of the effects of a teaching-skills program for family medicine residents or family medicine and other specialty trainees. The bibliographies of those articles were reviewed for unidentified studies. A total of 8 articles were identified for systematic review. Selection was limited to articles published in English. SYNTHESIS Teaching-skills training programs for family medicine residents vary from half-day curricula to a few months of training. Their content includes leadership skills, effective clinical teaching skills, technical teaching skills, as well as feedback and evaluation skills. Evaluations mainly assessed the programs’ effects on teaching behaviour, which was generally found to improve following participation in the programs. Evaluations of learner reactions and learning outcomes also suggested that the programs have positive effects. CONCLUSION Family medicine residency training programs differ from all other residency training programs in their shorter duration, usually 2 years, and the broader scope of learning within those 2 years. Few studies on teaching-skills training, however, were designed specifically for family medicine residents. Further studies assessing the effects of teaching-skills training in family medicine residents are needed to stimulate development of adapted programs for the discipline. Future research should also assess how residents’ teaching-skills training can affect their learners’ clinical training and eventually patient care. PMID:19752261

Maximizing the Impact of Systematic Reviews in Health Care Decision Making: A Systematic Scoping Review of Knowledge-Translation Resources

PubMed Central

Chambers, Duncan; Wilson, Paul M; Thompson, Carl A; Hanbury, Andria; Farley, Katherine; Light, Kate

2011-01-01

Context: Barriers to the use of systematic reviews by policymakers may be overcome by resources that adapt and present the findings in formats more directly tailored to their needs. We performed a systematic scoping review to identify such knowledge-translation resources and evaluations of them. Methods: Resources were eligible for inclusion in this study if they were based exclusively or primarily on systematic reviews and were aimed at health care policymakers at the national or local level. Resources were identified by screening the websites of health technology assessment agencies and systematic review producers, supplemented by an email survey. Electronic databases and proceedings of the Cochrane Colloquium and HTA International were searched as well for published and unpublished evaluations of knowledge-translation resources. Resources were classified as summaries, overviews, or policy briefs using a previously published classification. Findings: Twenty knowledge-translation resources were identified, of which eleven were classified as summaries, six as overviews, and three as policy briefs. Resources added value to systematic reviews by, for example, evaluating their methodological quality or assessing the reliability of their conclusions or their generalizability to particular settings. The literature search found four published evaluation studies of knowledge-translation resources, and the screening of abstracts and contact with authors found three more unpublished studies. The majority of studies reported on the perceived usefulness of the service, although there were some examples of review-based resources being used to assist actual decision making. Conclusions: Systematic review producers provide a variety of resources to help policymakers, of which focused summaries are the most common. More evaluations of these resources are required to ensure users’ needs are being met, to demonstrate their impact, and to justify their funding. PMID:21418315

Enhancing navigation in biomedical databases by community voting and database-driven text classification

PubMed Central

Duchrow, Timo; Shtatland, Timur; Guettler, Daniel; Pivovarov, Misha; Kramer, Stefan; Weissleder, Ralph

2009-01-01

Background The breadth of biological databases and their information content continues to increase exponentially. Unfortunately, our ability to query such sources is still often suboptimal. Here, we introduce and apply community voting, database-driven text classification, and visual aids as a means to incorporate distributed expert knowledge, to automatically classify database entries and to efficiently retrieve them. Results Using a previously developed peptide database as an example, we compared several machine learning algorithms in their ability to classify abstracts of published literature results into categories relevant to peptide research, such as related or not related to cancer, angiogenesis, molecular imaging, etc. Ensembles of bagged decision trees met the requirements of our application best. No other algorithm consistently performed better in comparative testing. Moreover, we show that the algorithm produces meaningful class probability estimates, which can be used to visualize the confidence of automatic classification during the retrieval process. To allow viewing long lists of search results enriched by automatic classifications, we added a dynamic heat map to the web interface. We take advantage of community knowledge by enabling users to cast votes in Web 2.0 style in order to correct automated classification errors, which triggers reclassification of all entries. We used a novel framework in which the database "drives" the entire vote aggregation and reclassification process to increase speed while conserving computational resources and keeping the method scalable. In our experiments, we simulate community voting by adding various levels of noise to nearly perfectly labelled instances, and show that, under such conditions, classification can be improved significantly. Conclusion Using PepBank as a model database, we show how to build a classification-aided retrieval system that gathers training data from the community, is completely controlled by the database, scales well with concurrent change events, and can be adapted to add text classification capability to other biomedical databases. The system can be accessed at . PMID:19799796

Protein Bioinformatics Databases and Resources

PubMed Central

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

2017-01-01

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

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources materials. Supplement 31, 1987.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

The Environmental Quality Instructional Resources Center in Columbus, Ohio, acquires, reviews, indexes, and announces both print (books, modules, units, etc.) and non-print (films, slides, video tapes, etc.) materials related to water quality and water resources education and instruction. This publication contains abstracts and indexes to selected…

Sustainable Development of Natural Resources in the Third World: Technological and Institutional Challenges. An International Symposium (Columbus, OH, September 3-6, 1985).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. School of Natural Resources.

This booket contains abstracts of papers presented at a symposium which focused on sustainable development of natural resources in third world countries. The abstracts are organized under these headings: (1) factors affecting individual's resource use decisions; (2) resource conservation and economic development; (3) research on alternative…

Mathematical Notation in Bibliographic Databases.

ERIC Educational Resources Information Center

Pasterczyk, Catherine E.

1990-01-01

Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

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.

Current Abstracts Nuclear Reactors and Technology

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

Bales, J.D.; Hicks, S.C.

1993-01-01

This publication Nuclear Reactors and Technology (NRT) announces on a monthly basis the current worldwide information available from the open literature on nuclear reactors and technology, including all aspects of power reactors, components and accessories, fuel elements, control systems, and materials. This publication contains the abstracts of DOE reports, journal articles, conference papers, patents, theses, and monographs added to the Energy Science and Technology Database during the past month. Also included are US information obtained through acquisition programs or interagency agreements and international information obtained through acquisition programs or interagency agreements and international information obtained through the International Energy Agency`smore » Energy Technology Data Exchange or government-to-government agreements. The digests in NRT and other citations to information on nuclear reactors back to 1948 are available for online searching and retrieval on the Energy Science and Technology Database and Nuclear Science Abstracts (NSA) database. Current information, added daily to the Energy Science and Technology Database, is available to DOE and its contractors through the DOE Integrated Technical Information System. Customized profiles can be developed to provide current information to meet each user`s needs.« less

Database resources of the National Center for Biotechnology Information

PubMed Central

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

2008-01-01

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

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

PubMed Central

Misra, Namrata; Parida, Bikram Kumar

2013-01-01

Abstract Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other “omic” approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of “omics” in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of “omic” approaches in the metabolic pathway studies for microalgal biofuel production. PMID:24044362

Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics

PubMed Central

Fukunishi, Yoshifumi; Mashimo, Tadaaki; Misoo, Kiyotaka; Wakabayashi, Yoshinori; Miyaki, Toshiaki; Ohta, Seiji; Nakamura, Mayu; Ikeda, Kazuyoshi

2016-01-01

Abstract: Background Computer-aided drug design is still a state-of-the-art process in medicinal chemistry, and the main topics in this field have been extensively studied and well reviewed. These topics include compound databases, ligand-binding pocket prediction, protein-compound docking, virtual screening, target/off-target prediction, physical property prediction, molecular simulation and pharmacokinetics/pharmacodynamics (PK/PD) prediction. Message and Conclusion: However, there are also a number of secondary or miscellaneous topics that have been less well covered. For example, methods for synthesizing and predicting the synthetic accessibility (SA) of designed compounds are important in practical drug development, and hardware/software resources for performing the computations in computer-aided drug design are crucial. Cloud computing and general purpose graphics processing unit (GPGPU) computing have been used in virtual screening and molecular dynamics simulations. Not surprisingly, there is a growing demand for computer systems which combine these resources. In the present review, we summarize and discuss these various topics of drug design. PMID:27075578

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.

Effects of climate change on water abstraction restrictions for irrigation during droughts - The UK case

NASA Astrophysics Data System (ADS)

Rey Vicario, D.; Holman, I.

2016-12-01

The use of water for irrigation and on-farm reservoir filling is globally important for agricultural production. In humid climates, like the UK, supplemental irrigation can be critical to buffer the effects of rainfall variability and to achieve high quality crops. Given regulatory efforts to secure sufficient environmental river flows and meet rising water demands due to population growth and climate change, increasing water scarcity is likely to compound the drought challenges faced by irrigated agriculture in this region. Currently, water abstraction from surface waters for agricultural irrigation can be restricted by the Environment Agency during droughts under Section 57 of the Water Resources Act (1991), based on abnormally low river flow levels and rainfall forecast, causing significant economic impacts on irrigated agricultural production. The aim of this study is to assess the impact that climate change may have on agricultural abstraction in the UK within the context of the abstraction restriction triggers currently in place. These triggers have been applied to the `Future Flows hydrology' database to assess the likelihood of increasing restrictions on agricultural abstraction in the future by comparing the probability of voluntary and compulsory restrictions in the baseline (1961-1990) and future period (2071-2098) for 282 catchments throughout the whole of the UK. The results of this study show a general increase in the probability of future agricultural irrigation abstraction restrictions in the UK in the summer, particularly in the South West, although there is significant variability between the 11 ensemble members. The results also indicate that UK winters are likely to become wetter in the future, although in some catchments the probability of abstraction restriction in the reservoir refilling winter months (November-February) could increase slightly. An increasing frequency of drought events due to climate change is therefore likely to lead to more water abstraction restrictions, increasing the need for irrigators to adapt their businesses to increase drought resilience and hence food security.

Database resources of the National Center for Biotechnology Information

PubMed Central

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

2001-01-01

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

Applications of Technology to CAS Data-Base Production.

ERIC Educational Resources Information Center

Weisgerber, David W.

1984-01-01

Reviews the economic importance of applying computer technology to Chemical Abstracts Service database production from 1973 to 1983. Database building, technological applications for editorial processing (online editing, Author Index Manufacturing System), and benefits (increased staff productivity, reduced rate of increase of cost of services,…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement VIII.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials; related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and…

Coupling Radar Rainfall to Hydrological Models for Water Abstraction Management

NASA Astrophysics Data System (ADS)

Asfaw, Alemayehu; Shucksmith, James; Smith, Andrea; MacDonald, Ken

2015-04-01

The impacts of climate change and growing water use are likely to put considerable pressure on water resources and the environment. In the UK, a reform to surface water abstraction policy has recently been proposed which aims to increase the efficiency of using available water resources whilst minimising impacts on the aquatic environment. Key aspects to this reform include the consideration of dynamic rather than static abstraction licensing as well as introducing water trading concepts. Dynamic licensing will permit varying levels of abstraction dependent on environmental conditions (i.e. river flow and quality). The practical implementation of an effective dynamic abstraction strategy requires suitable flow forecasting techniques to inform abstraction asset management. Potentially the predicted availability of water resources within a catchment can be coupled to predicted demand and current storage to inform a cost effective water resource management strategy which minimises environmental impacts. The aim of this work is to use a historical analysis of UK case study catchment to compare potential water resource availability using modelled dynamic abstraction scenario informed by a flow forecasting model, against observed abstraction under a conventional abstraction regime. The work also demonstrates the impacts of modelling uncertainties on the accuracy of predicted water availability over range of forecast lead times. The study utilised a conceptual rainfall-runoff model PDM - Probability-Distributed Model developed by Centre for Ecology & Hydrology - set up in the Dove River catchment (UK) using 1km2 resolution radar rainfall as inputs and 15 min resolution gauged flow data for calibration and validation. Data assimilation procedures are implemented to improve flow predictions using observed flow data. Uncertainties in the radar rainfall data used in the model are quantified using artificial statistical error model described by Gaussian distribution and propagated through the model to assess its influence on the forecasted flow uncertainty. Furthermore, the effects of uncertainties at different forecast lead times on potential abstraction strategies are assessed. The results show that over a 10 year period, an average of approximately 70 ML/d of potential water is missed in the study catchment under a convention abstraction regime. This indicates a considerable potential for the use of flow forecasting models to effectively implement advanced abstraction management and more efficiently utilize available water resources in the study catchment.

Emission & Generation Resource Integrated Database (eGRID)

EPA Pesticide Factsheets

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

SABER: The Searchable Annotated Bibliography of Education Research in Astronomy

NASA Astrophysics Data System (ADS)

Bruning, David H.; Bailey, J. M.; Brissenden, G.

2006-12-01

Starting a new research project in astronomy education is hard because the literature is scattered throughout many journals. Relevant astronomy education research may be in psychology journals, science education journals, physics education journals, or even in science journals themselves. Tracking the vast realm of literature is difficult, especially since libraries do not carry many of these journals and related abstracting services. SABER is an online resource (http://astronomy.uwp.edu/saber/) that was started in 2001 specifically to reduce this “scatter” by compiling into one place an annotated bibliography of relevant education research articles. The database now includes more than 150 articles specifically addressing astronomy education research. Visit SABER and see what it can do for you.

National Vulnerability Database (NVD)

National Institute of Standards and Technology Data Gateway

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

STEM Education Related Dissertation Abstracts: A Bounded Qualitative Meta-Study

ERIC Educational Resources Information Center

Banning, James; Folkestad, James E.

2012-01-01

This article utilizes a bounded qualitative meta-study framework to examine the 101 dissertation abstracts found by searching the ProQuest Dissertation and Theses[TM] digital database for dissertations abstracts from 1990 through 2010 using the search terms education, science, technology, engineer, and STEM/SMET. Professional search librarians…

Incomplete evidence: the inadequacy of databases in tracing published adverse drug reactions in clinical trials

PubMed Central

Derry, Sheena; Kong Loke, Yoon; Aronson, Jeffrey K

2001-01-01

Background We would expect information on adverse drug reactions in randomised clinical trials to be easily retrievable from specific searches of electronic databases. However, complete retrieval of such information may not be straightforward, for two reasons. First, not all clinical drug trials provide data on the frequency of adverse effects. Secondly, not all electronic records of trials include terms in the abstract or indexing fields that enable us to select those with adverse effects data. We have determined how often automated search methods, using indexing terms and/or textwords in the title or abstract, would fail to retrieve trials with adverse effects data. Methods We used a sample set of 107 trials known to report frequencies of adverse drug effects, and measured the proportion that (i) were not assigned the appropriate adverse effects indexing terms in the electronic databases, and (ii) did not contain identifiable adverse effects textwords in the title or abstract. Results Of the 81 trials with records on both MEDLINE and EMBASE, 25 were not indexed for adverse effects in either database. Twenty-six trials were indexed in one database but not the other. Only 66 of the 107 trials reporting adverse effects data mentioned this in the abstract or title of the paper. Simultaneous use of textword and indexing terms retrieved only 82/107 (77%) papers. Conclusions Specific search strategies based on adverse effects textwords and indexing terms will fail to identify nearly a quarter of trials that report on the rate of drug adverse effects. PMID:11591220

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

PubMed Central

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

2011-01-01

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

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

PubMed Central

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

2011-01-01

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

MNDR v2.0: an updated resource of ncRNA–disease associations in mammals

PubMed Central

Cui, Tianyu; Zhang, Lin; Huang, Yan; Yi, Ying; Tan, Puwen; Zhao, Yue; Hu, Yongfei

2018-01-01

Abstract Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA–disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA–disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA–disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework. The new developments in MNDR v2.0 include (i) an over 220-fold increase in ncRNA–disease associations enhancement compared with the previous version (including lncRNA, miRNA, piRNA, snoRNA and more than 1400 diseases); (ii) integrating experimental and prediction evidence from 14 resources and prediction algorithms for each ncRNA–disease association; (iii) mapping disease names to the Disease Ontology and Medical Subject Headings (MeSH); (iv) providing a confidence score for each ncRNA–disease association and (v) an increase of species coverage to six mammals. Finally, MNDR v2.0 intends to provide the scientific community with a resource for efficient browsing and extraction of the associations between diverse ncRNAs and diseases, including >260 000 ncRNA–disease associations. PMID:29106639

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome

PubMed Central

Liu, Hui; Wang, Huaizhi; Wei, Zhen; Zhang, Songyao; Hua, Gang; Zhang, Shao-Wu; Zhang, Lin; Gao, Shou-Jiang

2018-01-01

Abstract Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. Since its inception in 2014, the Met-DB (Liu, H., Flores, M.A., Meng, J., Zhang, L., Zhao, X., Rao, M.K., Chen, Y. and Huang, Y. (2015) MeT-DB: a database of transcriptome methylation in mammalian cells. Nucleic Acids Res., 43, D197–D203), has become an important resource for methyltranscriptome, especially in the N6-methyl-adenosine (m6A) research community. Here, we report Met-DB v2.0, the significantly improved second version of Met-DB, which is entirely redesigned to focus more on elucidating context-specific m6A functions. Met-DB v2.0 has a major increase in context-specific m6A peaks and single-base sites predicted from 185 samples for 7 species from 26 independent studies. Moreover, it is also integrated with a new database for targets of m6A readers, erasers and writers and expanded with more collections of functional data. The redesigned Met-DB v2.0 web interface and genome browser provide more friendly, powerful, and informative ways to query and visualize the data. More importantly, MeT-DB v2.0 offers for the first time a series of tools specifically designed for understanding m6A functions. Met-DB V2.0 will be a valuable resource for m6A methyltranscriptome research. The Met-DB V2.0 database is available at http://compgenomics.utsa.edu/MeTDB/ and http://www.xjtlu.edu.cn/metdb2. PMID:29126312

Identifying known unknowns using the US EPA's CompTox Chemistry Dashboard.

PubMed

McEachran, Andrew D; Sobus, Jon R; Williams, Antony J

2017-03-01

Chemical features observed using high-resolution mass spectrometry can be tentatively identified using online chemical reference databases by searching molecular formulae and monoisotopic masses and then rank-ordering of the hits using appropriate relevance criteria. The most likely candidate "known unknowns," which are those chemicals unknown to an investigator but contained within a reference database or literature source, rise to the top of a chemical list when rank-ordered by the number of associated data sources. The U.S. EPA's CompTox Chemistry Dashboard is a curated and freely available resource for chemistry and computational toxicology research, containing more than 720,000 chemicals of relevance to environmental health science. In this research, the performance of the Dashboard for identifying known unknowns was evaluated against that of the online ChemSpider database, one of the primary resources used by mass spectrometrists, using multiple previously studied datasets reported in the peer-reviewed literature totaling 162 chemicals. These chemicals were examined using both applications via molecular formula and monoisotopic mass searches followed by rank-ordering of candidate compounds by associated references or data sources. A greater percentage of chemicals ranked in the top position when using the Dashboard, indicating an advantage of this application over ChemSpider for identifying known unknowns using data source ranking. Additional approaches are being developed for inclusion into a non-targeted analysis workflow as part of the CompTox Chemistry Dashboard. This work shows the potential for use of the Dashboard in exposure assessment and risk decision-making through significant improvements in non-targeted chemical identification. Graphical abstract Identifying known unknowns in the US EPA's CompTox Chemistry Dashboard from molecular formula and monoisotopic mass inputs.

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

NASA Astrophysics Data System (ADS)

Wang, Jian

2017-01-01

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

Content Independence in Multimedia Databases.

ERIC Educational Resources Information Center

de Vries, Arjen P.

2001-01-01

Investigates the role of data management in multimedia digital libraries, and its implications for the design of database management systems. Introduces the notions of content abstraction and content independence. Proposes a blueprint of a new class of database technology, which supports the basic functionality for the management of both content…

The CIS Database: Occupational Health and Safety Information Online.

ERIC Educational Resources Information Center

Siegel, Herbert; Scurr, Erica

1985-01-01

Describes document acquisition, selection, indexing, and abstracting and discusses online searching of the CIS database, an online system produced by the International Occupational Safety and Health Information Centre. This database comprehensively covers information in the field of occupational health and safety. Sample searches and search…

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

PubMed

Ridyard, Colin H; Hughes, Dyfrig A

2012-01-01

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

Remote Sensing of Earth Resources: A literature survey with indexes (1970 - 1973 supplement). Section 1: Abstracts

NASA Technical Reports Server (NTRS)

1975-01-01

Abstracts of reports, articles, and other documents introduced into the NASA scientific and technical information system between March 1970 and December 1973 are presented in the following areas: agriculture and forestry, environmental changes and cultural resources, geodesy and cartography, geology and mineral resources, oceanography and marine resources, hydrology and water management, data processing and distribution systems, instrumentation and sensors, and economic analysis.

Text processing through Web services: calling Whatizit.

PubMed

Rebholz-Schuhmann, Dietrich; Arregui, Miguel; Gaudan, Sylvain; Kirsch, Harald; Jimeno, Antonio

2008-01-15

Text-mining (TM) solutions are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of resources (e.g. available controlled vocabularies), with the amount of literature to be processed (e.g. about 17 million documents in PubMed) and with the demands of the user community (e.g. different methods for fact extraction). These demands motivated the development of a server-based solution for literature analysis. Whatizit is a suite of modules that analyse text for contained information, e.g. any scientific publication or Medline abstracts. Special modules identify terms and then link them to the corresponding entries in bioinformatics databases such as UniProtKb/Swiss-Prot data entries and gene ontology concepts. Other modules identify a set of selected annotation types like the set produced by the EBIMed analysis pipeline for proteins. In the case of Medline abstracts, Whatizit offers access to EBI's in-house installation via PMID or term query. For large quantities of the user's own text, the server can be operated in a streaming mode (http://www.ebi.ac.uk/webservices/whatizit).

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 28, 1986.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and nonprint materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 29, 1987.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources, Supplement XIV (1983).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 23 (1985).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement XII.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement XIX (1984).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 25 (1986).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to hazardous wastes and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS). A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement XVI.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement IX.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 24 (l985).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS). A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement XIII.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS). A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement XV.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement XI.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement X.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 26, 1986.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of governmental, private concerns, and…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement XX (1984).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 22 (1985).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS). A Compilation of Abstracts to Water Quality and Water Resources Materials. Supplement XVII.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 21 (1985).

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement 27, 1986.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials, Supplement XVIII.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracted/indexed materials include all levels of government, private concerns, and educational…

Abstracts of SIG Sessions.

ERIC Educational Resources Information Center

Proceedings of the ASIS Annual Meeting, 1997

1997-01-01

Presents abstracts of SIG Sessions. Highlights include digital collections; information retrieval methods; public interest/fair use; classification and indexing; electronic publication; funding; globalization; information technology projects; interface design; networking in developing countries; metadata; multilingual databases; networked…

The Microphysiology Systems Database for Analyzing and Modeling Compound Interactions with Human and Animal Organ Models

PubMed Central

Vernetti, Lawrence; Bergenthal, Luke; Shun, Tong Ying; Taylor, D. Lansing

2016-01-01

Abstract Microfluidic human organ models, microphysiology systems (MPS), are currently being developed as predictive models of drug safety and efficacy in humans. To design and validate MPS as predictive of human safety liabilities requires safety data for a reference set of compounds, combined with in vitro data from the human organ models. To address this need, we have developed an internet database, the MPS database (MPS-Db), as a powerful platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. The present study demonstrates the capability of the MPS-Db in early safety testing using a human liver MPS to relate the effects of tolcapone and entacapone in the in vitro model to human in vivo effects. These two compounds were chosen to be evaluated as a representative pair of marketed drugs because they are structurally similar, have the same target, and were found safe or had an acceptable risk in preclinical and clinical trials, yet tolcapone induced unacceptable levels of hepatotoxicity while entacapone was found to be safe. Results demonstrate the utility of the MPS-Db as an essential resource for relating in vitro organ model data to the multiple biochemical, preclinical, and clinical data sources on in vivo drug effects. PMID:28781990

SCPortalen: human and mouse single-cell centric database

PubMed Central

Noguchi, Shuhei; Böttcher, Michael; Hasegawa, Akira; Kouno, Tsukasa; Kato, Sachi; Tada, Yuhki; Ura, Hiroki; Abe, Kuniya; Shin, Jay W; Plessy, Charles; Carninci, Piero

2018-01-01

Abstract Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database ‘SCPortalen’ (http://single-cell.clst.riken.jp/). The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available. The target users of SCPortalen are all researchers interested in specific cell types or population heterogeneity. Through the web interface of SCPortalen users are easily able to search, explore and download the single-cell datasets of their interests. PMID:29045713

A neotropical Miocene pollen database employing image-based search and semantic modeling1

PubMed Central

Han, Jing Ginger; Cao, Hongfei; Barb, Adrian; Punyasena, Surangi W.; Jaramillo, Carlos; Shyu, Chi-Ren

2014-01-01

• Premise of the study: Digital microscopic pollen images are being generated with increasing speed and volume, producing opportunities to develop new computational methods that increase the consistency and efficiency of pollen analysis and provide the palynological community a computational framework for information sharing and knowledge transfer. • Methods: Mathematical methods were used to assign trait semantics (abstract morphological representations) of the images of neotropical Miocene pollen and spores. Advanced database-indexing structures were built to compare and retrieve similar images based on their visual content. A Web-based system was developed to provide novel tools for automatic trait semantic annotation and image retrieval by trait semantics and visual content. • Results: Mathematical models that map visual features to trait semantics can be used to annotate images with morphology semantics and to search image databases with improved reliability and productivity. Images can also be searched by visual content, providing users with customized emphases on traits such as color, shape, and texture. • Discussion: Content- and semantic-based image searches provide a powerful computational platform for pollen and spore identification. The infrastructure outlined provides a framework for building a community-wide palynological resource, streamlining the process of manual identification, analysis, and species discovery. PMID:25202648

NNDC Data Services

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

Tuli, J.K.; Sonzogni,A.

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

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

USGS Publications Warehouse

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

2014-01-01

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

A Database Evaluation Based on Information Needs of Academic Social Scientists.

ERIC Educational Resources Information Center

Buterbaugh, Nancy Toth

This study evaluates two databases, "Historical Abstracts" and REESWeb, to determine their effectiveness in supporting academic social science research. While many performance evaluations gather quantitative data from isolated query and response transactions, this study is a qualitative evaluation of the databases in the context of…

NCCDPHP PUBLICATION DATABASE

EPA Science Inventory

This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

Systematic review of the links between human resource management practices and performance.

PubMed

Patterson, M; Rick, J; Wood, S; Carroll, C; Balain, S; Booth, A

2010-10-01

In recent years human resource management (HRM) has been seen as an important factor in the successful realisation of organisational change programmes. The UK NHS is undergoing substantial organisational change and there is a need to establish which human resource (HR) initiatives may be most effective. To assess the results from a wide-ranging series of systematic reviews of the evidence on HRM and performance. The first part assesses evidence on use of HRM in the UK and fidelity of practice implemented. The second part considers evidence for the impact of HRM practices on intermediate outcomes, which can impact on final outcomes, such as organisational performance or patient care. The following databases were searched: Applied Social Sciences Index and Abstracts (ASSIA), British Nursing Index (BNI), Business Source Premier, Campbell Collaboration, Cochrane Central Register of Controlled Trials (CENTRAL), Cochrane Database of Systematic Reviews (CDSR), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Database of Abstracts of Reviews of Effectiveness (DARE), DH-Data, EMBASE, Health Management Information Consortium (HMIC), International Bibliography of the Social Sciences (IBSS), King's Fund database, MEDLINE, NHS Economic Evaluation Database (NHS EED), National Research Register (NRR), PREMEDLINE, PsycINFO, ReFeR, Social Sciences Citation Index (SSCI) and Science Citation Index (SCI). The searches were conducted in May/June 2006. Broad categories of HRM interventions and intermediate outcomes were generated: 10 HRM categories and 12 intermediate outcome categories. Seven patient final outcomes were derived from the NHS Performance Indicators and the NHS Improvement Plan. The quality criteria used to select papers incorporated a longitudinal study design filter to provide evidence of the causal direction of relationships between HRM and relevant outcomes. Single HRM practices were considered. Within the health-specific literature, focus was on the impact of HRM on patient outcomes. Information is presented on the reliability of measures in each of the intermediate outcome areas. Work design practices that enhance employee autonomy and control influenced a number of outcomes and there was consistent evidence for the positive impact of increased job control on employee outcomes, such as job satisfaction, absence and health. For employee participation, the small number of studies reviewed supported the involvement of employees in design/implementation of changes that affect their work. In health literature in particular, employee involvement through quality improvement teams resulted in improved patient outcomes. Findings were positive for the impact of training on the intended outcomes of the initiatives. Support for the impact of performance management practices was apparent, in particular feedback on performance outcomes and the use of participative goal setting. Strong associations were found among all intermediate outcomes, and the relationship between most intermediate behaviours and outcomes were significant. Limited evidence was available on the use of HRM and on the implementation of policy. Also, the specific practices studied within each HRM category differ so there was little evidence to show whether similar practices have the same effects in health and non-health settings. Some potentially effective practices for both health and non-health areas were identified, and HRM methods could be used to support change processes within the NHS; the findings relating to work organisation are particularly promising with regard to changes in methods of service delivery. Using training to support the implementation of change is highlighted. However, future multilevel studies that embrace the individual, team and organisational level are needed. Studies should look into interventions aimed at improving HR outcomes and performance, and allow for pre- and post-intervention measurement of practices and outcomes.

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials.

ERIC Educational Resources Information Center

Office of Water Program Operations (EPA), Cincinnati, OH. National Training and Operational Technology Center.

Presented is a compilation of over 3,000 abstracts on print and non-print materials related to water quality and water resources education. Entries are included from all levels of governmental sources, private concerns, and educational institutions. Each entry includes: title, author, cross references, descriptors, and availability. (CLS)

dSED: A database tool for modeling sediment early diagenesis

NASA Astrophysics Data System (ADS)

Katsev, S.; Rancourt, D. G.; L'Heureux, I.

2003-04-01

Sediment early diagenesis reaction transport models (RTMs) are becoming powerful tools in providing kinetic descriptions of the metal and nutrient diagenetic cycling in marine, lacustrine, estuarine, and other aquatic sediments, as well as of exchanges with the water column. Whereas there exist several good database/program combinations for thermodynamic equilibrium calculations in aqueous systems, at present there exist no database tools for classification and analysis of the kinetic data essential to RTM development. We present a database tool that is intended to serve as an online resource for information about chemical reactions, solid phase and solute reactants, sorption reactions, transport mechanisms, and kinetic and equilibrium parameters that are relevant to sediment diagenesis processes. The list of reactive substances includes but is not limited to organic matter, Fe and Mn oxides and oxyhydroxides, sulfides and sulfates, calcium, iron, and manganese carbonates, phosphorus-bearing minerals, and silicates. Aqueous phases include dissolved carbon dioxide, oxygen, methane, hydrogen sulfide, sulfate, nitrate, phosphate, some organic compounds, and dissolved metal species. A number of filters allow extracting information according to user-specified criteria, e.g., about a class of substances contributing to the cycling of iron. The database also includes bibliographic information about published diagenetic models and the reactions and processes that they consider. At the time of preparing this abstract, dSED contained 128 reactions and 12 pre-defined filters. dSED is maintained by the Lake Sediment Structure and Evolution (LSSE) group at the University of Ottawa (www.science.uottawa.ca/LSSE/dSED) and we invite input from the geochemical community.

Ten Years Experience In Geo-Databases For Linear Facilities Risk Assessment (Lfra)

NASA Astrophysics Data System (ADS)

Oboni, F.

2003-04-01

Keywords: geo-environmental, database, ISO14000, management, decision-making, risk, pipelines, roads, railroads, loss control, SAR, hazard identification ABSTRACT: During the past decades, characterized by the development of the Risk Management (RM) culture, a variety of different RM models have been proposed by governmental agencies in various parts of the world. The most structured models appear to have originated in the field of environmental RM. These models are briefly reviewed in the first section of the paper focusing the attention on the difference between Hazard Management and Risk Management and the need to use databases in order to allow retrieval of specific information and effective updating. The core of the paper reviews a number of different RM approaches, based on extensions of geo-databases, specifically developed for linear facilities (LF) in transportation corridors since the early 90s in Switzerland, Italy, Canada, the US and South America. The applications are compared in terms of methodology, capabilities and resources necessary to their implementation. The paper then focuses the attention on the level of detail that applications and related data have to attain. Common pitfalls related to decision making based on hazards rather than on risks are discussed. The paper focuses the last sections on the description of the next generation of linear facility RA application, including examples of results and discussion of future methodological research. It is shown that geo-databases should be linked to loss control and accident reports in order to maximize their benefits. The links between RA and ISO 14000 (environmental management code) are explicitly considered.

An automatic method to generate domain-specific investigator networks using PubMed abstracts.

PubMed

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

2007-06-20

Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70-90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. We successfully created a web-based prototype capable of creating domain-specific investigator networks based on an application that accurately generates detailed investigator profiles from PubMed abstracts combined with robust standard vocabularies. This approach could be used for other biomedical fields to efficiently establish domain-specific investigator networks.

An automatic method to generate domain-specific investigator networks using PubMed abstracts

PubMed Central

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

2007-01-01

Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a web-based prototype capable of creating domain-specific investigator networks based on an application that accurately generates detailed investigator profiles from PubMed abstracts combined with robust standard vocabularies. This approach could be used for other biomedical fields to efficiently establish domain-specific investigator networks. PMID:17584920

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

USDA-ARS?s Scientific Manuscript database

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

Database resources of the National Center for Biotechnology Information.

PubMed

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

2007-01-01

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

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

PubMed

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

2014-07-01

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

Resources | Office of Cancer Genomics

Cancer.gov

OCG provides a variety of scientific and educational resources for both cancer researchers and members of the general public. These resources are divided into the following types: OCG-Supported Resources: Tools, databases, and reagents generated by initiated and completed OCG programs for researchers, educators, and students. (Note: Databases for current OCG programs are available through program-specific data matrices)

Water Quality Instructional Resources Information System (IRIS): A Compilation of Abstracts to Water Quality and Water Resources Materials. Includes May 1979 edition and Supplements 1-15.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus, OH. Information Reference Center for Science, Mathematics, and Environmental Education.

Compiled are abstracts and indexes to selected print and non-print materials related to wastewater treatment and water quality education and instruction, as well as materials related to pesticides, hazardous wastes, and public participation. Sources of abstracts/indexed materials include all levels of government, private concerns, and educational…

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

PubMed Central

Onwubiko, J.; Zaru, R.; Rosanoff, S.; Antunes, R.; Bingley, M.; Watkins, X.; O'Donovan, C.; Martin, M. J.

2017-01-01

Abstract Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al., (2013), BMC Bioinformatics, 14 (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al., Nucleic Acids Res.2016; 44, D385–D395) Rhea—a database of enzyme-catalysed reactions (Morgat, A., et al., Nucleic Acids Res. 2015; 43, D459-D464), Reactome—a database of biochemical pathways (Fabregat, A., et al., Nucleic Acids Res. 2016; 44, D481–D487), IntEnz—a resource with enzyme nomenclature information (Fleischmann, A., et al., Nucleic Acids Res. 2004 32, D434–D437) and ChEBI (Hastings, J., et al., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al., Nucleic Acids Res. 201442, 1083–1090)—resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. PMID:28158609

Literature searching for clinical and cost-effectiveness studies used in health technology assessment reports carried out for the National Institute for Clinical Excellence appraisal system.

PubMed

Royle, P; Waugh, N

2003-01-01

To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. A sample of 20 recent TARs. All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.

CottonDB: A resource for cotton genome research

USDA-ARS?s Scientific Manuscript database

CottonDB (http://cottondb.org/) is a database and web resource for cotton genomic and genetic research. Created in 1995, CottonDB was among the first plant genome databases established by the USDA-ARS. Accessed through a website interface, the database aims to be a convenient, inclusive medium of ...

Smart home technologies for health and social care support.

PubMed

Martin, Suzanne; Kelly, Greg; Kernohan, W George; McCreight, Bernadette; Nugent, Christopher

2008-10-08

The integration of smart home technology to support health and social care is acquiring an increasing global significance. Provision is framed within the context of a rapidly changing population profile, which is impacting on the number of people requiring health and social care, workforce availability and the funding of healthcare systems. To explore the effectiveness of smart home technologies as an intervention for people with physical disability, cognitive impairment or learning disability, who are living at home, and to consider the impact on the individual's health status and on the financial resources of health care. We searched the following databases for primary studies: (a) the Cochrane Effective Practice and Organisation of Care (EPOC) Group Register, (b) the Cochrane Central Register of Controlled Trials (CENTRAL), (The Cochrane Library, issue 1, 2007), and (c) bibliographic databases, including MEDLINE (1966 to March 2007), EMBASE (1980 to March 2007) and CINAHL (1982 to March 2007). We also searched the Database of Abstracts of Reviews of Effectiveness (DARE). We searched the electronic databases using a strategy developed by the EPOC Trials Search Co-ordinator. We included randomised controlled trials (RCTs), quasi-experimental studies, controlled before and after studies (CBAs) and interrupted time series analyses (ITS). Participants included adults over the age of 18, living in their home in a community setting. Participants with a physical disability, dementia or a learning disability were included. The included interventions were social alarms, electronic assistive devices, telecare social alert platforms, environmental control systems, automated home environments and 'ubiquitous homes'. Outcome measures included any objective measure that records an impact on a participant's quality of life, healthcare professional workload, economic outcomes, costs to healthcare provider or costs to participant. We included measures of service satisfaction, device satisfaction and healthcare professional attitudes or satisfaction. One review author completed the search strategy with the support of a life and health sciences librarian. Two review authors independently screened titles and abstracts of results. No studies were identified which met the inclusion criteria. This review highlights the current lack of empirical evidence to support or refute the use of smart home technologies within health and social care, which is significant for practitioners and healthcare consumers.

CBD: a biomarker database for colorectal cancer

PubMed Central

Zhang, Xueli; Sun, Xiao-Feng; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Abstract Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD. Database URL: http://sysbio.suda.edu.cn/CBD/ PMID:29846545

Resources in Education (RIE). Volume 36, Number 11.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 12.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community, including researchers, teachers, students, school board members, school administrators, counselors, parents, etc. Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 10.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 7.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 2.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 5.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 3.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 9.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 8.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 4.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 1.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

Resources in Education (RIE). Volume 36, Number 6.

ERIC Educational Resources Information Center

Resources in Education, 2001

2001-01-01

"Resources in Education" (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, parents, etc.). Each issue announces approximately 1000 documents and provides…

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

USGS Publications Warehouse

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

2000-01-01

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

Computing through Scientific Abstractions in SysBioPS

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

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

2004-10-13

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

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

PubMed

Kodama, Yuichi; Mashima, Jun; Kaminuma, Eli; Gojobori, Takashi; Ogasawara, Osamu; Takagi, Toshihisa; Okubo, Kousaku; Nakamura, Yasukazu

2012-01-01

The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

Multi-terminology indexing for the assignment of MeSH descriptors to medical abstracts in French.

PubMed

Pereira, Suzanne; Sakji, Saoussen; Névéol, Aurélie; Kergourlay, Ivan; Kerdelhué, Gaétan; Serrot, Elisabeth; Joubert, Michel; Darmoni, Stéfan J

2009-11-14

To facilitate information retrieval in the biomedical domain, a system for the automatic assignment of Medical Subject Headings to documents curated by an online quality-controlled health gateway was implemented. The French Multi-Terminology Indexer (F-MTI) implements a multiterminology approach using nine main medical terminologies in French and the mappings between them. This paper presents recent efforts to assess the added value of (a) integrating four new terminologies (Orphanet, ATC, drug names, MeSH supplementary concepts) into F-MTI's knowledge sources and (b) performing the automatic indexing on the titles and abstracts (vs. title only) of the online health resources. F-MTI was evaluated on a CISMeF corpus comprising 18,161 manually indexed resources. The performance of F-MTI including nine health terminologies on CISMeF resources with Title only was 27.9% precision and 19.7% recall, while the performance on CISMeF resources with Title and Abstract is 14.9 % precision (-13.0%) and 25.9% recall (+6.2%). In a few weeks, CISMeF will launch the indexing of resources based on title and abstract, using nine terminologies.

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.

PubMed

Jeffryes, James G; Colastani, Ricardo L; Elbadawi-Sidhu, Mona; Kind, Tobias; Niehaus, Thomas D; Broadbelt, Linda J; Hanson, Andrew D; Fiehn, Oliver; Tyo, Keith E J; Henry, Christopher S

2015-01-01

In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography-mass spectrometry (LC-MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC-MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. Furthermore, MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures. Graphical abstractMINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.

The current state of epilepsy guidelines: A systematic review.

PubMed

Sauro, Khara M; Wiebe, Samuel; Dunkley, Colin; Janszky, Jozsef; Kumlien, Eva; Moshé, Solomon; Nakasato, Nobukazu; Pedley, Timothy A; Perucca, Emilio; Senties, Horacio; Thomas, Sanjeev V; Wang, Yuping; Wilmshurst, Jo; Jetté, Nathalie

2016-01-01

The International League Against Epilepsy (ILAE) Epilepsy Guidelines Task Force, composed of 14 international members, was established in 2011 to identify, using systematic review methodology, international epilepsy clinical care guidelines, assess their quality, and determine gaps in areas of need of development. A systematic review of the literature (1985-2014) was performed in six electronic databases (e.g. Medline, Embase) using a broad search strategy without initial limits to language or study design. Six gray literature databases (e.g., American Academy of Neurology [AAN], ILAE) were also searched to minimize publication bias. Two independent reviewers screened abstracts, reviewed full text articles, and performed data abstraction. Descriptive statistics and a meta-analysis were generated. The search identified 10,926 abstracts. Of the 410 articles selected for full text review, 63 met our eligibility criteria for a guideline. Of those included, 54 were in English and 9 were in other languages (French, Spanish, and Italian). Of all guidelines, 29% did not specify the target age groups, 27% were focused on adults, 22% included only children, and 6% specifically addressed issues related to women with epilepsy. Guidelines included in the review were most often aimed at guiding clinical practice for status epilepticus (n = 7), first seizure (n = 6), drug-resistant epilepsy (n = 5), and febrile seizures (n = 4), among others. Most of the guidelines were therapeutic (n = 35) or diagnostic (n = 16) in nature. The quality of the guidelines using a 1-7 point scale (7 = highest) varied and was moderate overall (mean = 4.99 ± 1.05 [SD]). We identified substantial gaps in topics (e.g., epilepsy in the elderly) and there was considerable heterogeneity in methodologic quality. The findings should offer a valuable resource for health professionals caring for people with epilepsy, since they will help guide the prioritization, development, and dissemination of future epilepsy-related guidelines. Wiley Periodicals, Inc. © 2015 International League Against Epilepsy.

Content Is King: Databases Preserve the Collective Information of Science.

PubMed

Yates, John R

2018-04-01

Databases store sequence information experimentally gathered to create resources that further science. In the last 20 years databases have become critical components of fields like proteomics where they provide the basis for large-scale and high-throughput proteomic informatics. Amos Bairoch, winner of the Association of Biomolecular Resource Facilities Frederick Sanger Award, has created some of the important databases proteomic research depends upon for accurate interpretation of data.

Database resources of the National Center for Biotechnology Information

PubMed Central

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

2006-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Database resources of the National Center for Biotechnology Information

PubMed Central

Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

2014-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429

Database resources of the National Center for Biotechnology

PubMed Central

Wheeler, David L.; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana A.; Wagner, Lukas

2003-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519941

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

PubMed Central

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

2002-01-01

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

Systems and methods for automatically identifying and linking names in digital resources

DOEpatents

Parker, Charles T.; Lyons, Catherine M.; Roston, Gerald P.; Garrity, George M.

2017-06-06

The present invention provides systems and methods for automatically identifying name-like-strings in digital resources, matching these name-like-string against a set of names held in an expertly curated database, and for those name-like-strings found in said database, enhancing the content by associating additional matter with the name, wherein said matter includes information about the names that is held within said database and pointers to other digital resources which include the same name and it synonyms.

Second Annual Conference on Astronomical Data Analysis Software and Systems. Abstracts

NASA Technical Reports Server (NTRS)

1992-01-01

Abstracts from the conference are presented. The topics covered include the following: next generation software systems and languages; databases, catalogs, and archives; user interfaces/visualization; real-time data acquisition/scheduling; and IRAF/STSDAS/PROS status reports.

Physicians utilisation of internet medical databases at the tertiary health institutions in Osun State, south west, Nigeria.

PubMed

Shabi, Iwok N; Shabi, Olabode M; Akewukereke, Modupe A; Udofia, Emem P

2011-12-01

To determine the extent, purpose, determinants and the impact of the utilization of Internet medical databases among the respondents. A descriptive cross sectional survey of 540 randomly selected physicians at the two tertiary health institutions in Osun State, south west, Nigeria. A total of 444 (82.2%) physicians completed the questionnaires. All the respondents have used the internet medical databases within the last 4 weeks of the study. Majority, (53.8%) used the internet resources at least once in 2 weeks, while 12.2% used the resources every day. The online resources are mainly sought for Routine patient care and for Research purposes. pubmed (70.3%), hinari (69.0%), and Free medical journals (60.1%) are the frequently used online databases/digital archives. The internet resources has positively impacted the Clinical practice (40.0%) and Research output (65.5%) of the physicians. There had been considerable increase in the extent and quality of utilization of online medical databases which has positively impacted on the Clinical practice and Research output of the physicians. Ease of finding the needed information and the availability of evidence based resources are the major determinants of the databases utilized. © 2011 The authors. Health Information and Libraries Journal © 2011 Health Libraries Group.

Administrative health data in Canada: lessons from history.

PubMed

Lucyk, Kelsey; Lu, Mingshan; Sajobi, Tolulope; Quan, Hude

2015-08-19

Health decision-making requires evidence from high-quality data. As one example, the Discharge Abstract Database (DAD) compiles data from the majority of Canadian hospitals to form one of the most comprehensive and highly regarded administrative health databases available for health research, internationally. However, despite the success of this and other administrative health data resources, little is known about their history or the factors that have led to their success. The purpose of this paper is to provide an historical overview of Canadian administrative health data for health research to contribute to the institutional memory of this field. We conducted a qualitative content analysis of approximately 20 key sources to construct an historical narrative of administrative health data in Canada. Specifically, we searched for content related to key events, individuals, challenges, and successes in this field over time. In Canada, administrative health data for health research has developed in tangent with provincial research centres. Interestingly, the lessons learned from this history align with the original recommendations of the 1964 Royal Commission on Health Services: (1) standardization, and (2) centralization of data resources, that is (3) facilitated through governmental financial support. The overview history provided here illustrates the need for longstanding partnerships between government and academia, for classification, terminology and standardization are time-consuming and ever-evolving processes. This paper will be of interest to those who work with administrative health data, and also for countries that are looking to build or improve upon their use of administrative health data for decision-making.

Estimating the Burden of Osteoarthritis to Plan for the Future.

PubMed

Marshall, Deborah A; Vanderby, Sonia; Barnabe, Cheryl; MacDonald, Karen V; Maxwell, Colleen; Mosher, Dianne; Wasylak, Tracy; Lix, Lisa; Enns, Ed; Frank, Cy; Noseworthy, Tom

2015-10-01

With aging and obesity trends, the incidence and prevalence of osteoarthritis (OA) is expected to rise in Canada, increasing the demand for health resources. Resource planning to meet this increasing need requires estimates of the anticipated number of OA patients. Using administrative data from Alberta, we estimated OA incidence and prevalence rates and examined their sensitivity to alternative case definitions. We identified cases in a linked data set spanning 1993 to 2010 (population registry, Discharge Abstract Database, physician claims, Ambulatory Care Classification System, and prescription drug data) using diagnostic codes and drug identification numbers. In the base case, incident cases were captured for patients with an OA diagnostic code for at least 2 physician visits within 2 years or any hospital admission. Seven alternative case definitions were applied and compared. Age- and sex-standardized incidence and prevalence rates were estimated to be 8.6 and 80.3 cases per 1,000 population, respectively, in the base case. Physician claims data alone captured 88% of OA cases. Prevalence rate estimates required 15 years of longitudinal data to plateau. Compared to the base case, estimates are sensitive to alternative case definitions. Administrative databases are a key source for estimating the burden and epidemiologic trends of chronic diseases such as OA in Canada. Despite their limitations, these data provide valuable information for estimating disease burden and planning health services. Estimates of OA are mostly defined through physician claims data and require a long period of longitudinal data. © 2015, American College of Rheumatology.

Resources in Education (RIE). Volume 27, Number 10.

ERIC Educational Resources Information Center

Resources in Education, 1992

1992-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 8.

ERIC Educational Resources Information Center

Resources in Education, 1992

1992-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 6.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 9.

ERIC Educational Resources Information Center

Resources in Education, 1992

1992-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 8.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 5.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 2.

ERIC Educational Resources Information Center

Resources in Education, 1991

1991-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 12.

ERIC Educational Resources Information Center

Resources in Education, 1992

1992-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 1.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 7.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 11.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 3.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 3.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 9.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 10.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 1.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 2.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 4.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 2.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 7.

ERIC Educational Resources Information Center

Resources in Education, 1992

1992-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 29, Number 1.

ERIC Educational Resources Information Center

Resources in Education, 1994

1994-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 6.

ERIC Educational Resources Information Center

Resources in Education, 1991

1991-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 7.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 9.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 5.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 3.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 24, Number 12.

ERIC Educational Resources Information Center

Resources in Education, 1989

1989-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 12.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 10.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 11.

ERIC Educational Resources Information Center

Resources in Education, 1992

1992-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 1.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 5.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 10.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 24, Number 10.

ERIC Educational Resources Information Center

Resources in Education, 1989

1989-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 29, Number 2.

ERIC Educational Resources Information Center

Resources in Education, 1994

1994-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 9.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 4.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 7.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 6.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 4.

ERIC Educational Resources Information Center

Resources in Education, 1991

1991-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 27, Number 4.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 24, Number 11.

ERIC Educational Resources Information Center

Resources in Education, 1989

1989-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 8.

ERIC Educational Resources Information Center

ERIC Processing and Reference Facility, Rockville, MD.

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 26, Number 3.

ERIC Educational Resources Information Center

Resources in Education, 1991

1991-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 28, Number 6.

ERIC Educational Resources Information Center

Resources in Education, 1993

1993-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 2.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

Resources in Education (RIE). Volume 25, Number 8.

ERIC Educational Resources Information Center

Resources in Education, 1990

1990-01-01

Resources in Education (RIE) is a monthly abstract journal that announces (catalogs, indexes, abstracts) documents of interest to the educational community (including researchers, teachers, students, school board members, school administrators, counselors, etc.). Each issue announces approximately 1,100 documents and provides indexes by Subject,…

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

PubMed Central

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

PubMed

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/

Rule-Based Statistical Calculations on a Database Abstract.

DTIC Science & Technology

1983-06-01

quadruples 17 L.6.6. Our methds ~ in distributed systems 17 L.6.7. Easy extensions 17 17. The datibms abstract as a database 17 17.1.w S orae mu is 1.7.2...the largest item in the intersection of two sets cannot be any larger that the minima of the maxima of the two sets for some numeric attribute. On the...from "range analysis" of arbitrary numeric attributes. Suppose the length range of tankers is from 300 to 1000 feet and that of American ships 50 to

Measurement tools for the diagnosis of nasal septal deviation: a systematic review

PubMed Central

2014-01-01

Objective To perform a systematic review of measurement tools utilized for the diagnosis of nasal septal deviation (NSD). Methods Electronic database searches were performed using MEDLINE (from 1966 to second week of August 2013), EMBASE (from 1966 to second week of August 2013), Web of Science (from 1945 to second week of August 2013) and all Evidence Based Medicine Reviews Files (EBMR); Cochrane Database of Systematic Review (CDSR), Cochrane Central Register of Controlled Trials (CCTR), Cochrane Methodology Register (CMR), Database of Abstracts of Reviews of Effects (DARE), American College of Physicians Journal Club (ACP Journal Club), Health Technology Assessments (HTA), NHS Economic Evaluation Database (NHSEED) till the second quarter of 2013. The search terms used in database searches were ‘nasal septum’, ‘deviation’, ‘diagnosis’, ‘nose deformities’ and ‘nose malformation’. The studies were reviewed using the updated Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Results Online searches resulted in 23 abstracts after removal of duplicates that resulted from overlap of studies between the electronic databases. An additional 15 abstracts were excluded due to lack of relevance. A total of 8 studies were systematically reviewed. Conclusions Diagnostic modalities such as acoustic rhinometry, rhinomanometry and nasal spectral sound analysis may be useful in identifying NSD in anterior region of the nasal cavity, but these tests in isolation are of limited utility. Compared to anterior rhinoscopy, nasal endoscopy, and imaging the above mentioned index tests lack sensitivity and specificity in identifying the presence, location, and severity of NSD. PMID:24762010

Quantifying Data Quality for Clinical Trials Using Electronic Data Capture

PubMed Central

Nahm, Meredith L.; Pieper, Carl F.; Cunningham, Maureen M.

2008-01-01

Background Historically, only partial assessments of data quality have been performed in clinical trials, for which the most common method of measuring database error rates has been to compare the case report form (CRF) to database entries and count discrepancies. Importantly, errors arising from medical record abstraction and transcription are rarely evaluated as part of such quality assessments. Electronic Data Capture (EDC) technology has had a further impact, as paper CRFs typically leveraged for quality measurement are not used in EDC processes. Methods and Principal Findings The National Institute on Drug Abuse Treatment Clinical Trials Network has developed, implemented, and evaluated methodology for holistically assessing data quality on EDC trials. We characterize the average source-to-database error rate (14.3 errors per 10,000 fields) for the first year of use of the new evaluation method. This error rate was significantly lower than the average of published error rates for source-to-database audits, and was similar to CRF-to-database error rates reported in the published literature. We attribute this largely to an absence of medical record abstraction on the trials we examined, and to an outpatient setting characterized by less acute patient conditions. Conclusions Historically, medical record abstraction is the most significant source of error by an order of magnitude, and should be measured and managed during the course of clinical trials. Source-to-database error rates are highly dependent on the amount of structured data collection in the clinical setting and on the complexity of the medical record, dependencies that should be considered when developing data quality benchmarks. PMID:18725958

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

Common Database Interface for Heterogeneous Software Engineering Tools.

DTIC Science & Technology

1987-12-01

SUB-GROUP Database Management Systems ;Programming(Comuters); 1e 05 Computer Files;Information Transfer;Interfaces; 19. ABSTRACT (Continue on reverse...Air Force Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Information Systems ...Literature ..... 8 System 690 Configuration ......... 8 Database Functionis ............ 14 Software Engineering Environments ... 14 Data Manager

Using glycome databases for drug discovery.

PubMed

Aoki-Kinoshita, Kiyoko F

2008-08-01

The glycomics field has made great advancements in the last decade due to technologies for their synthesis and analysis including carbohydrate microarrays. Accordingly, databases for glycomics research have also emerged and been made publicly available by many major institutions worldwide. This review introduces these and other useful databases on which new methods for drug discovery can be developed. The scope of this review covers current documented and accessible databases and resources pertaining to glycomics. These were selected with the expectation that they may be useful for drug discovery research. There is a plethora of glycomics databases that have much potential for drug discovery. This may seem daunting at first but this review helps to put some of these resources into perspective. Additionally, some thoughts on how to integrate these resources to allow more efficient research are presented.

Measuring use patterns of online journals and databases

PubMed Central

De Groote, Sandra L.; Dorsch, Josephine L.

2003-01-01

Purpose: This research sought to determine use of online biomedical journals and databases and to assess current user characteristics associated with the use of online resources in an academic health sciences center. Setting: The Library of the Health Sciences–Peoria is a regional site of the University of Illinois at Chicago (UIC) Library with 350 print journals, more than 4,000 online journals, and multiple online databases. Methodology: A survey was designed to assess online journal use, print journal use, database use, computer literacy levels, and other library user characteristics. A survey was sent through campus mail to all (471) UIC Peoria faculty, residents, and students. Results: Forty-one percent (188) of the surveys were returned. Ninety-eight percent of the students, faculty, and residents reported having convenient access to a computer connected to the Internet. While 53% of the users indicated they searched MEDLINE at least once a week, other databases showed much lower usage. Overall, 71% of respondents indicated a preference for online over print journals when possible. Conclusions: Users prefer online resources to print, and many choose to access these online resources remotely. Convenience and full-text availability appear to play roles in selecting online resources. The findings of this study suggest that databases without links to full text and online journal collections without links from bibliographic databases will have lower use. These findings have implications for collection development, promotion of library resources, and end-user training. PMID:12883574

Extracting patterns of database and software usage from the bioinformatics literature

PubMed Central

Duck, Geraint; Nenadic, Goran; Brass, Andy; Robertson, David L.; Stevens, Robert

2014-01-01

Motivation: As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools. Results: We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice. Availability and implementation: The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/ Contact: robert.stevens@manchester.ac.uk PMID:25161253

DISEASES: text mining and data integration of disease-gene associations.

PubMed

Pletscher-Frankild, Sune; Pallejà, Albert; Tsafou, Kalliopi; Binder, Janos X; Jensen, Lars Juhl

2015-03-01

Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease-gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrences both within and between sentences. We show that this approach is able to extract half of all manually curated associations with a false positive rate of only 0.16%. Nonetheless, text mining should not stand alone, but be combined with other types of evidence. For this reason, we have developed the DISEASES resource, which integrates the results from text mining with manually curated disease-gene associations, cancer mutation data, and genome-wide association studies from existing databases. The DISEASES resource is accessible through a web interface at http://diseases.jensenlab.org/, where the text-mining software and all associations are also freely available for download. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Water management in the Roman world

NASA Astrophysics Data System (ADS)

Dermody, Brian J.; van Beek, Rens L. P. H.; Meeks, Elijah; Klein Goldewijk, Kees; Bierkens, Marc F. P.; Scheidel, Walter; Wassen, Martin J.; van der Velde, Ype; Dekker, Stefan C.

2014-05-01

Climate variability can have extreme impacts on societies in regions that are water-limited for agriculture. A society's ability to manage its water resources in such environments is critical to its long-term viability. Water management can involve improving agricultural yields through in-situ irrigation or redistributing water resources through trade in food. Here, we explore how such water management strategies affected the resilience of the Roman Empire to climate variability in the water-limited region of the Mediterranean. Using the large-scale hydrological model PCR-GLOBWB and estimates of landcover based on the Historical Database of the Global Environment (HYDE) we generate potential agricultural yield maps under variable climate. HYDE maps of population density in conjunction with potential yield estimates are used to develop maps of agricultural surplus and deficit. The surplus and deficit regions are abstracted to nodes on a water redistribution network based on the Stanford Geospatial Network Model of the Roman World (ORBIS). This demand-driven, water redistribution network allows us to quantitatively explore how water management strategies such as irrigation and food trade improved the resilience of the Roman Empire to climate variability.

Granular Activated Carbon Performance Capability and Availability.

DTIC Science & Technology

1983-06-01

services were surveyed to determine availability of data and to develop a strategy for later computerized searches: * Chemical Abstracts; * Engineering ...Chemical Abstracts; * Engineering Abstracts; * Environmental Abstracts; * Selected Water Resources Abstracts; * Pollution Abstracts; and * the U.S...chemicals addressed, and scientific and engineering methods used. Publications were also reviewed for quality and consistency with the bulk of available data

The ChEMBL database as linked open data

PubMed Central

2013-01-01

Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

"Is political behavior a viable coping strategy to perceived organizational politics? Unveiling the underlying resource dynamics": Correction to Sun and Chen (2017).

PubMed

2017-10-01

Reports an error in "Is Political Behavior a Viable Coping Strategy to Perceived Organizational Politics? Unveiling the Underlying Resource Dynamics" by Shuhua Sun and Huaizhong Chen ( Journal of Applied Psychology , Advanced Online Publication, May 22, 2017, np). In the article, Table 1 contained a formatting error. Correlation coefficient values in the last four cells of column 6 were misplaced with correlation coefficient values in the last four cells of column 7. All versions of this article have been corrected. (The following abstract of the original article appeared in record 2017-22542-001.) We conduct a theory-driven empirical investigation on whether political behavior, as a coping strategy to perceived organizational politics, creates resource trade-offs in moderating the relationship between perceived organizational politics and task performance. Drawing on conservation of resources theory, we hypothesize that political behavior mitigates the adverse effect of perceived organizational politics on task performance via psychological empowerment, yet exacerbates its adverse effect on task performance via emotional exhaustion. Three-wave multisource data from a sample of 222 employees and their 75 supervisors were collected for hypothesis testing. Findings supported our hypotheses. Our study enhances understandings of the complex resource dynamics of using political behavior to cope with perceived organizational politics and highlights the need to move stress-coping research from a focus on the stress-buffering effect of coping on outcomes to a focus on the underlying competing resource dynamics. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

PubMed

Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; Liu, Hongfang

2015-06-06

Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains 'locked' in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3% for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10% in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5%. Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating discourse level analysis significantly improved the performance of extracting the protein-mutation-disease association. Future work includes the extension of MutD for full text articles.

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

Genomics Community Resources | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

To facilitate genomic research and the dissemination of its products, National Human Genome Research Institute (NHGRI) supports genomic resources that are crucial for basic research, disease studies, model organism studies, and other biomedical research.  Awards under this FOA will support the development and distribution of genomic resources that will be valuable for the broad research community, using cost-effective approaches.  Such resources include (but are not limited to) databases and informatics resources (such as human and model organism databases, ontologies, and analysi

Multi-terminology indexing for the assignment of MeSH descriptors to medical abstracts in French

PubMed Central

Pereira, Suzanne; Sakji, Saoussen; Névéol, Aurélie; Kergourlay, Ivan; Kerdelhué, Gaétan; Serrot, Elisabeth; Joubert, Michel; Darmoni, Stéfan J.

2009-01-01

Background: To facilitate information retrieval in the biomedical domain, a system for the automatic assignment of Medical Subject Headings to documents curated by an online quality-controlled health gateway was implemented. The French Multi-Terminology Indexer (F-MTI) implements a multiterminology approach using nine main medical terminologies in French and the mappings between them. Objective: This paper presents recent efforts to assess the added value of (a) integrating four new terminologies (Orphanet, ATC, drug names, MeSH supplementary concepts) into F-MTI’s knowledge sources and (b) performing the automatic indexing on the titles and abstracts (vs. title only) of the online health resources. Methods: F-MTI was evaluated on a CISMeF corpus comprising 18,161 manually indexed resources. Results: The performance of F-MTI including nine health terminologies on CISMeF resources with Title only was 27.9% precision and 19.7% recall, while the performance on CISMeF resources with Title and Abstract is 14.9 % precision (−13.0%) and 25.9% recall (+6.2%). Conclusion: In a few weeks, CISMeF will launch the indexing of resources based on title and abstract, using nine terminologies. PMID:20351910

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

PubMed Central

Shimoyama, Mary; Smith, Jennifer R.; De Pons, Jeff; Tutaj, Marek; Khampang, Pawjai; Hong, Wenzhou; Erbe, Christy B.; Ehrlich, Garth D.; Bakaletz, Lauren O.; Kerschner, Joseph E.

2016-01-01

The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease. Database URL: http://crrd.mcw.edu PMID:27173523

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology

PubMed Central

Yue, Zongliang; Zheng, Qi; Neylon, Michael T; Yoo, Minjae; Shin, Jimin; Zhao, Zhiying; Tan, Aik Choon

2018-01-01

Abstract Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA. Specifically, we included 84 282 PAGs spanning 24 different data sources that cover human diseases, published gene-expression signatures, drug–gene, miRNA–gene interactions, pathways and tissue-specific gene expressions. We introduced a new normalized Cohesion Coefficient (nCoCo) score to assess the biological relevance of genes inside a PAG, and RP-score to rank genes and assign gene-specific weights inside a PAG. The companion web interface contains numerous features to help users query and navigate the database content. The database content can be freely downloaded and is compatible with third-party Gene Set Enrichment Analysis tools. We expect PAGER 2.0 to become a major resource in integrative GNPA. PAGER 2.0 is available at http://discovery.informatics.uab.edu/PAGER/. PMID:29126216

Database resources of the National Center for Biotechnology Information

PubMed Central

Sayers, Eric W.; Barrett, Tanya; Benson, Dennis A.; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M.; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D.; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A.; Wagner, Lukas; Wang, Yanli; Wilbur, W. John; Yaschenko, Eugene; Ye, Jian

2012-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:22140104

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

Database resources of the National Center for Biotechnology Information.

PubMed

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

2009-01-01

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

Database System Design and Implementation for Marine Air-Traffic-Controller Training

DTIC Science & Technology

2017-06-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. DATABASE SYSTEM DESIGN AND...thesis 4. TITLE AND SUBTITLE DATABASE SYSTEM DESIGN AND IMPLEMENTATION FOR MARINE AIR-TRAFFIC-CONTROLLER TRAINING 5. FUNDING NUMBERS 6. AUTHOR(S...12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This project focused on the design , development, and implementation of a centralized

RPA tree-level database users guide

Treesearch

Patrick D. Miles; Scott A. Pugh; Brad Smith; Sonja N. Oswalt

2014-01-01

The Forest and Rangeland Renewable Resources Planning Act (RPA) of 1974 calls for a periodic assessment of the Nation's renewable resources. The Forest Inventory and Analysis (FIA) program of the U.S. Forest Service supports the RPA effort by providing information on the forest resources of the United States. The RPA tree-level database (RPAtreeDB) was generated...

RNAcentral: A vision for an international database of RNA sequences

PubMed Central

Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian

2011-01-01

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

Development and operations of the astrophysics data system

NASA Technical Reports Server (NTRS)

Murray, Stephen S.; Oliversen, Ronald (Technical Monitor)

2005-01-01

Abstract service - Continued regular updates of abstracts in the databases, both at SA0 and at all mirror sites. - Modified loading scripts to accommodate changes in data format (PhyS) - Discussed data deliveries with providers to clear up problems with format or other errors (EGU) - Continued inclusion of large numbers of historical literature volumes and physics conference volumes xeroxed from the library. - Performed systematic fixes on some data sets in the database to account for changes in article numbering (AGU journals) - Implemented linking of ADS bibliographic records with multimedia files - Debugged and fixed obscure connection problems with the ADS Korean mirror site which were preventing successful updates of the data holdings. - Wrote procedure to parse citation data and characterize an ADS record based on its citation ratios within each database.

Research resource: Tissue-specific transcriptomics and cistromics of nuclear receptor signaling: a web research resource.

PubMed

Ochsner, Scott A; Watkins, Christopher M; LaGrone, Benjamin S; Steffen, David L; McKenna, Neil J

2010-10-01

Nuclear receptors (NRs) are ligand-regulated transcription factors that recruit coregulators and other transcription factors to gene promoters to effect regulation of tissue-specific transcriptomes. The prodigious rate at which the NR signaling field has generated high content gene expression and, more recently, genome-wide location analysis datasets has not been matched by a committed effort to archiving this information for routine access by bench and clinical scientists. As a first step towards this goal, we searched the MEDLINE database for studies, which referenced either expression microarray and/or genome-wide location analysis datasets in which a NR or NR ligand was an experimental variable. A total of 1122 studies encompassing 325 unique organs, tissues, primary cells, and cell lines, 35 NRs, and 91 NR ligands were retrieved and annotated. The data were incorporated into a new section of the Nuclear Receptor Signaling Atlas Molecule Pages, Transcriptomics and Cistromics, for which we designed an intuitive, freely accessible user interface to browse the studies. Each study links to an abstract, the MEDLINE record, and, where available, Gene Expression Omnibus and ArrayExpress records. The resource will be updated on a regular basis to provide a current and comprehensive entrez into the sum of transcriptomic and cistromic research in this field.

Assessment of the quality of reporting in abstracts of systematic reviews with meta-analyses in periodontology and implant dentistry.

PubMed

Faggion, C M; Liu, J; Huda, F; Atieh, M

2014-04-01

Proper scientific reporting is necessary to ensure the correct interpretation of study results by readers. The main objective of this study was to assess the quality of reporting in abstracts of systematic reviews (SRs) with meta-analyses in periodontology and implant dentistry. Differences in reporting of abstracts in Cochrane and paper-based reviews were also assessed. The PubMed electronic database and the Cochrane database for SRs were searched on November 11, 2012, independently and in duplicate, for SRs with meta-analyses related to interventions in periodontology and implant dentistry. Assessment of the quality of reporting was performed independently and in duplicate, taking into account items related to the effect direction, numerical estimates of effect size, measures of precision, probability and consistency. We initially screened 433 papers and included 146 (127 paper-based and 19 Cochrane reviews, respectively). The direction of evidence was reported in two-thirds of the abstracts while strength of evidence and measure of precision (i.e., confidence interval) were reported in less than half the selected abstracts. Measures of consistency such as I(2) statistics were reported in only 5% of the selected sample of abstracts. Cochrane abstracts reported the limitations of evidence and precision better than paper-based ones. Two items ("meta-analysis" in title and abstract, respectively), were nevertheless better reported in paper-based abstracts. Abstracts of SRs with meta-analyses in periodontology and implant dentistry currently have no uniform standard of reporting, which may hinder readers' understanding of study outcomes. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Effects of technical editing in biomedical journals: a systematic review.

PubMed

Wager, Elizabeth; Middleton, Philippa

2002-06-05

Technical editing supposedly improves the accuracy and clarity of journal articles. We examined evidence of its effects on research reports in biomedical journals. Subset of a systematic review using Cochrane methods, searching MEDLINE, EMBASE, and other databases from earliest entries to February 2000 by using inclusive search terms; hand searching relevant journals. We selected comparative studies of the effects of editorial processes on original research articles between acceptance and publication in biomedical journals. Two reviewers assessed each study and performed independent data extraction. The 11 studies on technical editing indicate that it improves the readability of articles slightly (as measured by Gunning Fog and Flesch reading ease scores), may improve other aspects of their quality, can increase the accuracy of references and quotations, and raises the quality of abstracts. Supplying authors with abstract preparation instructions had no discernible effect. Considering the time and resources devoted to technical editing, remarkably little is know about its effects or the effects of imposing different house styles. Studies performed at 3 journals employing relatively large numbers of professional technical editors suggest that their editorial processes are associated with increases in readability and quality of articles, but these findings may not be generalizable to other journals.

Bibliographic Databases Outside of the United States.

ERIC Educational Resources Information Center

McGinn, Thomas P.; And Others

1988-01-01

Eight articles describe the development, content, and structure of databases outside of the United States. Features discussed include library involvement, authority control, shared cataloging services, union catalogs, thesauri, abstracts, and distribution methods. Countries and areas represented are Latin America, Australia, the United Kingdom,…

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

RREL TREATABILITY DATABASE - VERSION 5.0

EPA Science Inventory

There is no abstract available for this product. If further information is requested, please refer to the bibliographic citation and contact the person listed under Contact field. This database can be obtained by contacting Tom Holdsworth, U.S. EPA, 26 West Martin Luther King D...

SERS internship: Spring 1994 abstracts and research papers

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

Goldman, B.

1994-05-06

This document contains abstracts from the science and engineering research semester from the Lawrence Livermore National Laboratory. Projects cover many areas in the fields of contaminant removal from the environment, physics, and genetics research. Individual projects were processed separately for the Department of Energy databases.

A CONCEPTUAL FRAMEWORK FOR INCORPORATING COGNITIVE PRINCIPLES INTO GEOGRAPHICAL DATABASE REPRESENTATION. (R825195)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

PubMed

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific information about genes or microRNAs is quick and easily accessible. Hence, this platform can support the ongoing OS research and biomarker discovery. Database URL: http://osteosarcoma-db.uni-muenster.de. © The Author(s) 2014. Published by Oxford University Press.

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation

PubMed Central

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific information about genes or microRNAs is quick and easily accessible. Hence, this platform can support the ongoing OS research and biomarker discovery. Database URL: http://osteosarcoma-db.uni-muenster.de PMID:24865352

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

PubMed

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

2009-11-01

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

HMDB 4.0: the human metabolome database for 2018

PubMed Central

Feunang, Yannick Djoumbou; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep; Arndt, David; Liang, Yonjie; Badran, Hasan; Grant, Jason; Serra-Cayuela, Arnau; Liu, Yifeng; Mandal, Rupa; Neveu, Vanessa; Pon, Allison; Knox, Craig; Wilson, Michael; Manach, Claudine; Scalbert, Augustin

2018-01-01

Abstract The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science. PMID:29140435

Rural Career Guidance: Abstracts of Current Research, Materials, and Practices.

ERIC Educational Resources Information Center

Far West Lab. for Educational Research and Development, San Francisco, CA.

The annotated bibliography provides a guide to the latest resource material, research findings, and/or developments in rural career guidance found in the ERIC system. Section I contains 158 citations and abstracts which have appeared in "Resources in Education" (RIE). RIE document resumes include the ERIC accession number, author(s), title,…

A Selected Annotated Bibliography on the Analysis of Water Resources System, Volume 2.

ERIC Educational Resources Information Center

Kriss, Carol; And Others

Presented is an annotated bibliography of some recent selected publications pertaining to the application of systems analysis techniques for defining and evaluating alternative solutions to water resource problems. Both subject and author indices are provided. Keywords are listed at the end of each abstract. The abstracted material emphasizes the…

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.

PubMed

Rigden, Daniel J; Fernández, Xosé M

2018-01-04

The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Parent's Guide to the ERIC Database. Where To Turn with Your Questions about Schooling. Revised Edition.

ERIC Educational Resources Information Center

Howley, Craig B.; And Others

This guide explains what the Educational Resources Information Center (ERIC) database is and how it can be used by parents to learn more about schooling and parenting. The guide also presents sample records of 55 documents in the ERIC database. The cited resources are particularly relevant to parents' concerns about meeting children's basic needs,…

Publication Rates of Abstracts Presented at Five National Pharmacy Association Meetings

PubMed Central

Prohaska, Emily; Generali, Joyce; Zak, Kevin; Grauer, Dennis

2013-01-01

Background: Abstract presentations at professional meetings provide a medium for disseminating the findings of scholarly activity. Rates of abstract publication from various biomedical disciplines have been evaluated, with pharmacy noted to be lower than other specialties. Previous research on pharmacy abstract publication rates was conducted for a limited number of professional meetings but has not been assessed using Google Scholar. Objective: To determine the full publication rate of abstracts presented at the 2005 American College of Clinical Pharmacy (ACCP) Spring and Annual Meetings, American Pharmacists Association (APhA) Annual Meeting, and American Society of Health-System Pharmacists (ASHP) Summer and Midyear Clinical Meetings. Methods: Publication status was assessed for abstracts presented during the 2005 ACCP Spring and Annual Meetings, APhA Annual Meeting, and ASHP Summer and Midyear Clinical Meetings using PubMed and Google Scholar. Data collected included abstract category, study category, practice site, database(s) in which publication appeared, time in months to publication, publication type, and journal of publication. Results: Evaluation of 2,000 abstracts presented in 2005 revealed an overall full publication rate of 19.8% (n = 384). Nearly all pharmacy abstracts were published as manuscripts (98.4%; n=378) and indexed in PubMed and Google Scholar (91.9%; n = 353), although a significant percentage were indexed in Google Scholar only (7.8%; n = 30). The mean time to full publication was 16.8 months (SD ±11.9 months). Conclusions: Results were consistent with previously reported full publication rates of abstracts from pharmacy association meetings, indicating that abstracts presented at pharmacy meetings continue to have a lower full publication rate than other health disciplines. PMID:24421465

SABER: The Searchable Annotated Bibliography of Education Research in Astronomy

NASA Astrophysics Data System (ADS)

Bruning, David; Bailey, Janelle M.; Brissenden, Gina

Starting a new research project can be a challenge, but especially so in education research because the literature is scattered throughout many journals. Relevant astronomy education research may be in psychology journals, science education journals, physics education journals, or even in science journals. Tracking the vast realm of literature is difficult, especially because libraries frequently do not subscribe to many of the relevant journals and abstracting services. The Searchable Annotated Bibliography of Education Research (SABER) is an online resource that was started to service the needs of the astronomy education community, specifically to reduce this "scatter" by compiling an annotated bibliography of education research articles in one electronic location. Although SABER started in 2001, the database has a new URL—http://astronom- y.uwp.edu/saber/—and has recently undergone a major update.

Techniques of Photometry and Astrometry with APASS, Gaia, and Pan-STARRs Results (Abstract)

NASA Astrophysics Data System (ADS)

Green, W.

2017-12-01

(Abstract only) The databases with the APASS DR9, Gaia DR1, and the Pan-STARRs 3pi DR1 data releases are publicly available for use. There is a bit of data-mining involved to download and manage these reference stars. This paper discusses the use of these databases to acquire accurate photometric references as well as techniques for improving results. Images are prepared in the usual way: zero, dark, flat-fields, and WCS solutions with Astrometry.net. Images are then processed with Sextractor to produce an ASCII table of identifying photometric features. The database manages photometics catalogs and images converted to ASCII tables. Scripts convert the files into SQL and assimilate them into database tables. Using SQL techniques, each image star is merged with reference data to produce publishable results. The VYSOS has over 13,000 images of the ONC5 field to process with roughly 100 total fields in the campaign. This paper provides the overview for this daunting task.

Database Changes (Post-Publication). ERIC Processing Manual, Section X.

ERIC Educational Resources Information Center

Brandhorst, Ted, Ed.

The purpose of this section is to specify the procedure for making changes to the ERIC database after the data involved have been announced in the abstract journals RIE or CIJE. As a matter of general ERIC policy, a document or journal article is not re-announced or re-entered into the database as a new accession for the purpose of accomplishing a…

Hydrogeology of the Judith River Formation in southwestern Saskatchewan, Canada

NASA Astrophysics Data System (ADS)

Ferris, David; Lypka, Morgan; Ferguson, Grant

2017-11-01

The Judith River Formation forms an important regional aquifer in southwestern Saskatchewan, Canada. This aquifer is used for domestic and agricultural purposes in some areas and supports oil and gas production in other areas. As a result, the available data come from a range of sources and integration is required to provide an overview of aquifer characteristics. Here, data from oil and gas databases are combined with data from groundwater resource assessments. Analysis of cores, drill-stem tests and pumping tests provide a good overview of the physical hydrogeology of the Judith River Aquifer. Water chemistry data from oil and gas databases were less helpful in understanding the chemical hydrogeology due contamination of samples and unreliable laboratory analyses. Analytical modeling of past pumping in the aquifer indicates that decreases in hydraulic head exceeding 2 m are possible over distances of 10s of kilometers. Similar decreases in head should be expected for additional large withdrawals of groundwater from the Judith River Aquifer. Long-term groundwater abstraction should be limited by low pumping rates. Higher pumping rates appear to be possible for short-term uses, such as those required by the oil and gas industry.

From print to digital (1985-2015): APA's evolving role in psychological publishing.

PubMed

VandenBos, Gary R

2017-11-01

Knowledge dissemination plays an important role in all scientific fields. The American Psychological Association's (APA) journal publication program was established in 1927. During the 1960s, the Psychological Abstracts publication was computerized. In the mid-1980s, a reenergizing of APA Publishing began, with the establishment of the APA Books Program, as well as the movement of abstracts to CD-ROMs. This article describes the 30-year program of expansion of APA Publishing, covering the period from 1985 through 2015. This period saw the journals program grow from 15 journals to 89 journals, the abstract program grow into an Internet-based delivery system, the creation of the APA's own PsycNET delivery platform, the creation of 6 addition databases, and the establishment of dictionaries and handbooks of psychology. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Concierge: Personal Database Software for Managing Digital Research Resources

PubMed Central

Sakai, Hiroyuki; Aoyama, Toshihiro; Yamaji, Kazutsuna; Usui, Shiro

2007-01-01

This article introduces a desktop application, named Concierge, for managing personal digital research resources. Using simple operations, it enables storage of various types of files and indexes them based on content descriptions. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. In this paper, we also introduce a few optional plug-ins: literature management, electronic laboratory notebook, and XooNlps client plug-ins. XooNIps is a content management system developed to share digital research resources among neuroscience communities. It has been adopted as the standard database system in Japanese neuroinformatics projects. Concierge, therefore, offers comprehensive support from management of personal digital research resources to their sharing in open-access neuroinformatics databases such as XooNIps. This interaction between personal and open-access neuroinformatics databases is expected to enhance the dissemination of digital research resources. Concierge is developed as an open source project; Mac OS X and Windows XP versions have been released at the official site (http://concierge.sourceforge.jp). PMID:18974800

PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords.

PubMed

Chen, Chou-Cheng; Ho, Chung-Liang

2014-01-01

While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research. http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx.

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.

How effects on health equity are assessed in systematic reviews of interventions.

PubMed

Welch, Vivian; Tugwell, Peter; Petticrew, Mark; de Montigny, Joanne; Ueffing, Erin; Kristjansson, Betsy; McGowan, Jessie; Benkhalti Jandu, Maria; Wells, George A; Brand, Kevin; Smylie, Janet

2010-12-08

Enhancing health equity has now achieved international political importance with endorsement from the World Health Assembly in 2009.  The failure of systematic reviews to consider effects on health equity is cited by decision-makers as a limitation to their ability to inform policy and program decisions.  To systematically review methods to assess effects on health equity in systematic reviews of effectiveness. We searched the following databases up to July 2 2010: MEDLINE, PsychINFO, the Cochrane Methodology Register, CINAHL, Education Resources Information Center, Education Abstracts, Criminal Justice Abstracts, Index to Legal Periodicals, PAIS International, Social Services Abstracts, Sociological Abstracts, Digital Dissertations and the Health Technology Assessment Database. We searched SCOPUS to identify articles that cited any of the included studies on October 7 2010. We included empirical studies of cohorts of systematic reviews that assessed methods for measuring effects on health inequalities. Data were extracted using a pre-tested form by two independent reviewers. Risk of bias was appraised for included studies according to the potential for bias in selection and detection of systematic reviews.  Thirty-four methodological studies were included.  The methods used by these included studies were: 1) Targeted approaches (n=22); 2) gap approaches (n=12) and gradient approach (n=1).  Gender or sex was assessed in eight out of 34 studies, socioeconomic status in ten studies, race/ethnicity in seven studies, age in seven studies, low and middle income countries in 14 studies, and two studies assessed multiple factors across health inequity may exist.Only three studies provided a definition of health equity. Four methodological approaches to assessing effects on health equity were identified: 1) descriptive assessment of reporting and analysis in systematic reviews (all 34 studies used a type of descriptive method); 2) descriptive assessment of reporting and analysis in original trials (12/34 studies); 3) analytic approaches (10/34 studies); and 4) applicability assessment (11/34 studies). Both analytic and applicability approaches were not reported transparently nor in sufficient detail to judge their credibility. There is a need for improvement in conceptual clarity about the definition of health equity, describing sufficient detail about analytic approaches (including subgroup analyses) and transparent reporting of judgments required for applicability assessments in order to assess and report effects on health equity in systematic reviews.

The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

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

Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass

2009-12-01

In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) establishedmore » a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online resources, and raw data have been deposited in PRIDE and PRIDE BioMart. Included in this database is an Arabidopsis proteome map that provides evidence for the expression of {approx}50% of all predicted gene models, including several alternative gene models that are not represented in The Arabidopsis Information Resource (TAIR) protein database. A set of organ-specific biomarkers is provided, as well as organ-specific proteotypic peptides for 4105 proteins that can be used to facilitate targeted quantitative proteomic surveys. In the future, the AtProteome database will be linked to additional existing resources developed by MASCP members, such as PPDB, ProMEX, and SUBA. The most comprehensive study on the Arabidopsis chloroplast proteome, which includes information on chloroplast sorting signals, posttranslational modifications (PTMs), and protein abundances (analyzed by high-accuracy MS [Orbitrap]), was recently published by the van Wijk lab.2 These and previous data are available via the plant proteome database (PPDB; http://ppdb.tc.cornell.edu) for A. thaliana and maize. PPDB provides genome-wide experimental and functional characterization of the A. thaliana and maize proteomes, including PTMs and subcellular localization information, with an emphasis on leaf and plastid proteins. Maize and Arabidopsis proteome entries are directly linked via internal BLAST alignments within PPDB. Direct links for each protein to TAIR, SUBA, ProMEX, and other resources are also provided.« less

Database resources of the National Center for Biotechnology Information.

PubMed

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian

2011-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

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.

Development and Implementation of Kumamoto Technopolis Regional Database T-KIND

NASA Astrophysics Data System (ADS)

Onoue, Noriaki

T-KIND (Techno-Kumamoto Information Network for Data-Base) is a system for effectively searching information of technology, human resources and industries which are necessary to realize Kumamoto Technopolis. It is composed of coded database, image database and LAN inside technoresearch park which is the center of R & D in the Technopolis. It constructs on-line system by networking general-purposed computers, minicomputers, optical disk file systems and so on, and provides the service through public telephone line. Two databases are now available on enterprise information and human resource information. The former covers about 4,000 enterprises, and the latter does about 2,000 persons.

Influenza research database: an integrated bioinformatics resource for influenza virus research

USDA-ARS?s Scientific Manuscript database

The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

The Hidden Dimensions of Databases.

ERIC Educational Resources Information Center

Jacso, Peter

1994-01-01

Discusses methods of evaluating commercial online databases and provides examples that illustrate their hidden dimensions. Topics addressed include size, including the number of records or the number of titles; the number of years covered; and the frequency of updates. Comparisons of Readers' Guide Abstracts and Magazine Article Summaries are…

Body of Knowledge: Tomorrow's Research Agenda.

ERIC Educational Resources Information Center

VanLeuven, James K.

1990-01-01

Reviews the history of the Public Relations Body of Knowledge Abstracts, a database of public relations research and literature. Describes the uses of the abstracts for research purposes, and reports assessments of new research directions as set forth by members of the Public Relations Society of America's permanent Body of Knowledge Board. (MM)

CONSTRUCTING KNOWLEDGE FROM MULTIVARIATE SPATIOTEMPORAL DATA: INTEGRATING GEOGRAPHIC VISUALIZATION WITH KNOWLEDGE DISCOVERY IN DATABASE METHODS. (R825195)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

The Resource Identification Initiative: A cultural shift in publishing.

PubMed

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

2015-01-01

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

The Resource Identification Initiative: a cultural shift in publishing.

PubMed

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

2016-01-01

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

The Resource Identification Initiative: A Cultural Shift in Publishing.

PubMed

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

2016-01-01

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

The Resource Identification Initiative: A cultural shift in publishing

DOE PAGES

Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S.; ...

2015-05-29

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

The Resource Identification Initiative: A cultural shift in publishing

PubMed Central

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

2015-01-01

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as “What other studies used resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources. PMID:26594330

The Resource Identification Initiative: A cultural shift in publishing

PubMed Central

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

2016-01-01

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

The Resource Identification Initiative: A Cultural Shift in Publishing.

PubMed

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

2016-04-01

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

The Resource Identification Initiative: A cultural shift in publishing

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

Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S.

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

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

PubMed Central

Manasa, Justen; Lessells, Richard; Rossouw, Theresa; Naidu, Kevindra; Van Vuuren, Cloete; Goedhals, Dominique; van Zyl, Gert; Bester, Armand; Skingsley, Andrew; Stott, Katharine; Danaviah, Siva; Chetty, Terusha; Singh, Lavanya; Moodley, Pravi; Iwuji, Collins; McGrath, Nuala; Seebregts, Christopher J.; de Oliveira, Tulio

2014-01-01

Abstract Substantial amounts of data have been generated from patient management and academic exercises designed to better understand the human immunodeficiency virus (HIV) epidemic and design interventions to control it. A number of specialized databases have been designed to manage huge data sets from HIV cohort, vaccine, host genomic and drug resistance studies. Besides databases from cohort studies, most of the online databases contain limited curated data and are thus sequence repositories. HIV drug resistance has been shown to have a great potential to derail the progress made thus far through antiretroviral therapy. Thus, a lot of resources have been invested in generating drug resistance data for patient management and surveillance purposes. Unfortunately, most of the data currently available relate to subtype B even though >60% of the epidemic is caused by HIV-1 subtype C. A consortium of clinicians, scientists, public health experts and policy markers working in southern Africa came together and formed a network, the Southern African Treatment and Resistance Network (SATuRN), with the aim of increasing curated HIV-1 subtype C and tuberculosis drug resistance data. This article describes the HIV-1 data curation process using the SATuRN Rega database. The data curation is a manual and time-consuming process done by clinical, laboratory and data curation specialists. Access to the highly curated data sets is through applications that are reviewed by the SATuRN executive committee. Examples of research outputs from the analysis of the curated data include trends in the level of transmitted drug resistance in South Africa, analysis of the levels of acquired resistance among patients failing therapy and factors associated with the absence of genotypic evidence of drug resistance among patients failing therapy. All these studies have been important for informing first- and second-line therapy. This database is a free password-protected open source database available on www.bioafrica.net. Database URL: http://www.bioafrica.net/regadb/ PMID:24504151

SZDB: A Database for Schizophrenia Genetic Research

PubMed Central

Wu, Yong; Yao, Yong-Gang

2017-01-01

Abstract Schizophrenia (SZ) is a debilitating brain disorder with a complex genetic architecture. Genetic studies, especially recent genome-wide association studies (GWAS), have identified multiple variants (loci) conferring risk to SZ. However, how to efficiently extract meaningful biological information from bulk genetic findings of SZ remains a major challenge. There is a pressing need to integrate multiple layers of data from various sources, eg, genetic findings from GWAS, copy number variations (CNVs), association and linkage studies, gene expression, protein–protein interaction (PPI), co-expression, expression quantitative trait loci (eQTL), and Encyclopedia of DNA Elements (ENCODE) data, to provide a comprehensive resource to facilitate the translation of genetic findings into SZ molecular diagnosis and mechanism study. Here we developed the SZDB database (http://www.szdb.org/), a comprehensive resource for SZ research. SZ genetic data, gene expression data, network-based data, brain eQTL data, and SNP function annotation information were systematically extracted, curated and deposited in SZDB. In-depth analyses and systematic integration were performed to identify top prioritized SZ genes and enriched pathways. Multiple types of data from various layers of SZ research were systematically integrated and deposited in SZDB. In-depth data analyses and integration identified top prioritized SZ genes and enriched pathways. We further showed that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted. The user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization. More important, SZDB provides convenient online tools for data search and browse, data integration, and customized data analyses. PMID:27451428

Gene annotation from scientific literature using mappings between keyword systems.

PubMed

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

2004-09-01

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

Exploring Short Linear Motifs Using the ELM Database and Tools.

PubMed

Gouw, Marc; Sámano-Sánchez, Hugo; Van Roey, Kim; Diella, Francesca; Gibson, Toby J; Dinkel, Holger

2017-06-27

The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource. We also cover how to use this resource in order to predict SLiMs in known as well as novel proteins, and how to interpret the results generated by the ELM prediction pipeline. The ELM database is a very rich resource, and in the following protocols we give helpful examples to demonstrate how this knowledge can be used to improve your own research. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Common Data Model for Neuroscience Data and Data Model Exchange

PubMed Central

Gardner, Daniel; Knuth, Kevin H.; Abato, Michael; Erde, Steven M.; White, Thomas; DeBellis, Robert; Gardner, Esther P.

2001-01-01

Objective: Generalizing the data models underlying two prototype neurophysiology databases, the authors describe and propose the Common Data Model (CDM) as a framework for federating a broad spectrum of disparate neuroscience information resources. Design: Each component of the CDM derives from one of five superclasses—data, site, method, model, and reference—or from relations defined between them. A hierarchic attribute-value scheme for metadata enables interoperability with variable tree depth to serve specific intra- or broad inter-domain queries. To mediate data exchange between disparate systems, the authors propose a set of XML-derived schema for describing not only data sets but data models. These include biophysical description markup language (BDML), which mediates interoperability between data resources by providing a meta-description for the CDM. Results: The set of superclasses potentially spans data needs of contemporary neuroscience. Data elements abstracted from neurophysiology time series and histogram data represent data sets that differ in dimension and concordance. Site elements transcend neurons to describe subcellular compartments, circuits, regions, or slices; non-neuroanatomic sites include sequences to patients. Methods and models are highly domain-dependent. Conclusions: True federation of data resources requires explicit public description, in a metalanguage, of the contents, query methods, data formats, and data models of each data resource. Any data model that can be derived from the defined superclasses is potentially conformant and interoperability can be enabled by recognition of BDML-described compatibilities. Such metadescriptions can buffer technologic changes. PMID:11141510

Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

ERIC Educational Resources Information Center

Tenopir, Carol

1985-01-01

This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

Biological Databases for Behavioral Neurobiology

PubMed Central

Baker, Erich J.

2014-01-01

Databases are, at their core, abstractions of data and their intentionally derived relationships. They serve as a central organizing metaphor and repository, supporting or augmenting nearly all bioinformatics. Behavioral domains provide a unique stage for contemporary databases, as research in this area spans diverse data types, locations, and data relationships. This chapter provides foundational information on the diversity and prevalence of databases, how data structures support the various needs of behavioral neuroscience analysis and interpretation. The focus is on the classes of databases, data curation, and advanced applications in bioinformatics using examples largely drawn from research efforts in behavioral neuroscience. PMID:23195119

Finding alternatives when a major database is gone*

PubMed Central

Hu, Estelle

2016-01-01

Question What to do when a major database ceases publication? Setting An urban, academic health sciences library with four campuses serves a university health sciences system, a college of medicine, and five other health sciences colleges. Methods Usage statistics of each e-book title in the resource were carefully analyzed. Purchase decisions were made based on the assessment of usage. Results Sustainable resources were acquired from other vendors, with perpetual access for library users. Conclusion This systematic process of finding alternative resources is an example of librarians' persistence in acquiring perpetual electronic resources when a major resource is cancelled. PMID:27076804

OReFiL: an online resource finder for life sciences.

PubMed

Yamamoto, Yasunori; Takagi, Toshihisa

2007-08-06

Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort. We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system. We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page.

OReFiL: an online resource finder for life sciences

PubMed Central

Yamamoto, Yasunori; Takagi, Toshihisa

2007-01-01

Background Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort. Description We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system. Conclusion We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page. PMID:17683589

Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

PubMed Central

Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

2013-01-01

The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

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

E-MSD: an integrated data resource for bioinformatics.

PubMed

Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Modeling Multiple Stresses Placed Upon A Groundwater System In A Semi-Arid Brackish Environment

NASA Astrophysics Data System (ADS)

Toll, M.; Salameh, E.; Sauter, M.

2008-12-01

In semi-arid areas groundwater systems are frequently not sufficiently characterized hydrogeologically and long term data records are generally not available. Long-term time series are necessary, however to design future groundwater abstraction scenarios or to predict the influence of future climate change effects on groundwater resources. To overcome these problems an integrated approach for the provision of a reliable database based on sparse and fuzzy data is proposed. This integrated approach is demonstrated in the lowermost area of the Jordan Valley. The Jordan Valley is part of the Jordan Dead Sea Wadi Araba Rift Valley, which extends from the Red Sea to lake Tiberias and beyond with a major 107 km sinistral strike-slip fault between the Arabian plate to the east and the northeastern part of the African plate to the west. Due to extensional forces a topographic depression was formed. As a result of an arid environment it is filled with evaporites, lacustrine sediments, and clastic fluvial components. A subtropical climate with hot, dry summers and mild humid winters with low amounts of rainfall provide excellent farming conditions. Therefore the Jordan Valley is considered as the food basket of Jordan and is used intensively for agriculture. As a result hundreds of shallow wells were drilled and large amounts of groundwater were abstracted since groundwater is the major source for irrigation. Consequently groundwater quality decreased rapidly since the sixties and signs of overpumping and an increase in soil salinity could clearly be seen. In order to achieve a sustainable state of water resources and to quantify the impact of climate change on water resources a proper assessment of the groundwater resources as well as their quality is a prerequisite. In order to sufficiently describe the complex hydrogeologic flow system an integrated approach, combining geological, geophysical, hydrogeological, historical, and chemical methods was chosen. The aquifer geometry and composition is described with the help of geological, hydochemical, and geophysical methods. As far as the water budget is concerned, the recharge to the considered aquifer is estimated with geological methods and available data sets, while the abstraction from the aquifer is estimated with the help of remote sensing techniques. A historical approach is used to detect the general conditions under which the groundwater system has been in the past. Afterwards this information is implemented into a flow model. On the basis of the findings a numerical 3-D transient model integrating all important features of the hydrogeological system was developed.3 In order to be able to give reliable predictions about the impacts of climate change scenarios on the groundwater system the flow model was tested against stress periods depicted during the historical review of the test area (model period: 1955 - 2008). These stress periods include periods of intense rainfall, of drought, and of anthropogenic impacts, like building of storage dams and of violent conflicts. Recommendations for future sustainable groundwater abstractions are given.

Space Resources Roundtable VI

NASA Technical Reports Server (NTRS)

2004-01-01

The topics addressed in the conference paper abstracts contained in this document include: extracting resources from the Moon and Mars, equipment for in situ resource utilization, mission planning for resource extraction, drilling on Mars, and simulants for lunar soil and minerals.

Advanced light source: Compendium of user abstracts and technical reports,1993-1996

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

None, None

1997-04-01

This compendium contains abstracts written by users summarizing research completed or in progress from 1993-1996, ALS technical reports describing ongoing efforts related to improvement in machine operations and research and development projects, and information on ALS beamlines planned through 1998. Two tables of contents organize the user abstracts by beamline and by area of research, and an author index makes abstracts accessible by author and by principal investigator. Technical details for each beamline including whom to contact for additional information can be found in the beamline information section. Separate abstracts have been indexed into the database for contributions to thismore » compendium.« less

In Situ Resource Utilization (ISRU 3) Technical Interchange Meeting: Abstracts

NASA Technical Reports Server (NTRS)

1999-01-01

This volume contains abstracts that have been accepted for presentation at the In Situ Resource Utilization (ISRU III) Technical Interchange Meeting, February 11-12, 1999, hosted by the Lockheed Martin Astronautics Waterton Facility, Denver, Colorado. Administration and publication support for this meeting were provided by the staff of the Publications and Program Services Department at the Lunar and Planetary Institute.

Designing Studies of Extension Program Results: A Resource for Program Leaders and Specialists. Volume II--Abstracts.

ERIC Educational Resources Information Center

Rivera, William M., Ed.; And Others

These abstracts of 42 studies of extension program results, which make up the second volume of a two-volume resource, are intended to advise state administrative program leaders and others with program evaluation responsibilities of how to design studies of cooperative extension programs. Designed to support volume I, which refers to these…

Assignment of adverse event indexing terms in randomized clinical trials involving spinal manipulative therapy: an audit of records in MEDLINE and EMBASE databases.

PubMed

Gorrell, Lindsay M; Engel, Roger M; Lystad, Reidar P; Brown, Benjamin T

2017-03-14

Reporting of adverse events in randomized clinical trials (RCTs) is encouraged by the authors of The Consolidated Standards of Reporting Trials (CONSORT) statement. With robust methodological design and adequate reporting, RCTs have the potential to provide useful evidence on the incidence of adverse events associated with spinal manipulative therapy (SMT). During a previous investigation, it became apparent that comprehensive search strategies combining text words with indexing terms was not sufficiently sensitive for retrieving records that were known to contain reports on adverse events. The aim of this analysis was to compare the proportion of articles containing data on adverse events associated with SMT that were indexed in MEDLINE and/or EMBASE and the proportion of those that included adverse event-related words in their title or abstract. A sample of 140 RCT articles previously identified as containing data on adverse events associated with SMT was used. Articles were checked to determine if: (1) they had been indexed with relevant terms describing adverse events in the MEDLINE and EMBASE databases; and (2) they mentioned adverse events (or any related terms) in the title or abstract. Of the 140 papers, 91% were MEDLINE records, 85% were EMBASE records, 81% were found in both MEDLINE and EMBASE records, and 4% were not in either database. Only 19% mentioned adverse event-related text words in the title or abstract. There was no significant difference between MEDLINE and EMBASE records in the proportion of available papers (p = 0.078). Of the 113 papers that were found in both MEDLINE and EMBASE records, only 3% had adverse event-related indexing terms assigned to them in both databases, while 81% were not assigned an adverse event-related indexing term in either database. While there was effective indexing of RCTs involving SMT in the MEDLINE and EMBASE databases, there was a failure of allocation of adverse event indexing terms in both databases. We recommend the development of standardized definitions and reporting tools for adverse events associated with SMT. Adequate reporting of adverse events associated with SMT will facilitate accurate indexing of these types of manuscripts in the databases.

Water resources thesaurus: A vocabulary for indexing and retrieving the literature of water resources research and development

USGS Publications Warehouse

,

1980-01-01

This Water Resources Thesaurus encompasses such broad research areas as the hydrologic cycle, supply of and demand for water, conservation and best use of available supplies of water, methods of increasing supplies, and the economic, legal, social, engineering, recreational, biological, geographical, ecological, and qualitative aspects of water resources. This volume represents a major revision of the previous edition of the Thesaurus, published in 1971. The principal source of terms for this edition has been the indexing used in Selected Water Resources Abstracts (SWRA). Since its inception in 1968, SWRA has indexed tens of thousands of publications. Its indexing terminology has been developed by expert abstracters and researchers, and represents the range of disciplines related to research, development, and management of water resources.

A Novel Approach: Chemical Relational Databases, and the ...

EPA Pesticide Factsheets

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as

Schwannomatosis

MedlinePlus

... Schwannomatosis Database Schwannomatosis Resources NF Registry International Schwannomatosis Database Because of the small number of people that ... and how to treat it, the International Schwannomatosis Database (ISD) project is proposing to bring together people ...

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.

SAO/NASA ADS at SAO: ADS Abstract Service

Science.gov Websites

Service provides a gateway to the online Astronomy and Physics literature. You can navigate this content filtering options as well as visualizations. Astronomy and Astrophysics Classic Search, an legacy interface which searches the 2,311,600 records currently in the Astronomy database, including 198,834 abstracts

"Social Work Abstracts" Fails Again: A Replication and Extension

ERIC Educational Resources Information Center

Holden, Gary; Barker, Kathleen; Covert-Vail, Lucinda; Rosenberg, Gary; Cohen, Stephanie A.

2009-01-01

Objective: According to a prior study, there are substantial lapses in journal coverage in the "Social Work Abstracts" (SWA) database. The current study provides a replication and extension. Method: The longitudinal pattern of coverage of thirty-three journals categorized in SWA as core journals (published in the 1989-1996 period) is examined.…

The Distribution of Information: The Role for Online Public Access Catalogs.

ERIC Educational Resources Information Center

Matthews, Joseph R.

1994-01-01

Describes the Online Public Access Catalog (OPAC) and the inclusion of abstracting and indexing industry databases in OPACs. Topics addressed include the implications of including abstracting and indexing tape and CD-ROM products in OPACs; the need for standards allowing library systems to communicate with dissimilar CD-ROM products; and computer,…

Database resources for the Tuberculosis community

PubMed Central

Lew, Jocelyne M.; Mao, Chunhong; Shukla, Maulik; Warren, Andrew; Will, Rebecca; Kuznetsov, Dmitry; Xenarios, Ioannis; Robertson, Brian D.; Gordon, Stephen V.; Schnappinger, Dirk; Cole, Stewart T.; Sobral, Bruno

2013-01-01

Summary Access to online repositories for genomic and associated “-omics” datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th–8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis. PMID:23332401

2008 Niday Perinatal Database quality audit: report of a quality assurance project.

PubMed

Dunn, S; Bottomley, J; Ali, A; Walker, M

2011-12-01

This quality assurance project was designed to determine the reliability, completeness and comprehensiveness of the data entered into Niday Perinatal Database. Quality of the data was measured by comparing data re-abstracted from the patient record to the original data entered into the Niday Perinatal Database. A representative sample of hospitals in Ontario was selected and a random sample of 100 linked mother and newborn charts were audited for each site. A subset of 33 variables (representing 96 data fields) from the Niday dataset was chosen for re-abstraction. Of the data fields for which Cohen's kappa statistic or intraclass correlation coefficient (ICC) was calculated, 44% showed substantial or almost perfect agreement (beyond chance). However, about 17% showed less than 95% agreement and a kappa or ICC value of less than 60% indicating only slight, fair or moderate agreement (beyond chance). Recommendations to improve the quality of these data fields are presented.

Field methods in medical record abstraction: assessing the properties of comparative effectiveness estimates.

PubMed

Cook, Elizabeth A; Schneider, Kathleen M; Robinson, Jennifer; Wilwert, June; Chrischilles, Elizabeth; Pendergast, Jane; Brooks, John

2014-09-15

Comparative effectiveness studies using Medicare claims data are vulnerable to treatment selection biases and supplemental data from a sample of patients has been recommended for examining the magnitude of this bias. Previous research using nationwide Medicare claims data has typically relied on the Medicare Current Beneficiary Survey (MCBS) for supplemental data. Because many important clinical variables for our specific research question are not available in the MCBS, we collected medical record data from a subsample of patients to assess the validity of assumptions and to aid in the interpretation of our estimates. This paper seeks to describe and document the process used to collect and validate this supplemental information. Medicare claims data files for all patients with fee-for-service Medicare benefits who had an acute myocardial infarction (AMI) in 2007 or 2008 were obtained. Medical records were obtained and abstracted for a stratified subsample of 1,601 of these patients, using strata defined by claims-based measures of physician prescribing practices and drug treatment combinations. The abstraction tool was developed collaboratively by study clinicians and researchers, leveraging important elements from previously validated tools. Records for 2,707 AMI patients were requested from the admitting hospitals and 1,751 were received for an overall response rate of 65%; 1,601 cases were abstracted by trained personnel at a contracted firm. Data were collected with overall 96% inter-abstractor agreement across all variables. Some non-response bias was detected at the patient and facility level. Although Medicare claims data are a potentially powerful resource for conducting comparative effectiveness analyses, observational databases are vulnerable to treatment selection biases. This study demonstrates that it is feasible to abstract medical records for Medicare patients nationwide and collect high quality data, to design the sampling purposively to address specific research questions, and to more thoroughly evaluate the appropriateness of care delivered to AMI patients.

Development of a personalized training system using the Lung Image Database Consortium and Image Database resource Initiative Database.

PubMed

Lin, Hongli; Wang, Weisheng; Luo, Jiawei; Yang, Xuedong

2014-12-01

The aim of this study was to develop a personalized training system using the Lung Image Database Consortium (LIDC) and Image Database resource Initiative (IDRI) Database, because collecting, annotating, and marking a large number of appropriate computed tomography (CT) scans, and providing the capability of dynamically selecting suitable training cases based on the performance levels of trainees and the characteristics of cases are critical for developing a efficient training system. A novel approach is proposed to develop a personalized radiology training system for the interpretation of lung nodules in CT scans using the Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) database, which provides a Content-Boosted Collaborative Filtering (CBCF) algorithm for predicting the difficulty level of each case of each trainee when selecting suitable cases to meet individual needs, and a diagnostic simulation tool to enable trainees to analyze and diagnose lung nodules with the help of an image processing tool and a nodule retrieval tool. Preliminary evaluation of the system shows that developing a personalized training system for interpretation of lung nodules is needed and useful to enhance the professional skills of trainees. The approach of developing personalized training systems using the LIDC/IDRL database is a feasible solution to the challenges of constructing specific training program in terms of cost and training efficiency. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Outline for Research in Large Data Base Resources.

ERIC Educational Resources Information Center

Kahn, Paul

This paper uses a hypothetical application entitled "VAPORTRAILS" to examine how an integrated application can be used to solve the problems of search and retrieval from a range of qualitatively different databases, and the organization of the resulting information into a personal database resource. In addition, four general classes of databases…

HOED: Hypermedia Online Educational Database.

ERIC Educational Resources Information Center

Duval, E.; Olivie, H.

This paper presents HOED, a distributed hypermedia client-server system for educational resources. The aim of HOED is to provide a library facility for hyperdocuments that is accessible via the world wide web. Its main application domain is education. The HOED database not only holds the educational resources themselves, but also data describing…

AIMES Final Technical Report

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

Katz, Daniel S; Jha, Shantenu; Weissman, Jon

2017-01-31

This is the final technical report for the AIMES project. Many important advances in science and engineering are due to large-scale distributed computing. Notwithstanding this reliance, we are still learning how to design and deploy large-scale production Distributed Computing Infrastructures (DCI). This is evidenced by missing design principles for DCI, and an absence of generally acceptable and usable distributed computing abstractions. The AIMES project was conceived against this backdrop, following on the heels of a comprehensive survey of scientific distributed applications. AIMES laid the foundations to address the tripartite challenge of dynamic resource management, integrating information, and portable and interoperablemore » distributed applications. Four abstractions were defined and implemented: skeleton, resource bundle, pilot, and execution strategy. The four abstractions were implemented into software modules and then aggregated into the AIMES middleware. This middleware successfully integrates information across the application layer (skeletons) and resource layer (Bundles), derives a suitable execution strategy for the given skeleton and enacts its execution by means of pilots on one or more resources, depending on the application requirements, and resource availabilities and capabilities.« less

AIMES Final Technical Report

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

Weissman, Jon; Katz, Dan; Jha, Shantenu

2017-01-31

This is the final technical report for the AIMES project. Many important advances in science and engineering are due to large scale distributed computing. Notwithstanding this reliance, we are still learning how to design and deploy large-scale production Distributed Computing Infrastructures (DCI). This is evidenced by missing design principles for DCI, and an absence of generally acceptable and usable distributed computing abstractions. The AIMES project was conceived against this backdrop, following on the heels of a comprehensive survey of scientific distributed applications. AIMES laid the foundations to address the tripartite challenge of dynamic resource management, integrating information, and portable andmore » interoperable distributed applications. Four abstractions were defined and implemented: skeleton, resource bundle, pilot, and execution strategy. The four abstractions were implemented into software modules and then aggregated into the AIMES middleware. This middleware successfully integrates information across the application layer (skeletons) and resource layer (Bundles), derives a suitable execution strategy for the given skeleton and enacts its execution by means of pilots on one or more resources, depending on the application requirements, and resource availabilities and capabilities.« less

HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors

National Institute of Standards and Technology Data Gateway

SRD 155 HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors (Web, free access)   The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB).

PrimateLit Database

Science.gov Websites

Primate Info Net Related Databases NCRR PrimateLit: A bibliographic database for primatology Top of any problems with this service. We welcome your feedback. The PrimateLit database is no longer being Resources, National Institutes of Health. The database is a collaborative project of the Wisconsin Primate

An international aerospace information system - A cooperative opportunity

NASA Technical Reports Server (NTRS)

Blados, Walter R.; Cotter, Gladys A.

1992-01-01

This paper presents for consideration new possibilities for uniting the various aerospace database efforts toward a cooperative international aerospace database initiative that can optimize the cost-benefit equation for all members. The development of astronautics and aeronautics in individual nations has led to initiatives for national aerospace databases. Technological developments in information technology and science, as well as the reality of scarce resources, makes it necessary to reconsider the mutually beneficial possibilities offered by cooperation and international resource sharing.

WAIS Searching of the Current Contents Database

NASA Astrophysics Data System (ADS)

Banholzer, P.; Grabenstein, M. E.

The Homer E. Newell Memorial Library of NASA's Goddard Space Flight Center is developing capabilities to permit Goddard personnel to access electronic resources of the Library via the Internet. The Library's support services contractor, Maxima Corporation, and their subcontractor, SANAD Support Technologies have recently developed a World Wide Web Home Page (http://www-library.gsfc.nasa.gov) to provide the primary means of access. The first searchable database to be made available through the HomePage to Goddard employees is Current Contents, from the Institute for Scientific Information (ISI). The initial implementation includes coverage of articles from the last few months of 1992 to present. These records are augmented with abstracts and references, and often are more robust than equivalent records in bibliographic databases that currently serve the astronomical community. Maxima/SANAD selected Wais Incorporated's WAIS product with which to build the interface to Current Contents. This system allows access from Macintosh, IBM PC, and Unix hosts, which is an important feature for Goddard's multiplatform environment. The forms interface is structured to allow both fielded (author, article title, journal name, id number, keyword, subject term, and citation) and unfielded WAIS searches. The system allows a user to: Retrieve individual journal article records. Retrieve Table of Contents of specific issues of journals. Connect to articles with similar subject terms or keywords. Connect to other issues of the same journal in the same year. Browse journal issues from an alphabetical list of indexed journal names.

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

Carr, F. Jr.; Mahaffey, J.A.

The purpose of the DOE/OHER Chernobyl Database project is to create and maintain an information system to provide usable information for research studies related to the nuclear accident. The system is the official United States repository for information about the Chernobyl accident and its consequences, and currently includes an extensive bibliography and diverse radiological measurements with supporting information. PNL has established two resources: original (not summarized) measurement data, currently about 80,000 measurements, with ancillary information; and about 2,200 bibliographic citations, some including abstracts. Major organizations that have contributed radiological measurement data include the Washington State Department of Social and Healthmore » Services; United States Environmental Protection Agency (domestic and foreign data); United States Nuclear Regulatory Commission; Stone Webster; Brookhaven National Laboratory; Commissariat A L'energie Atomique in France; Ministry of Agriculture, Fisheries, and Food in the United Kingdom; Japan National Institute of Radiological Sciences; and the Finnish Centre For Radiation and Nuclear Safety (STUK). Scientists in Australia, Austria, Belgium, Canada, China, Denmark, England, Federal Republic of Germany, Finland, France, Ireland, Italy, Japan, the Netherlands, Romania, Scotland, Spain, Sweden, Switzerland, United States, Wales, and Yugoslavia have made contributions. Bibliographic materials have been obtained from scientists in the above countries that have replied to requests. In addition, literature searches have been conducted, including a search of the DOE Energy Database. The last search was conducted in January, 1989. This document lists the bibliographic information in the DOE/OHER Chernobyl Database at the current time.« less

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases

PubMed Central

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia

2018-01-01

Abstract The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3′-UTRs, collectively called ‘miRSNPs’, represent a novel category of functional molecules. miRSNPs can lead to miRNA and its target gene dysregulation, and resulting in susceptibility to or onset of human diseases. A curated collection and summary of miRSNP-associated diseases is essential for a thorough understanding of the mechanisms and functions of miRSNPs. Here, we describe MSDD, which currently documents 525 associations among 182 human miRNAs, 197 SNPs, 153 genes and 164 human diseases through a review of more than 2000 published papers. Each association incorporates information on the miRNAs, SNPs, miRNA target genes and disease names, SNP locations and alleles, the miRNA dysfunctional pattern, experimental techniques, a brief functional description, the original reference and additional annotation. MSDD provides a user-friendly interface to conveniently browse, retrieve, download and submit novel data. MSDD will significantly improve our understanding of miRNA dysfunction in disease, and thus, MSDD has the potential to serve as a timely and valuable resource. PMID:29106642

Integrating evidence-based teaching into to clinical practice should improve outcomes.

PubMed

Richards, Derek

2005-01-01

Sources used were Medline, Embase, the Education Resources Information Centre , Cochrane Controlled Trials Register, Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects, Health Technology Assessment database, Best Evidence, Best Evidence Medical Education and Science Citation Index, along with reference lists of known systematic reviews. Studies were chosen for inclusion if they evaluated the effects of postgraduate evidence-based medicine (EBM) or critical appraisal teaching in comparison with a control group or baseline before teaching, using a measure of participants' learning achievements or patients' health gains as outcomes. Articles were graded as either level 1 (randomised controlled trials (RCT)) or level 2 (non-randomised studies that either had a comparison with a control group), or a before and after comparison without a control group. Learning achievement was assessed separately for knowledge, critical appraisal skills, attitudes and behaviour. Because of obvious heterogeneity in the features of individual studies, their quality and assessment tools used, a meta-analysis could not be carried out. Conclusions were weighted by methodological quality. Twenty-three relevant studies were identified, comprising four RCT, seven non-RCT, and 12 before and after comparison studies. Eighteen studies (including two RCT) evaluated a standalone teaching method and five studies (including two RCT) evaluated a clinically integrated teaching method. Standalone teaching improved knowledge but not skills, attitudes or behaviour. Clinically integrated teaching improved knowledge, skills, attitudes and behaviour. Teaching of EBM should be moved from classrooms to clinical practice to achieve improvements in substantial outcomes.

A Review of Equation of State Models, Chemical Equilibrium Calculations and CERV Code Requirements for SHS Detonation Modelling

DTIC Science & Technology

2009-10-01

parameters for a large number of species. These authors provide many sample calculations with the JCZS database incorporated in CHEETAH 2.0, including...FORM (highest classification of Title, Abstract, Keywords) DOCUMENT CONTROL DATA (Security classification of title, body of abstract and...CLASSIFICATION OF FORM 13. ABSTRACT (a brief and factual summary of the document. It may also appear elsewhere in the body of the document itself

Alternative treatment technology information center computer database system

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

Sullivan, D.

1995-10-01

The Alternative Treatment Technology Information Center (ATTIC) computer database system was developed pursuant to the 1986 Superfund law amendments. It provides up-to-date information on innovative treatment technologies to clean up hazardous waste sites. ATTIC v2.0 provides access to several independent databases as well as a mechanism for retrieving full-text documents of key literature. It can be accessed with a personal computer and modem 24 hours a day, and there are no user fees. ATTIC provides {open_quotes}one-stop shopping{close_quotes} for information on alternative treatment options by accessing several databases: (1) treatment technology database; this contains abstracts from the literature on all typesmore » of treatment technologies, including biological, chemical, physical, and thermal methods. The best literature as viewed by experts is highlighted. (2) treatability study database; this provides performance information on technologies to remove contaminants from wastewaters and soils. It is derived from treatability studies. This database is available through ATTIC or separately as a disk that can be mailed to you. (3) underground storage tank database; this presents information on underground storage tank corrective actions, surface spills, emergency response, and remedial actions. (4) oil/chemical spill database; this provides abstracts on treatment and disposal of spilled oil and chemicals. In addition to these separate databases, ATTIC allows immediate access to other disk-based systems such as the Vendor Information System for Innovative Treatment Technologies (VISITT) and the Bioremediation in the Field Search System (BFSS). The user may download these programs to their own PC via a high-speed modem. Also via modem, users are able to download entire documents through the ATTIC system. Currently, about fifty publications are available, including Superfund Innovative Technology Evaluation (SITE) program documents.« less

Occupational dose reduction at Department of Energy contractor facilities: Bibliography of selected readings in radiation protection and ALARA

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

Dionne, B.J.; Sullivan, S.G.; Baum, J.W.

1993-12-01

This bibliography contains abstracts relating to various aspects of ALARA program implementation and dose reduction activities, with a focus on DOE facilities. Abstracts included in this bibliography were selected from proceedings of technical meetings, journals, research reports, searches of the DOE Energy, Science and Technology Database (in general, the citation and abstract information is presented as obtained from this database), and reprints of published articles provided by the authors. Facility types and activities covered in the scope of this report include: radioactive waste, uranium enrichment, fuel fabrication, spent fuel storage and reprocessing, facility decommissioning, hot laboratories, tritium production, research, testmore » and production reactors, weapons fabrication and testing, fusion, uranium and plutonium processing, radiography, and aocelerators. Information on improved shielding design, decontamination, containments, robotics, source prevention and control, job planning, improved operational and design techniques, as well as on other topics, has been included. In addition, DOE/EH reports not included in previous volumes of the bibliography are in this volume (abstracts 611 to 684). This volume (Volume 5 of the series) contains 217 abstracts. An author index and a subject index are provided to facilitate use. Both indices contain the abstract numbers from previous volumes, as well as the current volume. Information that the reader feels might be included in the next volume of this bibliography should be submitted to the BNL ALARA Center.« less

bioDBnet - Biological Database Network

Cancer.gov

bioDBnet is a comprehensive resource of most of the biological databases available from different sites like NCBI, Uniprot, EMBL, Ensembl, Affymetrix. It provides a queryable interface to all the databases available, converts identifiers from one database into another and generates comprehensive reports.

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

Efficacy of Indexing and Abstracting Services for the Dissemination of Agricultural Information Resources in the Institure for Agricultural Research Library, Ahmadu Bello University, Zaria

NASA Astrophysics Data System (ADS)

Gabriel, KASA, M.

2012-10-01

The efficacy of Indexing and Abstracting service for effective organization, storage and retrieval of information resources for agricultural research in Ahmadu Bello University, Zaria necessitated examining the situation in Agricultural Library, Institute for Agricultural Research, Samaru. The study examines the processes, awareness and problems militating against the effective exploitation of the indexing and abstracting services in the Agricultural library established in 1975. The study was conducted ex post facto, data collected span from 2006 ñ 2010. Total sample sizes of 752 patrons and 20,236 intellectually indexed and abstracted resources were involved in the study. Data collected were subjected to descriptive and inferential statistics. The result revealed that a total of 644 articles were indexed and abstracted, 35% of these was done in 2010. Results for awareness show 452 (60.11%) to be aware in 2008. A total 584 articles were indexed and abstracted from which 167 (28.59%) was retrieved in 2006. Patrons, 270 (35.90%) attributed the poor use of the service to assumption it is a referral unit. The hypothesis testing revealed that there is significant association between articles indexed and abstracted with information consulted by patrons (?2cal,100.31>?2tab,9.488) at 5% level of probability and df, 4. In conclusion, enormous documents on Nigerian agriculture are indexed and abstracted in the unit, implying that the service is desirous and consistent. The study recommends that the unit should explore the use of modern technology, employ a permanent subject specialist, train and retrain the unit staff as well as intensify it general orientation campaigns to focus on awareness and use of the indexing and abstracting services.

Screening the Medicines for Malaria Venture Pathogen Box across Multiple Pathogens Reclassifies Starting Points for Open-Source Drug Discovery

PubMed Central

Sykes, Melissa L.; Jones, Amy J.; Shelper, Todd B.; Simpson, Moana; Lang, Rebecca; Poulsen, Sally-Ann; Sleebs, Brad E.

2017-01-01

ABSTRACT Open-access drug discovery provides a substantial resource for diseases primarily affecting the poor and disadvantaged. The open-access Pathogen Box collection is comprised of compounds with demonstrated biological activity against specific pathogenic organisms. The supply of this resource by the Medicines for Malaria Venture has the potential to provide new chemical starting points for a number of tropical and neglected diseases, through repurposing of these compounds for use in drug discovery campaigns for these additional pathogens. We tested the Pathogen Box against kinetoplastid parasites and malaria life cycle stages in vitro. Consequently, chemical starting points for malaria, human African trypanosomiasis, Chagas disease, and leishmaniasis drug discovery efforts have been identified. Inclusive of this in vitro biological evaluation, outcomes from extensive literature reviews and database searches are provided. This information encompasses commercial availability, literature reference citations, other aliases and ChEMBL number with associated biological activity, where available. The release of this new data for the Pathogen Box collection into the public domain will aid the open-source model of drug discovery. Importantly, this will provide novel chemical starting points for drug discovery and target identification in tropical disease research. PMID:28674055

Cholesterol Point-of-Care Testing for Community Pharmacies: A Review of the Current Literature.

PubMed

Haggerty, Lauren; Tran, Deanna

2017-08-01

To summarize the literature on cholesterol point-of-care tests (POCTs). This article would serve as a resource to assist community pharmacists in developing cholesterol point-of-care (POC) pharmacy services. A literature search was performed in MEDLINE Ovid, PubMed, EMBASE, and Cochrane database using the following medical subject headings (MeSH) terms: point-of-care test, cholesterol, blood chemical analysis, rapid testing, collaborative practice, community pharmacy, and ambulatory care. Additional resources including device manufacturer web sites were summarized to supplement the current literature. All human research articles, review articles, meta-analyses, and abstracts published in English through September 1, 2014, were considered. A total of 36 articles were applicable for review. Information was divided into the following categories to be summarized: devices, pharmacists' impact, and operational cost for the pharmacy. The current literature suggests that POCTs in community pharmacies assist with patient outcomes by providing screenings and referring patients with dyslipidemia for further evaluation. The majority of studies on cholesterol POC devices focused on accuracy, revealing the need for further studies to develop best practices and practice models with successful reimbursement. Accuracy, device specifications, required supplies, and patient preference should be considered when selecting a POC device for purchase.

Genome Variation Map: a data repository of genome variations in BIG Data Center

PubMed Central

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

The Effects of HMO Penetration on Preventable Hospitalizations

PubMed Central

Zhan, Chunliu; Miller, Marlene R; Wong, Herbert; Meyer, Gregg S

2004-01-01

Objective To examine the effects of health maintenance organization (HMO) penetration on preventable hospitalizations. Data Source Hospital inpatient discharge abstracts for 932 urban counties in 22 states from the Healthcare Cost and Utilization Project (HCUP) State Inpatient Databases (SID), hospital data from American Hospital Association (AHA) annual survey, and population characteristics and health care capacity data from Health Resources and Services Administration (HRSA) Area Resource File (ARF) for 1998. Methods Preventable hospitalizations due to 14 ambulatory care sensitive conditions were identified using the Agency for Healthcare Research and Quality (AHRQ) Prevention Quality Indicators. Multiple regressions were used to determine the association between preventable hospitalizations and HMO penetration while controlling for demographic and socioeconomic characteristics and health care capacity of the counties. Principal Findings A 10 percent increase in HMO penetration was associated with a 3.8 percent decrease in preventable hospitalizations (95 percent confidence interval, 2.0 percent–5.6 percent). Advanced age, female gender, poor health, poverty, more hospital beds, and fewer primary care physicians per capita were significantly associated with more preventable hospitalizations. Conclusions Our study suggests that HMO penetration has significant effects in reducing preventable hospitalizations due to some ambulatory care sensitive conditions. PMID:15032958

Automatic Summarization of MEDLINE Citations for Evidence–Based Medical Treatment: A Topic-Oriented Evaluation

PubMed Central

Fiszman, Marcelo; Demner-Fushman, Dina; Kilicoglu, Halil; Rindflesch, Thomas C.

2009-01-01

As the number of electronic biomedical textual resources increases, it becomes harder for physicians to find useful answers at the point of care. Information retrieval applications provide access to databases; however, little research has been done on using automatic summarization to help navigate the documents returned by these systems. After presenting a semantic abstraction automatic summarization system for MEDLINE citations, we concentrate on evaluating its ability to identify useful drug interventions for fifty-three diseases. The evaluation methodology uses existing sources of evidence-based medicine as surrogates for a physician-annotated reference standard. Mean average precision (MAP) and a clinical usefulness score developed for this study were computed as performance metrics. The automatic summarization system significantly outperformed the baseline in both metrics. The MAP gain was 0.17 (p < 0.01) and the increase in the overall score of clinical usefulness was 0.39 (p < 0.05). PMID:19022398

How Have States Used Executive Orders to Address Public Health?

PubMed

Gakh, Maxim; Callahan, Karen; Goodie, Aaliyah; Rutkow, Lainie

2018-06-07

Gubernatorial executive orders (GEOs) are important, yet poorly understood, public health tools. We analyzed health-related GEOs nationwide using a modified legal mapping approach. We searched Westlaw's Netscan Executive Orders database for orders issued between 2008 and 2014. Search terms were generated from the Healthy People 2020 Leading Health Indicators (LHIs). GEOs were screened with data abstracted and analyzed on the basis of LHIs, states, years, and characteristics identified in previous literature. We found differences in GEOs issued per LHI. Of the 303 unique orders, they ranged from 32 to 53 issued per year and 0 to 45 issued per state. Most GEOs managed governmental public health functions, required collaboration, and mandated studying problems. Fewer directly addressed health equity, chronic disease, and resource deployment. Gubernatorial authority and political and institutional factors appear relevant to GEO issuance. GEOs offer means to institute public health policies and should be considered by public health professionals.

Accelerating Precision Drug Development and Drug Repurposing by Leveraging Human Genetics

PubMed Central

Shirey-Rice, Jana K.; Lavieri, Robert R.; Jerome, Rebecca N.; Zaleski, Nicole M.; Aronoff, David M.; Bastarache, Lisa; Niu, Xinnan; Holroyd, Kenneth J.; Roden, Dan M.; Skaar, Eric P.; Niswender, Colleen M.; Marnett, Lawrence J.; Lindsley, Craig W.; Ekstrom, Leeland B.; Bentley, Alan R.; Bernard, Gordon R.; Hong, Charles C.; Denny, Joshua C.

2017-01-01

Abstract The potential impact of using human genetic data linked to longitudinal electronic medical records on drug development is extraordinary; however, the practical application of these data necessitates some organizational innovations. Vanderbilt has created resources such as an easily queried database of >2.6 million de-identified electronic health records linked to BioVU, which is a DNA biobank with more than 230,000 unique samples. To ensure these data are used to maximally benefit and accelerate both de novo drug discovery and drug repurposing efforts, we created the Accelerating Drug Development and Repurposing Incubator, a multidisciplinary think tank of experts in various therapeutic areas within both basic and clinical science as well as experts in legal, business, and other operational domains. The Incubator supports a diverse pipeline of drug indication finding projects, leveraging the natural experiment of human genetics. PMID:28379727

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

PubMed

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

2016-01-01

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

PaperBLAST: Text Mining Papers for Information about Homologs

PubMed Central

Arkin, Adam P.

2017-01-01

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

Managing Heterogeneous Information Systems through Discovery and Retrieval of Generic Concepts.

ERIC Educational Resources Information Center

Srinivasan, Uma; Ngu, Anne H. H.; Gedeon, Tom

2000-01-01

Introduces a conceptual integration approach to heterogeneous databases or information systems that exploits the similarity in metalevel information and performs metadata mining on database objects to discover a set of concepts that serve as a domain abstraction and provide a conceptual layer above existing legacy systems. Presents results of…

Students' Attitudes toward ABI/INFORM on CD-ROM: A Factor Analysis.

ERIC Educational Resources Information Center

Wang, Vicky; Lau, Shuk-fong

Two years after the introduction of CD-ROM bibliographic database searching in the Memphis State University libraries (Tennessee), a survey was conducted to examine students' attitudes toward the business database, ABI/INFORM. ABI/INFORM contains indexes and abstracts of articles from over 800 journals on management, accounting, banking, human…

Annual patents review, January-December 2004

Treesearch

Roland Gleisner; Karen Scallon; Michael Fleischmann; Julie Blankenburg; Marguerite Sykes

2005-01-01

This review summarizes patents related to paper recycling that first appeared in patent databases during the 2004. Two on-line databases, Claims/U.S. Patents Abstracts and Derwent World Patents Index, were searched for this review. This feature is intended to inform readers about recent developments in equipment design, chemicals, and process technologies for recycling...

New Directions in Library and Information Science Education. Final Report. Volume 2.5: Database Producer Professional Competencies.

ERIC Educational Resources Information Center

Griffiths, Jose-Marie; And Others

This document contains validated activities and competencies needed by librarians working in a database producer organization. The activities and competencies are organized according to the functions which these librarians perform: acquisitions; thesaurus development and control; indexing/abstracting; and publications and product management.…

Computerization of the Arkansas Fishes Database

Treesearch

Henry W. Robison; L. Gayle Henderson; Melvin L. Warren; Janet S. Rader

2004-01-01

Abstract - Until recently, distributional data for the fishes of Arkansas existed in the form of museum records, field notebooks of various ichthyologists, and published fish survey data; none of which was in a digital format. In 1995, a relational database system was used to design a PC platform data entry module for the capture of information on...

Database of Sources of Environmental Releases of Dioxin-Like Compounds in the United States

EPA Science Inventory

The Database of Sources of Environmental Releases of Dioxin-like Compounds in the United States (US)ARTI refrigerant database