Genomes and Genes
database management systems
Summary: Software designed to store, manipulate, manage, and control data for specific uses.
Publications332 found, 100 shown here
- Gene Expression Omnibus: NCBI gene expression and hybridization array data repositoryRon Edgar
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 30:207-10. 2002..A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo...
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsM Hucka
Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
Bioinformatics 19:524-31. 2003..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
- The human genome browser at UCSCW James Kent
Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
Genome Res 12:996-1006. 2002..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
- TM4: a free, open-source system for microarray data management and analysisA I Saeed
Institute for Genomic Research, Rockville, MD, USA
Biotechniques 34:374-8. 2003
- iRefIndex: a consolidated protein interaction database with provenanceSabry Razick
The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
BMC Bioinformatics 9:405. 2008..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...
- GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genesElizabeth I Boyle
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Bioinformatics 20:3710-5. 2004..GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script...
- SSAHA: a fast search method for large DNA databasesZ Ning
Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Res 11:1725-9. 2001..The SSAHA algorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly. Also, it provides Web-based sequence search facilities for Ensembl projects...
- The Bioperl toolkit: Perl modules for the life sciencesJason E Stajich
University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
Genome Res 12:1611-8. 2002..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
- Exploring the functional landscape of gene expression: directed search of large microarray compendiaMatthew A Hibbs
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
Bioinformatics 23:2692-9. 2007..This vast repository is still underutilized due to the lack of methods for fast, accurate exploration of the entire compendium...
- The Ensembl genome database projectT Hubbard
The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
Nucleic Acids Res 30:38-41. 2002..The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops...
- InterProScan--an integration platform for the signature-recognition methods in InterProE M Zdobnov
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bioinformatics 17:847-8. 2001..InterProScan is designed to be a scalable and extensible system with a robust internal architecture...
- Additional gene ontology structure for improved biological reasoningSimen Myhre
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology NO 7489 Trondheim, Norway
Bioinformatics 22:2020-7. 2006..Our aim was to connect the three subontologies to enable GO to cover more biological knowledge, enable a more consistent use of GO and provide new opportunities for biological reasoning...
- PISCES: a protein sequence culling serverGuoli Wang
Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
Bioinformatics 19:1589-91. 2003..PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output...
- TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasetsGeo Pertea
The Institute for Genomic Research, Rockville, MD 20850, USA
Bioinformatics 19:651-2. 2003..The system can run on multi-CPU architectures including SMP and PVM...
- TOPP--the OpenMS proteomics pipelineOliver Kohlbacher
Simulation of Biological Systems, Eberhard Karls University Tübingen Sand 14, 72076 Tubingen, Germany
Bioinformatics 23:e191-7. 2007..In order to facilitate these studies, it would be desirable to have a flexible 'toolbox' of versatile and user-friendly applications allowing for rapid construction of computational workflows in proteomics...
- Online predicted human interaction databaseKevin R Brown
Division of Cancer Informatics, Ontario Cancer Institute, University of Toronto, Canada
Bioinformatics 21:2076-82. 2005....
- FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factorsJongsun Park
Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151 921, Korea
Bioinformatics 24:1024-5. 2008..The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species...
- MPIDB: the microbial protein interaction databaseJohannes Goll
The J Craig Venter Institute, Rockville, MD 20850, USA
Bioinformatics 24:1743-4. 2008..In contrast to these databases, interactions in MPIDB are further supported by 8150 additional evidences based on interaction conservation, co-purification and 3D domain contacts (iPfam, 3did)...
- Circular genome visualization and exploration using CGViewPaul Stothard
Department of Biological Sciences and Computing Science, University of Alberta Edmonton, Alberta, Canada T6G 2E8
Bioinformatics 21:537-9. 2005..AVAILABILITY: CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/ CONTACT: email@example.com...
- The generic genome browser: a building block for a model organism system databaseLincoln D Stein
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
Genome Res 12:1599-610. 2002..GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org...
- BASE--2nd generation software for microarray data management and analysisJohan Vallon-Christersson
Department of Oncology, Clinical Sciences, Lund University, SE 221 84 Lund, Sweden
BMC Bioinformatics 10:330. 2009..To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2...
- Biocurators and biocuration: surveying the 21st century challengesSarah Burge
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Database (Oxford) 2012:bar059. 2012..DATABASE URL: http://biocurator.org...
- A reference ontology for biomedical informatics: the Foundational Model of AnatomyCornelius Rosse
Departments of Biological Structure, and Medical Education and Biomedical Informatics, Structural Informatics Group, University of Washington, Seattle, WA 98195, USA
J Biomed Inform 36:478-500. 2003....
- Literature mining and database annotation of protein phosphorylation using a rule-based systemZ Z Hu
Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
Bioinformatics 21:2759-65. 2005..While of great value, such information is limited in databases owing to the laborious process of literature-based curation. Computational literature mining holds promise to facilitate database curation...
- Pathway studio--the analysis and navigation of molecular networksAlexander Nikitin
Ariadne Genomics, Inc, 9700 Great Seneca Hgwy, Rockville, MD 20850, USA
Bioinformatics 19:2155-7. 2003..It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules...
- A comprehensive classification system for lipidsEoin Fahy
San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0505, USA
J Lipid Res 46:839-61. 2005..This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases...
- BioMart and Bioconductor: a powerful link between biological databases and microarray data analysisSteffen Durinck
Department of Electronical Engineering, ESAT SCD, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
Bioinformatics 21:3439-40. 2005..g. Ensembl). The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining...
- PharmGKB: the Pharmacogenetics Knowledge BaseMicheal Hewett
Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford, CA 94305 5479, USA
Nucleic Acids Res 30:163-5. 2002..The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001...
- The BioGRID Interaction Database: 2008 updateBobby Joe Breitkreutz
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
Nucleic Acids Res 36:D637-40. 2008..Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction...
- BioMart--biological queries made easyDamian Smedley
Ontario Institute for Cancer Research, MaRS Centre, 101 College Street, Toronto, Ontario, Canada
BMC Genomics 10:22. 2009..This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution...
- KAAS: an automatic genome annotation and pathway reconstruction serverYuki Moriya
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 35:W182-5. 2007..The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database...
- State of the nation in data integration for bioinformaticsCarole Goble
School of Computer Science, University of Manchester, Oxford Road, Manchester M139PL, UK
J Biomed Inform 41:687-93. 2008..The paper expands on that talk. We attempt to place some perspective on past efforts, highlight the reasons for success and failure, and indicate some pointers to the future...
- EGene: a configurable pipeline generation system for automated sequence analysisAlan M Durham
Depto de Ciências da Computação, Instituto de Matemática e Estatística São Paulo, SP, 05508 900, Brazil
Bioinformatics 21:2812-3. 2005..EGene comes with CoEd, a visual tool to facilitate pipeline construction and documentation. A series of components to build pipelines for sequence processing is provided...
- Recognizing names in biomedical texts: a machine learning approachGuodong Zhou
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
Bioinformatics 20:1178-90. 2004..In order to make organized and structured information available, automatically recognizing biomedical entity names becomes critical and is important for information retrieval, information extraction and automated knowledge acquisition...
- A posteriori quality control for the curation and reuse of public proteomics dataJoseph M Foster
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Proteomics 11:2182-94. 2011....
- Improved BLAST searches using longer words for protein seedingSergey A Shiryev
Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
Bioinformatics 23:2949-51. 2007..2.16 of blastall. A Linux executable used to produce the results herein is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/protein_longwords..
- MIFlowCyt: the minimum information about a Flow Cytometry ExperimentJamie A Lee
Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
Cytometry A 73:926-30. 2008..Adoptionof MIFlowCyt by the scientific and publishing communities will facilitate third-party understanding and reuse of FCM data...
- Toward a workbench for rodent brain image data: systems architecture and designIvar A Moene
Neural Systems and Graphics Computing Laboratory, Centre for Molecular Biology and Neuroscience and Institute of Basic Medical Sciences, University of Oslo, PO Box 1105 Blindern, N 0317 Oslo, Norway
Neuroinformatics 5:35-58. 2007..The FACCS application assumes standard animal brain atlas models and can be extended to future models. The system is available both for interactive use from a remote web-browser client as well as for download to a local server machine...
- Screensaver: an open source lab information management system (LIMS) for high throughput screening facilitiesAndrew N Tolopko
ICCB Longwood NSRB Screening Facility, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
BMC Bioinformatics 11:260. 2010....
- Molecular interactions and data standardisationSandra Orchard
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Methods Mol Biol 604:309-18. 2010..Finally, tools and frameworks have been created based on PSI-MI standards to facilitate the visualisation and analysis of molecular interaction data...
- Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysisClaire L Wilson
Paterson Institute for Cancer Research, Manchester M20 4BX, UK
Bioinformatics 21:3683-5. 2005..Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls...
- Systematic determination of patterns of gene expression during Drosophila embryogenesisPavel Tomancak
Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
Genome Biol 3:RESEARCH0088. 2002..Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription...
- ABNER: an open source tool for automatically tagging genes, proteins and other entity names in textBurr Settles
Department of Computer Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin Madison Madison, WI 52706, USA
Bioinformatics 21:3191-2. 2005..It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora...
- GMD@CSB.DB: the Golm Metabolome DatabaseJoachim Kopka
Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Golm, Germany
Bioinformatics 21:1635-8. 2005..AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html CONTACT: Steinhauser@mpimp-golm.mpg.de SUPPLEMENTARY INFORMATION: http://csbdb.mpimp-golm.mpg.de/..
- DATF: a database of Arabidopsis transcription factorsAnyuan Guo
Center for Bioinformatics, Beijing 100871, Peoples Republic of China
Bioinformatics 21:2568-9. 2005..AVAILABILITY: DATF is freely available at http://datf.cbi.pku.edu.cn..
- A Chado case study: an ontology-based modular schema for representing genome-associated biological informationChristopher J Mungall
Lawrence Berkeley National Laboratory, Lawrence Berkeley National Lab, Mail Stop 64R0121, Berkeley, CA 94720, USA
Bioinformatics 23:i337-46. 2007..Our question was whether we could create a relational database schema that would be successfully reused...
- MaGe: a microbial genome annotation system supported by synteny resultsDavid Vallenet
Atelier de Génomique Comparative, CNRS UMR8030, 2 rue Gaston Cremieux, 91057 Evry, Cedex, France
Nucleic Acids Res 34:53-65. 2006..In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage...
- ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomicsKenny Helsens
Department of Medical Protein Research, VIB, Ghent, Belgium
Proteomics 10:1261-4. 2010..We here present ms_lims (http://genesis.UGent.be/ms_lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses...
- Purdue ionomics information management system. An integrated functional genomics platformIvan Baxter
Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, USA
Plant Physiol 143:600-11. 2007..PiiMS is accessible at www.purdue.edu/dp/ionomics...
- Natural language processing in aid of FlyBase curatorsNikiforos Karamanis
Computer Laboratory, University of Cambridge, William Gates Building, Cambridge, CB3 0FD, UK
BMC Bioinformatics 9:193. 2008..Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear...
- MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactionsEmilie Chautard
UMR 5086 CNRS Université Lyon 1, 7 passage du Vercors, 69367 Lyon Cedex 07, France
Bioinformatics 25:690-1. 2009..The current version of MatrixDB contains 1972 interactions corresponding to 4412 experiments and involving 259 extracellular biomolecules...
- WikiPathways: pathway editing for the peopleAlexander R Pico
Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
PLoS Biol 6:e184. 2008
- Lessons from structural genomicsThomas C Terwilliger
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Annu Rev Biophys 38:371-83. 2009..Finally, rapid deposition of data in public databases has increased the impact and usefulness of the data and international cooperation has advanced the field and improved data sharing...
- IMG/M: a data management and analysis system for metagenomesVictor M Markowitz
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA
Nucleic Acids Res 36:D534-8. 2008..IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m...
- MedScan, a natural language processing engine for MEDLINE abstractsSvetlana Novichkova
Ariadne Genomics, Inc, 9100 Great Seneca HWY, Rockville, MD 20850, USA
Bioinformatics 19:1699-706. 2003..Most proposals to date make rather simplistic assumptions about the syntactic aspect of natural language. There is an urgent need for a system that has broad coverage and performs well in real-text applications...
- The SWAN biomedical discourse ontologyPaolo Ciccarese
Massachusetts General Hospital, Boston, MA 02129, USA Harvard Medical School, Boston, MA 02115, USA
J Biomed Inform 41:739-51. 2008..We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies...
- Systems Biology Toolbox for MATLAB: a computational platform for research in systems biologyHenning Schmidt
Fraunhofer Chalmers Research Centre for Industrial Mathematics, Chalmers Science Park, SE 41288 Göteborg, Sweden
Bioinformatics 22:514-5. 2006..The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis...
- The HMMTOP transmembrane topology prediction serverG E Tusnády
Institute of Enzymology, BRC, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary
Bioinformatics 17:849-50. 2001..This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments...
- Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasetsClaude Chelala
Centre for Molecular Oncology, Institute of Cancer and CR UK Clinical Centre, Barts and The London School of Medicine QMUL, Charterhouse Square London EC1M 6BQ, UK
BMC Genomics 8:439. 2007....
- PRIMe: a Web site that assembles tools for metabolomics and transcriptomicsKenji Akiyama
RIKEN Plant Science Center, Yokohama, Kanagawa, Japan
In Silico Biol 8:339-45. 2008....
- PDZBase: a protein-protein interaction database for PDZ-domainsThijs Beuming
Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave, New York, NY 10021, USA
Bioinformatics 21:827-8. 2005....
- Overview of BioCreAtIvE: critical assessment of information extraction for biologyLynette Hirschman
The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
BMC Bioinformatics 6:S1. 2005..The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation...
- Data extraction and ad hoc query of an entity-attribute-value databaseP M Nadkarni
Yale University, New Haven, Connecticut, USA
J Am Med Inform Assoc 5:511-27. 1998..The authors' work does not close the query problem, and they identify several complex subproblems that are still to be solved...
- GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway dataAndrey Rzhetsky
Columbia Genome Center, Columbia University, New York, NY 10032, USA
J Biomed Inform 37:43-53. 2004..GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information...
- Biomedical knowledge navigation by literature clusteringYasunori Yamamoto
Department of Computational Biology, University of Tokyo, Kibanto CB01, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8561, Japan
J Biomed Inform 40:114-30. 2007..McSyBi is freely available at http://textlens.hgc.jp/McSyBi/...
- Benefits of using the DCM4CHE DICOM archiveMax J Warnock
Diagnostic Radiology, University of Maryland School of Medicine, 22 South Greene Str, Baltimore, MD 21201, USA
J Digit Imaging 20:125-9. 2007
- Agile methods in biomedical software development: a multi-site experience reportDavid W Kane
SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA
BMC Bioinformatics 7:273. 2006..We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods...
- HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissuesPeter M Haverty
Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02115, USA
Nucleic Acids Res 30:214-7. 2002..We provide interactive tools for researchers to query and visualize our data over the Internet. To facilitate data analysis, we cross-reference each gene on the array with its annotation in the LocusLink database at NCBI...
- Corpus annotation for mining biomedical events from literatureJin Dong Kim
Department of Computer Science, School of Information Science and Technology, University of Tokyo, Tokyo, Japan
BMC Bioinformatics 9:10. 2008..However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation...
- Bioimage informatics for experimental biologyJason R Swedlow
Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
Annu Rev Biophys 38:327-46. 2009..In this article we present the recent efforts by the bioimage informatics community to tackle these challenges, and discuss our own vision for future development of bioimage informatics solutions...
- Life sciences on the Semantic Web: the Neurocommons and beyondAlan Ruttenberg
Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
Brief Bioinform 10:193-204. 2009..All components of the knowledge base are freely available at http://neurocommons.org/, enabling readers to reconstruct the knowledge base and experiment with this new technology...
- ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitroVadim P Valuev
Institute of Cytology and Genetics, Lavrentieva ave 10, Novosibirsk 630090, Russia and Istituto Tecnologie Biomediche Avanzate, Via Fratelli Cervi 93, 20090 Segrate, Italy
Nucleic Acids Res 30:200-2. 2002..Research tools of the ASPD allow the analysis of pairwise correlations in the sequences of proteins and peptides selected against one target. The URL for the ASPD database is http://www.sgi.sscc.ru/mgs/gnw/aspd/...
- Issues in learning an ontology from textChristopher Brewster
Aston Business School, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
BMC Bioinformatics 10:S1. 2009..We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus...
- The Integr8 project--a resource for genomic and proteomic dataManuela Pruess
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
In Silico Biol 5:179-85. 2005..Customisable statistics data are available from the BioMart application, and pre-prepared data can be downloaded from the FTP site...
- Rutabaga by any other name: extracting biological namesLynette Hirschman
The MITRE Corporation, MS K312, 202 Burlington Rd, Bedford, MA 01730, USA
J Biomed Inform 35:247-59. 2002..We conclude by outlining a research agenda to raise performance of named entity tagging to a level where it can be used to perform tasks of biological importance...
- Data management in a longitudinal cross-cultural studyR J Roberts
Department of Psychiatry, Indiana University School of Medicine, Indianapolis, USA
Stat Med 19:1645-9. 2000..Exchange visits have been needed to address data management issues and resolve unexpected problems. The data management on cross-cultural studies can be handled successfully, given careful planning...
- The Australian EEG databaseM Hunter
Department of Psychology, School of Behavioural Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
Clin EEG Neurosci 36:76-81. 2005..We anticipate that such data will be useful in not only helping to answer clinical questions but also in the field of mathematical modeling of the EEG...
- GeneTrail--advanced gene set enrichment analysisChristina Backes
Center for Bioinformatics, Saarland University, Building E1 1, 66041 Saarbrucken, Germany
Nucleic Acids Res 35:W186-92. 2007..GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de...
- Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMSHwanjo Yu
CSE Department, POSTECH, Pohang, South Korea
BMC Bioinformatics 11:S6. 2010..This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed...
- MedEvi: retrieving textual evidence of relations between biomedical concepts from MedlineJung Jae Kim
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
Bioinformatics 24:1410-2. 2008..MedEvi further identifies additional keywords of biological and statistical significance from local context of matching occurrences in order to help users reformulate their queries for better results...
- Terminology-driven mining of biomedical literatureGoran Nenadic
Computer Science, University of Salford, Salford M5 4WT, UK
Bioinformatics 19:938-43. 2003..Although the knowledge is organized around sets of domain-specific terms, few literature mining systems incorporate deep and dynamic terminology processing...
- TO-GO: a Java-based Gene Ontology navigation environmentUngsik Yu
National Genome Information Center, KRIBB, Oun 52, Yusong, Daejeon 305 333, Korea
Bioinformatics 21:3580-1. 2005..A copy/paste function is also implemented in order to facilitate data exchange between applications...
- UK Biobank: from concept to realityWilliam Ollier
Centre for Integrated Genomic Medical Research, The University of Manchester, UK
Pharmacogenomics 6:639-46. 2005..As such, it will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental and lifestyle factors on human morbidity, mortality and health...
- Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databasesTadashi Imanishi
Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2 42 Aomi, Koto ku, Tokyo 135 0064, Japan
Nucleic Acids Res 37:W17-22. 2009..We also developed the ID Converter System (ICS) for simply converting data IDs by using corresponding tables in the HMS. The HMS and ICS are freely available at http://biodb.jp/...
- Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)Selina S Dwight
Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5120, USA
Nucleic Acids Res 30:69-72. 2002..geneontology.org. SGD gene associations to GO can be found by visiting our site at http://genome-www.stanford.edu/Saccharomyces/...
- Bio2RDF: towards a mashup to build bioinformatics knowledge systemsFrançois Belleau
Centre de Recherche du CHUL, Universite Laval, 2705 Boulevard Laurier, Que, Canada G1V4G2
J Biomed Inform 41:706-16. 2008..The Bio2RDF repository can be queried at http://bio2rdf.org...
- BioInfer: a corpus for information extraction in the biomedical domainSampo Pyysalo
Turku Centre for Computer Science TUCS, University of Turku, Lemminkäisenkatu 14a, 20520 Turku, Finland
BMC Bioinformatics 8:50. 2007..The development and evaluation of such methods requires annotated domain corpora...
- AMiGA: the arthropodan mitochondrial genomes accessible databasePedro Cipriano Feijão
Laboratório de Genética Animal, Centro de Biologia Molecular e Engenharia Genética CBMEG, Universidade Estadual de Campinas UNICAMP, CP 6010, CEP 13035 875, Campinas, Sao Paulo, Brazil
Bioinformatics 22:902-3. 2006..AVAILABILITY: http://amiga.cbmeg.unicamp.br CONTACT: firstname.lastname@example.org SUPPLEMENTARY INFORMATION: Detailed information, including an illustrated tutorial, is available from the above URL...
- An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependenceSatya S Sahoo
Kno e sis Center, Wright State University, Dayton, OH, USA
J Biomed Inform 41:752-65. 2008..In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base...
- Project management system for structural and functional proteomics: SesameZsolt Zolnai
Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison Wisconsin 53706, USA
J Struct Funct Genomics 4:11-23. 2003..This software is available to parties interested in using it and assisting to guide its further development...
- Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabularyXizeng Mao
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing 100871, PR China
Bioinformatics 21:3787-93. 2005..Yet, while GO offers tremendous value, it also has certain limitations such as the lack of direct association with pathways...
- PRIDE: the proteomics identifications databaseLennart Martens
Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
Proteomics 5:3537-45. 2005..The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation...
- SNPper: retrieval and analysis of human SNPsA Riva
Children s Hospital Informatics Program, Children s Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
Bioinformatics 18:1681-5. 2002..Although large collections of SNPs exist in public databases, researchers need tools to effectively retrieve and manipulate them...
- ASRP: the Arabidopsis Small RNA Project DatabaseAdam M Gustafson
Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331, USA
Nucleic Acids Res 33:D637-40. 2005..0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu...
- Osprey: a network visualization systemBobby Joe Breitkreutz
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University Avenue, Toronto, M5G 1X5, Canada
Genome Biol 4:R22. 2003..Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods...
- Deciphering protein-protein interactions. Part I. Experimental techniques and databasesBenjamin A Shoemaker
Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States of America
PLoS Comput Biol 3:e42. 2007
- RelEx--relation extraction using dependency parse treesKatrin Fundel
Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
Bioinformatics 23:365-71. 2007..g. physical or regulatory interactions between genes and proteins. Most interactions mentioned in the free text of biomedical publications are not yet contained in structured databases...
- GenoMap, a circular genome data viewerNaoki Sato
Department of Molecular Biology, Faculty of Science, Saitama University, 255 Shimo ohkubo, Saitama, 338 8570 Japan
Bioinformatics 19:1583-4. 2003..An interactive interface facilitates easy identification of the expressed region. This software is also used for drawing genome-wide quantitative data...
- Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactionsSamuel Kerrien
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
BMC Biol 5:44. 2007....
- Using Laboratory Information Management Systems as central part of a proteomics data workflowChristian Stephan
Medizinisches Proteom Center, Ruhr Universitaet Bochum, Bochum, Germany
Proteomics 10:1230-49. 2010..Therefore, they enable community-wide data utilization and further Systems Biology discoveries...
- VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profilesPhilippe La Rosa
Institut Curie, Service Bioinformatique, 26 Rue d Ulm, Paris 75248 cedex 05, France
Bioinformatics 22:2066-73. 2006..This step requires visualization of the data in a meaningful way to visualize the results and to perform first level analyses...
- Development, Evaluation, and Testing of the Sesame LIMSZsolt Zolnai; Fiscal Year: 2012..We will ensure that the software runs on a variety of platforms, supports a variety of relational database management systems, and is firewall friendly...
- Continuation of the Longitudinal Assessment of Bariatric Surgery (LABS) - DCCSteven H Belle; Fiscal Year: 2013..This includes maintaining the distributed data entry and database management systems;maintaining contact with the NIDDK-supported biospecimen and data repositories;administering a ..
- HICSS-26 CONFERENCE--MINITRACK ON GENOME INFORMATICSCharles Lawrence; Fiscal Year: 1993..INTEGRATED SOFTWARE ENVIRONMENTS: Laboratory database management systems and software environments that integrate and support the process of large-scale mapping and sequencing.
- Building Web Services Infrastructure for Senior CitizensAthman Bouguettaya; Fiscal Year: 2004..Web services on the Web are poised to play the same role as data has played in database management systems. Two sites, Virginia Tech and VDA, will be used for the deployment of the Web Service middleware ..
- CONSORTIUM CANCER CENTER SUPPORT GRANTSHIRLEY LANSKY; Fiscal Year: 1993....
- Clinical Assessment in Neuropsychiatric Image DatabasesJOSE PARDO; Fiscal Year: 2004..Third, improved and more powerful database management systems (DBMS) and specialized computer interface must support such datasets and their query...
- BAYESIAN TEXTUAL AND MULTIMEDIA INFORMATION RETRIEVALGIOVANNI MARCHISIO; Fiscal Year: 2002..The Bayesian search and retrieval functions will become an add-on module to many database management systems. The ability to train the system to recognize visual concepts gives us a definite advantage In image ..
- EMERGENCY ROOM CANCER SCREENING PROGRAMHarold Freeman; Fiscal Year: 1991....
- ALCOHOL USE IN TECUMSEH, MICHIGAN: 1959-1978MaryFran Sowers; Fiscal Year: 1991..Computer files of alcohol use histories will be made for each person and for each family, using database management systems that facilitate use by other investigators...
- TB ANTIMICROBIAL ACQUISITION & COORDINATING FACILITYJOHN SECRIST; Fiscal Year: 1999..tuberculosis, (2) maintain computerized inventory and chemical database management systems. (3) receive, store, and ship compounds, (4) maintain confidentiality and coordinate correspondence ..
- DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASEPeter Karp; Fiscal Year: 2003....
- Robust Software Components for Model Organism DatabasesPeter Karp; Fiscal Year: 2003..Although Pathway Tools is particularly well adapted to microbial MODs, one goal of this application is to adapt the metabolic pathway part of Pathway Tools to work with MODs for higher organisms. ..
- Interoperation of Genome Databases and ToolsKei Hoi Cheung; Fiscal Year: 2005..We will extend our approach to other types of genomic data such as microarray data, which both laboratories and others will soon be generating in large quantities. ..
- Pathway Prediction and Assessment Integrating Multiple Evidence TypesPeter Karp; Fiscal Year: 2009..We will search the MetaCyc reaction space (comprising almost 6000 reactions) for novel subpathways, explicitly constraining our search using organism-specific evidence (i.e., homology, experimental evidence, etc.) at each step. ..
- Encyclopedia of E. Coli Genes and MetabolismPeter Karp; Fiscal Year: 2005..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
- VOCABULARY MANAGEMENT FOR CLINICAL RESEARCH DATABASESCynthia Brandt; Fiscal Year: 2005....
- DELIVERY OF THE CGN INFORMATION RESOURCE DATABASEPrakash Nadkarni; Fiscal Year: 2006..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
- ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASESPrakash Nadkarni; Fiscal Year: 2002..In particular, research will be performed on utilization of newer database technologies, such as new indexing methods, as well as parallel database implementations. ..
- DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASEPrakash Nadkarni; Fiscal Year: 2002..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
- Mediated Integration of Neuroscience ResourcesLuis Marenco; Fiscal Year: 2008..abstract_text> ..
- 2006 Diffraction Methods in Structual Biology ConferencePaul Adams; Fiscal Year: 2006..Junior participation will be encouraged with time for discussion after talks and a session devoted to talks selected from the poster-presentations. [unreadable] [unreadable] [unreadable] [unreadable]..
- Diffraction Methods in Structural Biology 2008 Gordon Research ConferencePaul Adams; Fiscal Year: 2008..There is a growing recognition that the use of such complementary techniques highly benefits the study of the increasingly complex assemblies of biological molecules now under investigation. [unreadable] [unreadable] [unreadable]..
- MOLECULAR AND GENETIC BASIS OF CELL PROLIFERATIONMICHAEL TYERS; Fiscal Year: 2005..The Gordon Conferences format provides a unique environment that encourages informal and open discussion among the participants and this in turn fosters initiation of collaborative efforts and stimulates future research directions. ..
- Assisting Systematic Review Preparation Using Automated Document ClassificationAaron Cohen; Fiscal Year: 2009..Since up-to-date systematic reviews are essential for establishing widespread high quality practice standards and guidelines, the overall public health will benefit from this work. ..
- Regulated Ligand Access in Control Receptor ProcessesH Wiley; Fiscal Year: 2004..In addition, they should provide some general insights into how other growth factor systems are regulated. ..
- Tool to Integrate Genomic and Proteomic Data of AgingZOE LACROIX; Fiscal Year: 2002..Aim 2: Enhance the access to information related to age-related diseases, disorders and disabilities through the exploration of multiple data sources. ..
- Androgen Signaling in Neoplastic Prostate GrowthPeter Nelson; Fiscal Year: 2006..abstract_text> ..
- dChip:Analysis and Visualization of Oligonucleotide Expression and SNP ArraysCheng Li; Fiscal Year: 2010....
- Physiological Genomics of Hypertensive Renal DiseaseHoward J Jacob; Fiscal Year: 2010..We are confident that we will either find the gene or narrow down the interval to a handful of genes when we complete the term of this grant. ..
- Fourier transform-ion cyclotron-resonance mass specDavid Goodlett; Fiscal Year: 2003..Furthermore there are no FTMS instruments in the greater Seattle area for us, or our collaborators, to use. ..
- Regulatory Role of Growth Hormone Secretagogue ReceptorRoy Smith; Fiscal Year: 2007..We hypothesize that clinical use of ghrelin mimetics will translate to improved cognitive function in the elderly. [unreadable] [unreadable] [unreadable]..
- Integrated Tool for Biological Parametric MappingJoseph Maldjian; Fiscal Year: 2007....
- Computational Methods for Transcriptional Mapping of Eukaryotic GenomesCharles Delisi; Fiscal Year: 2009..GABA is the major inhibitory neurotransmitter in the central nervous system (CNS), and plays a key role in CNS development and disease. ..
- VIRTUAL DENTAL PATIENTRalph DeLong; Fiscal Year: 2001..In light of these developments, an authenticated VDP seems not only possible and beneficial, but inevitable and of high program relevance. ..
- Novel algorithms and organisms for Onto-ToolsSorin Draghici; Fiscal Year: 2007..The enhanced Onto-Tools will continue to be freely available. Onto-Analyzer and the software evolution tools developed under this proposal will be made freely available to the research community, as well. ..
- Integrated Studies of 3'-UTR Mediated Gene RegulationJOEL GRABER; Fiscal Year: 2009..Our work will generate resources that facilitate the connection between regulatory activity and health implications. ..
- EVALUATION OF CHD IN MEN AND WOMEN PRIOR TO FIRST AMIBarbara Yawn; Fiscal Year: 2002..In addition, we will provide specific information on current gender-related practice patterns. This information can be used to inform future practice recommendations. ..
- Development of a Urological CD Cell Typing SystemPeter Nelson; Fiscal Year: 2009..These studies will involve the evaluation of in vitro growth characteristics, cellular gene expression, organ topography, inter-species conservation, and transgenic animal models. ..
- A Computational Genotyping System for Improved Influenza SurveillanceGuoqing Lu; Fiscal Year: 2010..With the genotyping database system, newly emerging influenza A viral genotypes can be identified in a timely and cost-effective manner. ..
- Controlled Vocabulary Design for Clinical ApplicationsPeter Elkin; Fiscal Year: 2004..g., implementation of guidelines), education of future clinicians (e.g., information acquisition techniques) and research (e.g., outcomes research) toward the evidence-based practice of medicine. ..
- A Literature Curation Tool for Organism DatabasesSeung Rhee; Fiscal Year: 2003..The system will be central to the curation efforts of the collaborating databases and will be useable as a whole or in parts by other existing or emerging MODs. ..
- Improving Reporting of Race, Ethnicity, and Language in CaliforniaDAVID SCOTT ZINGMOND; Fiscal Year: 2010..Results can be used to more accurately identify and address potential health and healthcare disparities arising through issues related to race, ethnicity, and language. ..
- Biosurveillance Utilizing SNOMED-CT Based Natural Language ProcessingPeter Elkin; Fiscal Year: 2007..The fruits of this research will assist our national initiatives to pave the way toward a safe and effective BioSecure biosurveillance solution. ..
- GENETIC ARCHITECTURE OF PLASMA T-PA AND PAI-1Jason Moore; Fiscal Year: 2004..This collaborative proposal provides a robust mechanism for highly focused translational research in the molecular genetics and biology of the role of the fibrinolytic system in arterial and cerebral thrombosis. ..
- Generic Software Modules for Microarray DataGavin Sherlock; Fiscal Year: 2003..Lastly, SMD will create and release a generic database table object that will provide a useful and simple architecture for data access that will be database platform-independent. ..
- Autonomic nervous system control of HIV-1 replicationSteve Cole; Fiscal Year: 2005..Such interventions would enhance the efficacy of current antiretroviral treatment regimens by opposing physiologic processes that support ongoing pathogenesis. ..
- COMBATING MULTI-DRUG RESISTANT BACTERIAPaul Hergenrother; Fiscal Year: 2010..abstract_text> ..
- Pathophysiology/Clinical Outcomes/Patients/EndocarditisChristopher Cabell; Fiscal Year: 2005..The findings of this study have implications not only for clinical care but will also provide a foundation of knowledge and network of investigators from which subsequent randomized trials can be conducted. ..
- Directory and Information System components for genomesDonald Gilbert; Fiscal Year: 2003..Such a module for automated, common-standard use of organism genome data is an important step toward a grid of data useable for the large-scale analyses desired bioscientists. ..
- TRANSCRIPTOME ANALYSIS IN NORMAL AND NEOPLASTIC PROSTATEPeter Nelson; Fiscal Year: 2002..The accomplishment of these aims will provide a genomics-based resource that defines cell type specific gene expression profiles associated with stages of normal development and neoplastic prostate growth. ..
- EMG-BASED METHODS FOR TESTING NON-KEYBOARD IMPUT DEVICESPaolo Bonato; Fiscal Year: 2002..Future studies by the applicant will focus on utilizing the innovation to gain a better understanding of overuse injury mechanisms related to work tasks and the operation of devices in the workplace. ..
- GENETIC DETERMINATES OF HIGH BLOOD PRESSUREHoward Jacob; Fiscal Year: 2004..The resulting synthesis of ideas and amassed data permits rigorous hypothesis testing not otherwise possible and will hasten understanding of the previously elusive genetic variation responsible for disease risk. ..
- Infrastructure equipment for gene expression analysisSorin Draghici; Fiscal Year: 2003..Furthermore, the system may be expanded in the future, to accommodate new investigators at a cost that is very feasible. ..
- Patient-Guided Tools to Promote Colon Cancer ScreeningWilson Pace; Fiscal Year: 2005..Furthermore, this method of education and tracking is not specific to CRC and could provide opportunities for increasing screening rates for other types of cancer. ..
- Uppsala ECD-ETD ConferenceDavid Goodlett; Fiscal Year: 2005..abstract_text> ..
- GENE EXPRESSION BASED CLASSIFICATION OF GLIAL TUMORSStanley Nelson; Fiscal Year: 2004..3)To develop a set of genes with prognostic importance in low grade astrocytomas. 4)To validate the importance of the genes from specific aims 2 and 3 in the prognosis of low grade astrocytomas. ..
- Defining the yeast transcriptome with custom microarraysGavin Sherlock; Fiscal Year: 2007..abstract_text> ..
- Lung Imaging Database Resource for Imaging ResearchMIKE MCNITT GRAY; Fiscal Year: 2006..SA-3 To provide a means for documentation and distribution of this database to researchers through the internet. ..
- STRUCTURAL ORGANIZATION AND PROTEOMICS OF TBThomas Terwilliger; Fiscal Year: 2005..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
- Neurophysiological Measurement in Aphasia TreatmentSteven Small; Fiscal Year: 2009..Outcomes are assessed by both physiological and behavioral measures, which are collected every three weeks starting six weeks before treatment and ending six weeks after completion of treatment. ..
- Assessing Penetrating Trauma Under UncertaintyOmolola Ogunyemi; Fiscal Year: 2004..We will also examine the system's performance in comparison to physicians at different stages of training, to assess its potential in providing educational value. ..
- WFU_Pickatlas InteroperabilityJoseph Maldjian; Fiscal Year: 2008..This project will build on the pickatlas software to provide automated neuroanatomical region of interest analyses for human imaging studies and studies of non-human primates. [unreadable] [unreadable]..
- Bioinformatics Infrastructure for Large Scale Studies of Aphasia RecoverySteven Small; Fiscal Year: 2007..Finally, this infrastructure and data will be shared, and a user of the system from virtually anywhere could pose such questions using the relational database query interface. ..
- COMMUNITY PREVENTION INTERVENTIONS FOR URBAN DEMOLITIONMark Farfel; Fiscal Year: 2002....