Genomes and Genes
Summary: A specified list of terms with a fixed and unalterable meaning, and from which a selection is made when CATALOGING; ABSTRACTING AND INDEXING; or searching BOOKS; JOURNALS; and other documents. The control is intended to avoid the scattering of related subjects under different headings (SUBJECT HEADINGS). The list may be altered or extended only by the publisher or issuing agency. (From Harrod's Librarians' Glossary, 7th ed, p163)
Publications283 found, 100 shown here
- 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...
- 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..Ontologies, such as the popular Gene Ontology (GO), provide a common controlled vocabulary for these types of automated analysis...
- A new method to measure the semantic similarity of GO termsJames Z Wang
School of Computing, Clemson University, Clemson, SC 29634, USA
Bioinformatics 23:1274-81. 2007....
- The OBO Foundry: coordinated evolution of ontologies to support biomedical data integrationBarry Smith
Department of Philosophy and New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, New York 14203, USA
Nat Biotechnol 25:1251-5. 2007..We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved...
- The GOA database in 2009--an integrated Gene Ontology Annotation resourceDaniel Barrell
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 37:D396-403. 2009..ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set...
- The Sequence Ontology: a tool for the unification of genome annotationsKaren Eilbeck
Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
Genome Biol 6:R44. 2005The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data...
- BioPortal: ontologies and integrated data resources at the click of a mouseNatalya F Noy
Stanford Center for Biomedical Informatics Research, Stanford University
Nucleic Acids Res 37:W170-3. 2009..Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources...
- 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....
- The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)Chris F Taylor
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
OMICS 10:145-51. 2006..Initiative (HUPO PSI), specifically, our work on reporting requirements, data exchange formats and controlled vocabulary terms...
- 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...
- The Arabidopsis Information Resource (TAIR): gene structure and function annotationDavid Swarbreck
Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA
Nucleic Acids Res 36:D1009-14. 2008..A total of 681 new genes and 1002 new splice variants were added. Overall, 10,098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release...
- Metrics for GO based protein semantic similarity: a systematic evaluationCatia Pesquita
XLDB, Departamento de Informatica, Faculdade de Ciencias da Universidade de Lisboa, Campo Grande Edifício C6, Lisboa, Portugal
BMC Bioinformatics 9:S4. 2008..Another issue, is whether electronic annotations should or not be used in semantic similarity calculations...
- 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...
- Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant speciesMarin Talbot Brewer
Department of Horticulture and Crop Science, The Ohio State University Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA
Plant Physiol 141:15-25. 2006..To facilitate consistent terminology pertaining to shape, a controlled vocabulary focusing specifically on fruit shape traits was developed...
- Correlation between gene expression and GO semantic similarityJosé L Sevilla
Strathmore University, Ole Sangale Road, Madaraka Estate, PO Box 59857, 00200 Nairobi, Kenya
IEEE/ACM Trans Comput Biol Bioinform 2:330-8. 2005..These results can be used to augment the knowledge provided by clustering algorithms and in the development of bioinformatic tools for finding and characterizing gene products...
- Functional annotation of the Arabidopsis genome using controlled vocabulariesTanya Z Berardini
Carnegie Institution, Department of Plant Biology, Stanford, California 94305, USA
Plant Physiol 135:745-55. 2004..We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-..
- The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic informationCynthia L Smith
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Genome Biol 6:R7. 2005..The MP Ontology is currently used by the Mouse Genome Database and Rat Genome Database to represent phenotypic data...
- 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...
- ChEBI: a database and ontology for chemical entities of biological interestKirill Degtyarenko
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nucleic Acids Res 36:D344-50. 2008..ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/..
- 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...
- Automated annotation of Drosophila gene expression patterns using a controlled vocabularyShuiwang Ji
Department of Computer Science and Engineering, Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
Bioinformatics 24:1881-8. 2008..The spatial and temporal patterns of gene expression are integrated by anatomical terms from a controlled vocabulary linking together intermediate tissues developed from one another...
- A new measure for functional similarity of gene products based on Gene OntologyAndreas Schlicker
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
BMC Bioinformatics 7:302. 2006..These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role...
- 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...
- Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI projectChris F Taylor
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nat Biotechnol 26:889-96. 2008
- Gene Ontology term overlap as a measure of gene functional similarityMeeta Mistry
Department of Psychiatry and Centre for High Throughput Biology, University of British Columbia, British Columbia, Canada
BMC Bioinformatics 9:327. 2008..A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO)...
- VectorBase: a data resource for invertebrate vector genomicsDaniel Lawson
European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nucleic Acids Res 37:D583-7. 2009..We have continued to develop both the software infrastructure and tools for interrogating the stored data...
- Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotationsXiaomei Wu
MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
Nucleic Acids Res 34:2137-50. 2006..This analysis is expected to provide a new approach for predicting the protein-protein interaction maps from other completely sequenced genomes with high-quality GO-based annotations...
- 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...
- 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...
- 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...
- A probabilistic generative model for GO enrichment analysisYong Lu
Computer Science Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213 USA
Nucleic Acids Res 36:e109. 2008..When used with microarray expression data and ChIP-chip data from yeast and human our method was able to correctly identify both general and specific enriched categories which were overlooked by other methods...
- 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...
- The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating dataTerry F Hayamizu
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Genome Biol 6:R29. 2005....
- Frontiers of biomedical text mining: current progressPierre Zweigenbaum
LIMSI CNRS, BP 133, 91403 Orsay Cedex, France
Brief Bioinform 8:358-75. 2007..In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year...
- GO PaD: the Gene Ontology Partition DatabaseGil Alterovitz
Division of Health Sciences and Technology Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA
Nucleic Acids Res 35:D322-7. 2007..med.harvard.edu/proj/gopart. The site also includes an online tutorial...
- Variations in Medical Subject Headings (MeSH) mapping: from the natural language of patron terms to the controlled vocabulary of mapped listsLora V Gault
The Library, Purdue University Calumet, Hammond, Indiana 46323 2590, USA
J Med Libr Assoc 90:173-80. 2002..This study compared the mapping of natural language patron terms to the Medical Subject Headings (MeSH) across six MeSH interfaces for the MEDLINE database...
- Medical subject headings used to search the biomedical literatureM H Coletti
Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
J Am Med Inform Assoc 8:317-23. 2001..MEDLINE is unique in that each reference to the medical literature is indexed under a controlled vocabulary called Medical Subject Headings (MeSH). These headings are the keys that unlock the medical literature...
- Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary testB L Humphreys
National Library of Medicine, Bethesda, MD 20894, USA
J Am Med Inform Assoc 4:484-500. 1997..of existing machine-readable health terminologies cover the concepts and terms needed for a comprehensive controlled vocabulary for health information systems by carrying out a distributed national experiment using the Internet and ..
- An environment for relation mining over richly annotated corpora: the case of GENIAFabio Rinaldi
Institute of Computational Linguistics, IFI, University of Zurich, Switzerland
BMC Bioinformatics 7:S3. 2006..There is a real need for support tools that 'digest' the published results and extract the most important information...
- Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoidG D Zhou
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
Int J Med Inform 75:456-67. 2006..1 and V3.0, respectively. In particular, our system achieves an F-measure of 77.8 on the "protein" class of GENIA V3.0. It also shows that our system outperforms the best-reported system on GENIA V1.1 and V3.0...
- A literature based method for identifying gene-disease connectionsLada A Adamic
HP Laboratories, HP, Palo Alto, CA, 94304, USA
Proc IEEE Comput Soc Bioinform Conf 1:109-17. 2002..The method is illustrated by finding genes related to breast cancer...
- Suregene, a scalable system for automated term disambiguation of gene and protein namesRaf M Podowski
Karolinska Institutet, SE 171 77 Stockholm, Sweden
J Bioinform Comput Biol 3:743-70. 2005..It is concluded that it is possible to achieve high quality gene disambiguation using scaleable automated techniques...
- Inferring pathways from gene lists using a literature-derived network of biological relationshipsDilip Rajagopalan
Bioinformatics Sciences, GlaxoSmithKline Pharmaceuticals R and D, 709 Swedeland Road, UW2230, King of Prussia, Pa 19406 0939, USA
Bioinformatics 21:788-93. 2005..Finding such subnetworks that maximally include all proteins from the query set but few others is the focus for this paper...
- Information extraction from full text scientific articles: where are the keywords?Parantu K Shah
Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
BMC Bioinformatics 4:20. 2003..Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant...
- Extracting synonymous gene and protein terms from biological literatureHong Yu
Department of Computer Science, Columbia University, New York, NY, USA
Bioinformatics 19:i340-9. 2003..Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance...
- Integrating high dimensional bi-directional parsing models for gene mention taggingChun Nan Hsu
Institute of Information Science, Academia Sinica, Taipei, Taiwan
Bioinformatics 24:i286-94. 2008..Our tagger is interesting because it accomplished the highest F-scores among CRF-based methods and second over all. Moreover, we obtained our results by mostly applying open source packages, making it easy to duplicate our results...
- An ontology for cell typesJonathan Bard
Department of Biomedical Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
Genome Biol 6:R21. 2005..The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA...
- BioThesaurus: a web-based thesaurus of protein and gene namesHongfang Liu
Department of Information Systems, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
Bioinformatics 22:103-5. 2006..The BioThesaurus web site allows the retrieval of synonymous names of given protein entries and the identification of protein entries sharing the same names...
- Text processing through Web services: calling WhatizitDietrich Rebholz-Schuhmann
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Bioinformatics 24:296-8. 2008..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)...
- Relations in biomedical ontologiesBarry Smith
Institute for Formal Ontology and Medical Information Science, Saarland University, D 66041 Saarbrucken, Germany
Genome Biol 6:R46. 2005..The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena...
- Using ontologies to describe mouse phenotypesGeorgios V Gkoutos
Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire, OX11 0RD, UK
Genome Biol 6:R8. 2005..This produces a framework with greater flexibility, power and economy than previous approaches. We discuss some of the issues this approach raises...
- Ontology-driven indexing of public datasets for translational bioinformaticsNigam H Shah
Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 10:S1. 2009..The key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts...
- KOBAS server: a web-based platform for automated annotation and pathway identificationJianmin Wu
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China
Nucleic Acids Res 34:W720-4. 2006..We have previously demonstrated the KEGG Orthology (KO) as an effective alternative controlled vocabulary and developed a standalone KO-Based Annotation System (KOBAS)...
- Desiderata for controlled medical vocabularies in the twenty-first centuryJ J Cimino
Department of Medical Informatics, Columbia University, New York, USA
Methods Inf Med 37:394-403. 1998..Standards developers are beginning to recognize and address these desiderata and adapt their offerings to meet them...
- Exploring and developing consumer health vocabulariesQing T Zeng
Department of Radiology, Decision Systems Group, Thorn 309, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
J Am Med Inform Assoc 13:24-9. 2006....
- PRIDE: a public repository of protein and peptide identifications for the proteomics communityPhilip Jones
EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Nucleic Acids Res 34:D659-63. 2006..Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML...
- The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotationsShulamit Avraham
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Nucleic Acids Res 36:D449-54. 2008..plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants...
- A critical review of PASBio's argument structures for biomedical verbsK Bretonnel Cohen
Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
BMC Bioinformatics 7:S5. 2006..Here, we quantitatively evaluate several dimensions of the initial PASBio propositional structure repository...
- Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomicsDaniel H Haft
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Bioinformatics 21:293-306. 2005..Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics...
- Annotation and query of tissue microarray data using the NCI ThesaurusNigam H Shah
Stanford Medical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 8:296. 2007..These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult...
- CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysisJohannes Rainer
Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
Nucleic Acids Res 34:W498-503. 2006..The web application is implemented in Java based on the latest J2EE (Java 2 Enterprise Edition) software technology. CARMAweb is freely available at https://carmaweb.genome.tugraz.at...
- Comparative analysis of five protein-protein interaction corporaSampo Pyysalo
Turku Centre for Computer Science TUCS, Department of IT, University of Turku, Joukahaisenkatu 3 5, 20520 Turku, Finland
BMC Bioinformatics 9:S6. 2008..However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate...
- Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approachesSampo Pyysalo
Turku Centre for Computer Science TUCS and University of Turku, Lemminkäisenkatu 14 A, 20520 Turku, Finland
BMC Bioinformatics 7:S2. 2006..We evaluate each approach separately for its effect on parsing performance and consider combinations of these approaches...
- The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopesVeronika Vincze
University of Szeged, Department of Informatics, Human Language Technology Group, Arpád tér 2, Szeged, Hungary
BMC Bioinformatics 9:S9. 2008..This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus)...
- Evaluation of controlled vocabulary resources for development of a consumer entry vocabulary for diabetesT B Patrick
Department of Health Management and Informatics and Center for Family Medicine Science, University of Missouri Columbia, USA
J Med Internet Res 3:E24. 2001..One way to address this problem is to develop a consumer entry vocabulary for health care communications...
- A multi-aspect comparison study of supervised word sense disambiguationHongfang Liu
Department of Information Systems, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
J Am Med Inform Assoc 11:320-31. 2004....
- Of truth and pathways: chasing bits of information through myriads of articlesMichael Krauthammer
Department of Medical Informatics, Columbia University, New York, NY 10032, USA
Bioinformatics 18:S249-57. 2002..We hope that in the future such a model can be useful for automatically producing consensus views of molecular interaction data...
- Derivation and evaluation of a document-naming nomenclatureS H Brown
Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA
J Am Med Inform Assoc 8:379-90. 2001..The authors' objective was to develop a document-naming nomenclature (DNN) that creates informative, structured note titles that improve information access...
- Identifying gene and protein mentions in text using conditional random fieldsRyan McDonald
Department of Computer and Information Science, University of Pennsylvania, Levine Hall, 3330 Walnut Street, Philadelphia, Pennsylvania 19104, USA
BMC Bioinformatics 6:S6. 2005..The mechanics of CRFs and their relationship to maximum entropy are discussed in detail...
- Automated recognition of malignancy mentions in biomedical literatureYang Jin
Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
BMC Bioinformatics 7:492. 2006....
- The Ontology Lookup Service: more data and better tools for controlled vocabulary queriesRichard G Côté
EMBL Outstation, European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Nucleic Acids Res 36:W372-6. 2008..Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries...
- Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse usersHagit Shatkay
The Computational Biology and Machine Learning Lab, School of Computing, Queen s University, Kingston, Ontario, Canada
Bioinformatics 24:2086-93. 2008....
- MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction dataAndrew Chatr-Aryamontri
Department of Biology, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
Genome Biol 9:S5. 2008..The 2006 BioCreative competition was aimed at evaluating text-mining procedures in comparison with manual annotation of protein-protein interactions...
- A relation based measure of semantic similarity for Gene Ontology annotationsBrendan Sheehan
Systems Research Group, School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland
BMC Bioinformatics 9:468. 2008..These approaches introduce assumptions about how semantic similarity of terms relates to the semantic similarity of annotations that do not necessarily reflect how terms relate to each other...
- Conceptual biology: a semantic issue and moreJulie C Barnes
Nature 417:587-8. 2002
- SEMEDA: ontology based semantic integration of biological databasesJacob Köhler
AG Bioinformatics, Technical Faculty, Bielefeld University, Germany
Bioinformatics 19:2420-7. 2003..g. the use of different terms for the same things, different names for equivalent database attributes and missing links between relevant entries in different databases...
- Survey-based naming conventions for use in OBO Foundry ontology developmentDaniel Schober
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
BMC Bioinformatics 10:125. 2009....
- Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologiesRobert Hoehndorf
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
BMC Bioinformatics 8:377. 2007..Currently, there is no support for a correct and consistent integration of such ontologies...
- Modeling a description logic vocabulary for cancer researchFrank W Hartel
National Cancer Institute Center for Bioinformatics, 6116 Executive Blvd, Suite 403, Bethesda, MD 20892 8335, USA
J Biomed Inform 38:114-29. 2005..The artifacts and processes developed by NCI for collaboration may be useful in other biomedical terminology development efforts...
- CoPub Mapper: mining MEDLINE based on search term co-publicationBlaise T F Alako
Department of Molecular Design and Informatics, Organon NV, P O Box 20, 5340 BH Oss, The Netherlands
BMC Bioinformatics 6:51. 2005..In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned...
- Representation of change in controlled medical terminologiesD E Oliver
Stanford Medical Informatics MSOB, Stanford University School of Medicine, CA 94305 5479, USA
Artif Intell Med 15:53-76. 1999..We are currently implementing our modeling approach within a computational architecture...
- POSBIOTM-NER: a trainable biomedical named-entity recognition systemYu Song
Department of CSE, POSTECH Pohang, 790 784, Korea
Bioinformatics 21:2794-6. 2005..GENIA-NER was trained based on GENIA Corpus, GENE-NER based on BioCreative data and GPCR-NER based on our own POSBIOTM/NE corpus, respectively, which would be used in GPCR-related pathway extraction...
- Representing the UMLS as an object-oriented database: modeling issues and advantagesH Gu
Department of Health Informatics, University of Medicine and Dentistry of New Jersey, School of Health Related Professions, Newark 07107 3001, USA
J Am Med Inform Assoc 7:66-80. 2000..However, the UMLS is very large and complex and poses serious comprehension problems for users and maintenance personnel. The authors present a representation to support the user's comprehension and navigation of the UMLS...
- Literature-based concept profiles for gene annotation: the issue of weightingRob Jelier
Erasmus University Medical Centre, Department of Medical Informatics, P O Box 2040, 3000 CA Rotterdam, The Netherlands
Int J Med Inform 77:354-62. 2008..Various schemes have been proposed to determine these weights, but no comparative studies of the different approaches are available. Here we compare several weighting approaches in a large scale classification experiment...
- Clinical classification and terminology: some history and current observationsC G Chute
Mayo Foundation, Rochester, Minnesota 55905, USA
J Am Med Inform Assoc 7:298-303. 2000..The inescapable conclusion is that we are amidst a major revolution in the role and capabilities of health terminologies, entering an age of large-scale systems for health concept representation with international implications...
- Identifying biological concepts from a protein-related corpus with a probabilistic topic modelBin Zheng
Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29405, USA
BMC Bioinformatics 7:58. 2006..The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE titles and abstracts by applying a probabilistic topic model...
- Gramene: a bird's eye view of cereal genomesPankaj Jaiswal
Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA
Nucleic Acids Res 34:D717-23. 2006..Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication...
- Zone analysis in biology articles as a basis for information extractionYoko Mizuta
National Institute of Informatics, 2 1 2 Hitotsubashi, 101 8430 Tokyo, Japan
Int J Med Inform 75:468-87. 2006..We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework...
- FlyBase: anatomical data, images and queriesGary Grumbling
Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405 7005, USA
Nucleic Acids Res 34:D484-8. 2006....
- From concepts to clinical reality: an essay on the benchmarking of biomedical terminologiesBarry Smith
Department of Philosophy and National Center for Biomedical Ontology, University at Buffalo, Buffalo, NY 14260, USA
J Biomed Inform 39:288-98. 2006..We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support...
- Normalizing biomedical terms by minimizing ambiguity and variabilityYoshimasa Tsuruoka
School of Computer Science, The University of Manchester, MIB, 131 Princess Street, Manchester, M1 7DN, UK
BMC Bioinformatics 9:S2. 2008..The development of good heuristic rules, however, requires extensive knowledge of the terminology in question and thus is the bottleneck of the normalization approach...
- Thesaurus-based disambiguation of gene symbolsBob J A Schijvenaars
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P O Box 1738, 3000 DR Rotterdam, The Netherlands
BMC Bioinformatics 6:149. 2005..Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck...
- Biomedical ontologies: a functional perspectiveDaniel L Rubin
Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
Brief Bioinform 9:75-90. 2008....
- MILANO--custom annotation of microarray results using automatic literature searchesRan Rubinstein
Department of Molecular Biology, Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
BMC Bioinformatics 6:12. 2005..Literature mining--the process of representing literature data in a fashion that is easy to relate to genomic data--is one solution to this problem...
- VIRGO: computational prediction of gene functionsNaveed Massjouni
660 McBryde Hall, Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Nucleic Acids Res 34:W340-4. 2006..For each prediction, VIRGO also provides an informative 'propagation diagram' that traces the flow of information in the FLN that led to the prediction. VIRGO is available at http://whipple.cs.vt.edu:8080/virgo...
- JAFA: a protein function annotation meta-serverIddo Friedberg
Burnham Institute for Medical Research, Program in Bioinformatics and Systems Biology, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
Nucleic Acids Res 34:W379-81. 2006..JAFA also offers its own output, and the individual programs' predictions for further processing. JAFA is available for use from http://jafa.burnham.org...
- Controlled vocabularies for consumer healthRita D Zielstorff
HEALTHvision, Inc, Waltham, MA, USA
J Biomed Inform 36:326-33. 2003..In addition, the presence of terms for which no representation currently exists in nursing terminologies could serve as a stimulus for developing new knowledge about patient phenomena not previously recognized...
- An entity tagger for recognizing acquired genomic variations in cancer literatureRyan T McDonald
Department of Computer and Information Science, University of Pennsylvania, 3330 Walnut Street, Philadelphia, PA 19104, USA
Bioinformatics 20:3249-51. 2004..VTag was tested with 345 training and 200 evaluation documents pertaining to cancer genetics. Our experiments resulted in 0.8541 precision, 0.7870 recall and 0.8192 F-measure on the evaluation set...
- caCORE: a common infrastructure for cancer informaticsPeter A Covitz
National Cancer Institute Center for Bioinformatics, National Institutes of Health, U S Department of Health and Human Services, 6116 Executive Boulevard, Suite 403, Rockville MD 20852, USA
Bioinformatics 19:2404-12. 2003..Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications...
- NCI Thesaurus: using science-based terminology to integrate cancer research resultsSherri de Coronado
Center for Bioinformatics, National Cancer Institute, 6116 Executive Boulevard 403, Rockville, MD 20892, USA
Stud Health Technol Inform 107:33-7. 2004..As a scalable, formal terminology, the deployed Thesaurus, and associated applications and interfaces, are a model for some of the standards required for the NHII (National Health Information Infrastructure) and the Semantic Web...
- Bio-ontologies: current trends and future directionsOlivier Bodenreider
National Library of Medicine, Bethesda, MD 20894, USA
Brief Bioinform 7:256-74. 2006..With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine...
- Patterned Gene Expression in Drosophila DevelopmentSusan E Celniker; Fiscal Year: 2013..spatial and temporal embryonic expression patterns, annotations of the patterns using a standardized, controlled vocabulary, based on an anatomical ontology and a standardized virtual representation of the patterns...
- Incorporating microRNA data and analyses into the leading cancer genomics portalDaniel R Rhodes; Fiscal Year: 2012..metadata curation strategy for 3 micro-RNA profiling datasets to demonstrate feasibility of applying a controlled vocabulary and ontology to miRNA sample metadata;2) Establish and implement platform mapping strategy for 3 micro-RNA ..
- Vector Surveillance Ontology and Vector Management OntologySaul Lozano Fuentes; Fiscal Year: 2010..Vocabularies (sets of standardized and defined terms) and Ontologies (sets of standardized and defined controlled vocabulary terms and their inter-relationships)...
- Enhancing the Biomedical Computing Platform for Pancreatic Cancer ResearchSimon Sherman; Fiscal Year: 2013..To achieve this objective, the following aims will be accomplished. Aim 1: Development of a controlled vocabulary and ontology for the PCCR System...
- Computational Methods for Expression Image AnalysisJieping Ye; Fiscal Year: 2013..b) Develop machine learning methods to describe expression patterns in words by using the existing controlled vocabulary. These descriptions will enable the use of efficient text-mining tools to identify genes expressed in ..
- Ontology-Driven Methods for Knowledge Acquisition and Knowledge DiscoveryXinghua Lu; Fiscal Year: 2013..likely provide evidence regarding the function of genes/proteins and map the extracted information to a controlled vocabulary. Specific Aim 3...
- Automatic Literature-based Protein AnnotationXinghua Lu; Fiscal Year: 2009..articles about the protein, extracting biological concepts from the articles and mapping the concept to a controlled vocabulary. We envision that achieving these goals will result in advances with broader impact which not only ..
- Bioassay Ontology and Software Tools to Integrate and Analyze Diverse Data SetsSTEPHAN C SCHURER; Fiscal Year: 2012..An ontology is a controlled vocabulary representation of the objects and concepts and their properties and relationships...
- ICTVdB: The Universal Virus Information SystemLois Blaine; Fiscal Year: 2004..A comprehensive controlled vocabulary is used for the virus descriptions, allowing for vocabulary switching or mapping to similar descriptors in ..
- Tissue Microarray Informatics Standards WorkshopMary Edgerton; Fiscal Year: 2001..We anticipate that standards for imaging, fabrication, controlled vocabulary and ontologies, data analysis, and XML for tissue microarray data will be issues for this group to address ..
- GKB: An Integrative Resource for Genome BiologyLincoln Stein; Fiscal Year: 2006..summation will be associated with a set of assertions that present the core facts of the field using a controlled vocabulary and grammar, as well as diagrams, animations and other graphics...
- THESAURUS FOR AIDS BEHAVIORAL INTERVENTION INFORMATIONKAREN LEVITAN; Fiscal Year: 1990..local levels; 2) developing a preliminary thesaurus including conceptual and classification structures, controlled vocabulary and lead-in vocabulary reflecting AIDS behavioral Interventions; ) planning future development, Including ..
- INDEXING AND RETRIEVING INFORMATIONJOHN VRIES; Fiscal Year: 1990..The expert system will then be integrated into a comprehensive medical information system under development at the University of Pittsburgh...
- ANALYZING TOBACCO DOCUMENTS ON CIGARETTE DESIGNLynn Kozlowski; Fiscal Year: 2004..Collections (with standardized abstracts controlled vocabulary terms) will be made available on the Internet. Reports will be submitted to peer-reviewed journals...
- 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. ..
- A Framework Based Clinical Documentation Evaluation MethodSAMUEL T ROSENBLOOM; Fiscal Year: 2010..The proposed project will transition the PI from his current National Library of Medicine supported period of career development to an independent informatics investigator. ..
- 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. ..
- Mediated Integration of Neuroscience ResourcesLuis Marenco; Fiscal Year: 2008..abstract_text> ..
- LATENT SEMANTIC INDEXING IN SUPPORT OF DATA RETRIEVALCHRISTOPHER CHUTE; Fiscal Year: 2001..We commit these activities to remain compliant with emerging standards for medical concept representation arising from the Canon efforts and the standardization processes at ANSI-HISPP, CEN TC251 and the CPRI initiatives. ..
- Intelligent Data Storage ResourceCHRISTOPHER CHUTE; Fiscal Year: 2005..Centralizing such access to a secure data warehouse ensures our continued commitment to patient confidentiality and compliance with federal and state regulations. ..
- Development and Evaluation of Terminology ServicesCHRISTOPHER CHUTE; Fiscal Year: 2004....
- Biomedical Computing Tools for Pancreatic Cancer Res.Simon Sherman; Fiscal Year: 2007..The IBCT to be developed in this project can also be used as an infrastructural foundation for research of other types of cancer and chronic diseases. [unreadable] [unreadable]..
- IMMUNOGENIC TUMOR ASSOCIATED MUCIN PEPTIDESSimon Sherman; Fiscal Year: 2004....
- EMILIE--INTEGRATED INFORMATION FOR COLLABORATIVE CAREJudy Ozbolt; Fiscal Year: 2003....
- 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. ..
- Telemedical Diagnosis of Retinopathy of PrematurityMichael Chiang; Fiscal Year: 2007..Columbia University has a strong existing framework in medical information systems, telemedicine, and public health, which will be leveraged to complete this training and research program successfully. ..
- Terminological Systems for Representing Patient StatusMarcelline Harris; Fiscal Year: 2004..At the end of this study, we intend to make available a scalable resource for this field. This work does not duplicate any existing work in terminology and information modeling work, rather extensively builds on existing work. ..
- WOMEN'S ALTERNATIVE MEDICINE USE--MULTIETHNIC SURVEYFredi Kronenberg; Fiscal Year: 2001..Such factors ma include age, health status, educational attainment, level of acculturation, and attitudes. ..
- After-hours communication support for hospice family caregivers and patientsKaren Courtney; Fiscal Year: 2009..We will explore if using a videophone for after-hours phone calls between hospice nurses and family caregivers leads to better caregiver and patient management of pain and higher levels of quality of life for both. ..
- MOMENT (Monitoring for Outpatient Medication Effects and New Toxicities) in TIMERANDOLPH MILLER; Fiscal Year: 2009..The project will develop tools and algorithms to detect the patient symptoms, physical exam signs, test results, and medical diagnoses that may indicate drug-induced injury. ..
- Environmental Impact on Perinatal Lung MetabolismOliver Fiehn; Fiscal Year: 2009..abstract_text> ..
- IMPROVING THE MATCH OF PERSON AND MOBILITY TECHNOLOGYMarcia Scherer; Fiscal Year: 2003..Upon validation, these products can be distributed privately through existing publishers of interactive instruction and assessments and promoted by relevant professional organizations. ..
- Data Structuring and Visualization System for Neuro-oncologyRicky K Taira; Fiscal Year: 2010..The structuring tools should lead to improvements in the quality of clinical research databases. ..
- Enhancing Clinical Effectiveness Research with Natural Language Processing of EMRBRIAN L HAZLEHURST; Fiscal Year: 2010..We will demonstrate the utility of this infrastructure by conducting CER studies investigating the effectiveness of interventions in asthma and smoking, across the 6 participating health systems. ..
- Taxonomies Supporting Orientation, Navigation and Auditing of TerminologiesYehoshua Perl; Fiscal Year: 2010..We will demonstrate the utility of our taxonomy-based methodologies by defining various complexity measures with respect to the underlying terminology networks and by tracking terminology evolution. ..
- A Toxicological Knowledge Base PrototypeNikolai Daraselia; Fiscal Year: 2007..We believe that such a knowledge base can facilitate research in the pharmaceutical and drug discovery fields and will be highly useful to many researchers in these areas. [unreadable] [unreadable] [unreadable]..
- Automated Literature Mining for Validation of High-Throughput Function PredictionKARIN MARIA VERSPOOR; Fiscal Year: 2010..It is time to truly integrate the biological literature into the protein function prediction problem. By doing so, we will enable a critical advance in high-throughput protein function prediction ..
- VOCABULARY MANAGEMENT FOR CLINICAL RESEARCH DATABASESCynthia Brandt; Fiscal Year: 2005....
- EVALUATION OF NURSING SENSITIVE PATIENT OUTCOME MEASURESMarion Johnson; Fiscal Year: 2001..Fehring (1987) content validity scores will be used to evaluate the content validity of new outcomes. ..
- A Multifaceted Adaptive Testing Approach to Health Literacy in Older AdultsDavid Kaufman; Fiscal Year: 2009..The tool has the potential to be used to support research on health literacy, develop screening tools for clinicians and tailor health education materials for older adult patients and consumers at varying levels of literacy. ..
- Automating Assessment of Asthma Care QualityBrian Hazlehurst; Fiscal Year: 2008..Finally, we will evaluate the association between ACQ measures of recommended asthma care and actual clinical outcomes using extensive longitudinal patient data available at the KPNW study site. [unreadable] [unreadable] [unreadable]..
- PubAssist - an NLP-based document search systemNikolai Daraselia; Fiscal Year: 2005..Customers who install the server-based semantic indexing engine in addition to the PubAssist client will be able to process their proprietary documents and customize the NLP algorithm. ..
- CENTER FOR CAM RESEARCH IN AGINGFredi Kronenberg; Fiscal Year: 2005..abstract_text> ..
- Improving Match of Person/Assistive Cognitive TechnologyMarcia Scherer; Fiscal Year: 2006..unreadable] [unreadable]..
- Integrative Pain MedicineFredi Kronenberg; Fiscal Year: 2006..abstract_text> ..
- HIT Support for Safe Nursing CareGail Keenan; Fiscal Year: 2006..h.r.). ..
- Minorities and CAM Use: A Health Services PerspectiveFredi Kronenberg; Fiscal Year: 2006..abstract_text> ..
- Flexible NLP system for MEDLINE information extractionNikolai Daraselia; Fiscal Year: 2003..We will also extend our approach to other areas including pharmacogenomics and extraction of clinically relevant information. ..
- Mobile Decision Support for Advanced Practice NursingSuzanne Bakken; Fiscal Year: 2007..Such tools have the potential to increase CPG adherence, enhance evidence-based practice, promote patient safety, and in the long term improve patient outcomes. ..
- Communicating probabilities through interactive computer graphicsRita Kukafka; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- MGED 9&10 Student Travel AwardsCatherine Ball; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Outcomes of ICU Working ConditionsPatricia Stone; Fiscal Year: 2003..In addition, obtaining NNIS and Medicare data creates an opportunity to explore the sensitivity and specificity of identifying NI through claims data. ..
- Analyzing Nurses' Impact on Outcomes Using Detailed DataMarcelline Harris; Fiscal Year: 2008..Subsequently, this study can provide heretofore missing evidence needed to define nurse staffing levels associated with patient safety in U.S. hospitals. [unreadable] [unreadable] [unreadable]..
- Computer Adaptive Testing for OA Clinical TrialsAlan Jette; Fiscal Year: 2006..We expect the gains in precision and efficiency of score estimation to be superior over traditional fixed forms of assessments and transform outcomes monitoring in OA clinical trials research. ..
- Protein Self-Assembly in Model MicroorganismsJames Hu; Fiscal Year: 2004..cerevisiae and E. coli) and important human pathogens (M. tuberculosis and A. fumigatus), and new drug targets based on protein-protein interactions. ..
- 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. ..
- 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. ..
- Innovative Methods for Function and Disability AssessmentAlan Jette; Fiscal Year: 2007..The public health research and clinical communities would be the likely markets [unreadable] interested in the CAT technology that would be developed and evaluated in this STTR. [unreadable] [unreadable] [unreadable] [unreadable]..
- 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. ..