controlled vocabulary

Summary

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)

Top Publications

  1. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth I Boyle
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3710-5. 2004
  2. ncbi Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
    Xizeng 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
  3. ncbi A new method to measure the semantic similarity of GO terms
    James Z Wang
    School of Computing, Clemson University, Clemson, SC 29634, USA
    Bioinformatics 23:1274-81. 2007
  4. pmc The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Barry 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
  5. pmc The GOA database in 2009--an integrated Gene Ontology Annotation resource
    Daniel Barrell
    Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D396-403. 2009
  6. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
  7. pmc BioPortal: ontologies and integrated data resources at the click of a mouse
    Natalya F Noy
    Stanford Center for Biomedical Informatics Research, Stanford University
    Nucleic Acids Res 37:W170-3. 2009
  8. ncbi A reference ontology for biomedical informatics: the Foundational Model of Anatomy
    Cornelius 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
  9. ncbi 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
  10. ncbi Recognizing names in biomedical texts: a machine learning approach
    Guodong Zhou
    Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
    Bioinformatics 20:1178-90. 2004

Detail Information

Publications283 found, 100 shown here

  1. pmc GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    Elizabeth 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...
  2. ncbi Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
    Xizeng 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...
  3. ncbi A new method to measure the semantic similarity of GO terms
    James Z Wang
    School of Computing, Clemson University, Clemson, SC 29634, USA
    Bioinformatics 23:1274-81. 2007
    ....
  4. pmc The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    Barry 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...
  5. pmc The GOA database in 2009--an integrated Gene Ontology Annotation resource
    Daniel 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...
  6. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
    The 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...
  7. pmc BioPortal: ontologies and integrated data resources at the click of a mouse
    Natalya 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...
  8. ncbi A reference ontology for biomedical informatics: the Foundational Model of Anatomy
    Cornelius 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
    ....
  9. ncbi 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...
  10. ncbi Recognizing names in biomedical texts: a machine learning approach
    Guodong 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...
  11. pmc The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    David 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...
  12. pmc Metrics for GO based protein semantic similarity: a systematic evaluation
    Catia 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...
  13. ncbi ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text
    Burr 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...
  14. pmc Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species
    Marin 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...
  15. ncbi Correlation between gene expression and GO semantic similarity
    José 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...
  16. pmc Functional annotation of the Arabidopsis genome using controlled vocabularies
    Tanya 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-..
  17. pmc The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
    Cynthia 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...
  18. pmc Natural language processing in aid of FlyBase curators
    Nikiforos 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...
  19. pmc ChEBI: a database and ontology for chemical entities of biological interest
    Kirill 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/..
  20. ncbi MedScan, a natural language processing engine for MEDLINE abstracts
    Svetlana 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...
  21. pmc Automated annotation of Drosophila gene expression patterns using a controlled vocabulary
    Shuiwang 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...
  22. pmc A new measure for functional similarity of gene products based on Gene Ontology
    Andreas 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...
  23. ncbi Additional gene ontology structure for improved biological reasoning
    Simen 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...
  24. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  25. pmc Gene Ontology term overlap as a measure of gene functional similarity
    Meeta 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)...
  26. pmc VectorBase: a data resource for invertebrate vector genomics
    Daniel 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...
  27. pmc Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations
    Xiaomei 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...
  28. ncbi GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data
    Andrey 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...
  29. pmc Corpus annotation for mining biomedical events from literature
    Jin 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...
  30. ncbi Rutabaga by any other name: extracting biological names
    Lynette 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...
  31. pmc A probabilistic generative model for GO enrichment analysis
    Yong 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...
  32. ncbi Bio2RDF: towards a mashup to build bioinformatics knowledge systems
    François 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...
  33. pmc The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data
    Terry F Hayamizu
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
    Genome Biol 6:R29. 2005
    ....
  34. pmc Frontiers of biomedical text mining: current progress
    Pierre 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...
  35. pmc GO PaD: the Gene Ontology Partition Database
    Gil 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...
  36. pmc Variations in Medical Subject Headings (MeSH) mapping: from the natural language of patron terms to the controlled vocabulary of mapped lists
    Lora 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...
  37. pmc Medical subject headings used to search the biomedical literature
    M 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...
  38. pmc Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary test
    B 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 ..
  39. pmc An environment for relation mining over richly annotated corpora: the case of GENIA
    Fabio 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...
  40. ncbi Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid
    G 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...
  41. ncbi A literature based method for identifying gene-disease connections
    Lada 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...
  42. ncbi Suregene, a scalable system for automated term disambiguation of gene and protein names
    Raf 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...
  43. ncbi Inferring pathways from gene lists using a literature-derived network of biological relationships
    Dilip 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...
  44. pmc 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...
  45. ncbi Extracting synonymous gene and protein terms from biological literature
    Hong 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...
  46. pmc Integrating high dimensional bi-directional parsing models for gene mention tagging
    Chun 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...
  47. pmc An ontology for cell types
    Jonathan 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...
  48. ncbi BioThesaurus: a web-based thesaurus of protein and gene names
    Hongfang 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...
  49. ncbi Text processing through Web services: calling Whatizit
    Dietrich 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)...
  50. pmc Relations in biomedical ontologies
    Barry 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...
  51. pmc Using ontologies to describe mouse phenotypes
    Georgios 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...
  52. pmc Ontology-driven indexing of public datasets for translational bioinformatics
    Nigam 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...
  53. pmc KOBAS server: a web-based platform for automated annotation and pathway identification
    Jianmin 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)...
  54. pmc Desiderata for controlled medical vocabularies in the twenty-first century
    J 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...
  55. pmc Exploring and developing consumer health vocabularies
    Qing 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
    ....
  56. pmc PRIDE: a public repository of protein and peptide identifications for the proteomics community
    Philip 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...
  57. pmc The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
    Shulamit 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...
  58. pmc A critical review of PASBio's argument structures for biomedical verbs
    K 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...
  59. ncbi Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
    Daniel 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...
  60. pmc Annotation and query of tissue microarray data using the NCI Thesaurus
    Nigam 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...
  61. pmc CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis
    Johannes 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...
  62. pmc Comparative analysis of five protein-protein interaction corpora
    Sampo 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...
  63. pmc Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches
    Sampo 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...
  64. pmc The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes
    Veronika 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)...
  65. pmc Evaluation of controlled vocabulary resources for development of a consumer entry vocabulary for diabetes
    T 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...
  66. pmc A multi-aspect comparison study of supervised word sense disambiguation
    Hongfang 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
    ....
  67. ncbi Of truth and pathways: chasing bits of information through myriads of articles
    Michael 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...
  68. pmc Derivation and evaluation of a document-naming nomenclature
    S 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...
  69. pmc Identifying gene and protein mentions in text using conditional random fields
    Ryan 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...
  70. pmc Automated recognition of malignancy mentions in biomedical literature
    Yang Jin
    Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Bioinformatics 7:492. 2006
    ....
  71. pmc The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
    Richard 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...
  72. pmc Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users
    Hagit Shatkay
    The Computational Biology and Machine Learning Lab, School of Computing, Queen s University, Kingston, Ontario, Canada
    Bioinformatics 24:2086-93. 2008
    ....
  73. pmc MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
    Andrew 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...
  74. pmc A relation based measure of semantic similarity for Gene Ontology annotations
    Brendan 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...
  75. ncbi Conceptual biology: a semantic issue and more
    Julie C Barnes
    Nature 417:587-8. 2002
  76. ncbi SEMEDA: ontology based semantic integration of biological databases
    Jacob 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...
  77. pmc Survey-based naming conventions for use in OBO Foundry ontology development
    Daniel Schober
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:125. 2009
    ....
  78. pmc Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies
    Robert 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...
  79. ncbi Modeling a description logic vocabulary for cancer research
    Frank 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...
  80. pmc CoPub Mapper: mining MEDLINE based on search term co-publication
    Blaise 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...
  81. ncbi Representation of change in controlled medical terminologies
    D 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...
  82. ncbi POSBIOTM-NER: a trainable biomedical named-entity recognition system
    Yu 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...
  83. pmc Representing the UMLS as an object-oriented database: modeling issues and advantages
    H 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...
  84. ncbi Literature-based concept profiles for gene annotation: the issue of weighting
    Rob 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...
  85. pmc Clinical classification and terminology: some history and current observations
    C 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...
  86. pmc Identifying biological concepts from a protein-related corpus with a probabilistic topic model
    Bin 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...
  87. pmc Gramene: a bird's eye view of cereal genomes
    Pankaj 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...
  88. ncbi Zone analysis in biology articles as a basis for information extraction
    Yoko 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...
  89. pmc FlyBase: anatomical data, images and queries
    Gary Grumbling
    Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405 7005, USA
    Nucleic Acids Res 34:D484-8. 2006
    ....
  90. ncbi From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies
    Barry 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...
  91. pmc Normalizing biomedical terms by minimizing ambiguity and variability
    Yoshimasa 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...
  92. pmc Thesaurus-based disambiguation of gene symbols
    Bob 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...
  93. ncbi Biomedical ontologies: a functional perspective
    Daniel L Rubin
    Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
    Brief Bioinform 9:75-90. 2008
    ....
  94. pmc MILANO--custom annotation of microarray results using automatic literature searches
    Ran 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...
  95. pmc VIRGO: computational prediction of gene functions
    Naveed 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...
  96. pmc JAFA: a protein function annotation meta-server
    Iddo 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...
  97. ncbi Controlled vocabularies for consumer health
    Rita 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...
  98. ncbi An entity tagger for recognizing acquired genomic variations in cancer literature
    Ryan 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...
  99. ncbi caCORE: a common infrastructure for cancer informatics
    Peter 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...
  100. ncbi NCI Thesaurus: using science-based terminology to integrate cancer research results
    Sherri 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...
  101. pmc Bio-ontologies: current trends and future directions
    Olivier 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...

Research Grants62

  1. Patterned Gene Expression in Drosophila Development
    Susan 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...
  2. Incorporating microRNA data and analyses into the leading cancer genomics portal
    Daniel 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 ..
  3. Vector Surveillance Ontology and Vector Management Ontology
    Saul 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)...
  4. Enhancing the Biomedical Computing Platform for Pancreatic Cancer Research
    Simon 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...
  5. Computational Methods for Expression Image Analysis
    Jieping 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 ..
  6. Ontology-Driven Methods for Knowledge Acquisition and Knowledge Discovery
    Xinghua 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...
  7. Automatic Literature-based Protein Annotation
    Xinghua 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 ..
  8. Bioassay Ontology and Software Tools to Integrate and Analyze Diverse Data Sets
    STEPHAN C SCHURER; Fiscal Year: 2012
    ..An ontology is a controlled vocabulary representation of the objects and concepts and their properties and relationships...
  9. ICTVdB: The Universal Virus Information System
    Lois Blaine; Fiscal Year: 2004
    ..A comprehensive controlled vocabulary is used for the virus descriptions, allowing for vocabulary switching or mapping to similar descriptors in ..
  10. Tissue Microarray Informatics Standards Workshop
    Mary 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 ..
  11. GKB: An Integrative Resource for Genome Biology
    Lincoln 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...
  12. THESAURUS FOR AIDS BEHAVIORAL INTERVENTION INFORMATION
    KAREN 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 ..
  13. INDEXING AND RETRIEVING INFORMATION
    JOHN VRIES; Fiscal Year: 1990
    ..The expert system will then be integrated into a comprehensive medical information system under development at the University of Pittsburgh...
  14. ANALYZING TOBACCO DOCUMENTS ON CIGARETTE DESIGN
    Lynn 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...
  15. ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASES
    Prakash 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. ..
  16. DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASE
    Prakash 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. ..
  17. A Framework Based Clinical Documentation Evaluation Method
    SAMUEL 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. ..
  18. DELIVERY OF THE CGN INFORMATION RESOURCE DATABASE
    Prakash 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. ..
  19. Mediated Integration of Neuroscience Resources
    Luis Marenco; Fiscal Year: 2008
    ..abstract_text> ..
  20. LATENT SEMANTIC INDEXING IN SUPPORT OF DATA RETRIEVAL
    CHRISTOPHER 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. ..
  21. Intelligent Data Storage Resource
    CHRISTOPHER 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. ..
  22. Development and Evaluation of Terminology Services
    CHRISTOPHER CHUTE; Fiscal Year: 2004
    ....
  23. 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]..
  24. IMMUNOGENIC TUMOR ASSOCIATED MUCIN PEPTIDES
    Simon Sherman; Fiscal Year: 2004
    ....
  25. EMILIE--INTEGRATED INFORMATION FOR COLLABORATIVE CARE
    Judy Ozbolt; Fiscal Year: 2003
    ....
  26. Assisting Systematic Review Preparation Using Automated Document Classification
    Aaron 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. ..
  27. Telemedical Diagnosis of Retinopathy of Prematurity
    Michael 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. ..
  28. Terminological Systems for Representing Patient Status
    Marcelline 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. ..
  29. WOMEN'S ALTERNATIVE MEDICINE USE--MULTIETHNIC SURVEY
    Fredi Kronenberg; Fiscal Year: 2001
    ..Such factors ma include age, health status, educational attainment, level of acculturation, and attitudes. ..
  30. After-hours communication support for hospice family caregivers and patients
    Karen 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. ..
  31. MOMENT (Monitoring for Outpatient Medication Effects and New Toxicities) in TIME
    RANDOLPH 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. ..
  32. Environmental Impact on Perinatal Lung Metabolism
    Oliver Fiehn; Fiscal Year: 2009
    ..abstract_text> ..
  33. IMPROVING THE MATCH OF PERSON AND MOBILITY TECHNOLOGY
    Marcia 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. ..
  34. Data Structuring and Visualization System for Neuro-oncology
    Ricky K Taira; Fiscal Year: 2010
    ..The structuring tools should lead to improvements in the quality of clinical research databases. ..
  35. Enhancing Clinical Effectiveness Research with Natural Language Processing of EMR
    BRIAN 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. ..
  36. Taxonomies Supporting Orientation, Navigation and Auditing of Terminologies
    Yehoshua 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. ..
  37. A Toxicological Knowledge Base Prototype
    Nikolai 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]..
  38. Automated Literature Mining for Validation of High-Throughput Function Prediction
    KARIN 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 ..
  39. VOCABULARY MANAGEMENT FOR CLINICAL RESEARCH DATABASES
    Cynthia Brandt; Fiscal Year: 2005
    ....
  40. EVALUATION OF NURSING SENSITIVE PATIENT OUTCOME MEASURES
    Marion Johnson; Fiscal Year: 2001
    ..Fehring (1987) content validity scores will be used to evaluate the content validity of new outcomes. ..
  41. A Multifaceted Adaptive Testing Approach to Health Literacy in Older Adults
    David 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. ..
  42. Automating Assessment of Asthma Care Quality
    Brian 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]..
  43. PubAssist - an NLP-based document search system
    Nikolai 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. ..
  44. CENTER FOR CAM RESEARCH IN AGING
    Fredi Kronenberg; Fiscal Year: 2005
    ..abstract_text> ..
  45. Improving Match of Person/Assistive Cognitive Technology
    Marcia Scherer; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  46. Integrative Pain Medicine
    Fredi Kronenberg; Fiscal Year: 2006
    ..abstract_text> ..
  47. HIT Support for Safe Nursing Care
    Gail Keenan; Fiscal Year: 2006
    ..h.r.). ..
  48. Minorities and CAM Use: A Health Services Perspective
    Fredi Kronenberg; Fiscal Year: 2006
    ..abstract_text> ..
  49. Flexible NLP system for MEDLINE information extraction
    Nikolai Daraselia; Fiscal Year: 2003
    ..We will also extend our approach to other areas including pharmacogenomics and extraction of clinically relevant information. ..
  50. Mobile Decision Support for Advanced Practice Nursing
    Suzanne 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. ..
  51. Communicating probabilities through interactive computer graphics
    Rita Kukafka; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  52. MGED 9&10 Student Travel Awards
    Catherine Ball; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  53. Outcomes of ICU Working Conditions
    Patricia 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. ..
  54. Analyzing Nurses' Impact on Outcomes Using Detailed Data
    Marcelline 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]..
  55. Computer Adaptive Testing for OA Clinical Trials
    Alan 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. ..
  56. Protein Self-Assembly in Model Microorganisms
    James 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. ..
  57. Interoperation of Genome Databases and Tools
    Kei 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. ..
  58. Controlled Vocabulary Design for Clinical Applications
    Peter 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. ..
  59. Innovative Methods for Function and Disability Assessment
    Alan 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]..
  60. Biosurveillance Utilizing SNOMED-CT Based Natural Language Processing
    Peter 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. ..