controlled vocabulary

Summary

Alias: controlled vocabulary, controlled thesauri, controlled thesaurus, thesauri
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)

Webpages

  1. the university of adelaide library | environmental health
    www.library.adelaide.edu.au/guide/med/pubhealth/environ.html
  2. mouse tumor biology system (mtb
    tumor.informatics.jax.org/mtbwi/index.do

Research Grants

  1. Patterned Gene Expression in Drosophila Development
    Susan Celniker; Fiscal Year: 2009
  2. Development of a Cognitive Paradigm Ontology: BrainMap and BIRN Intergration
    Angela Laird; Fiscal Year: 2009
  3. ANALYZING TOBACCO DOCUMENTS ON CIGARETTE DESIGN
    Lynn Kozlowski; Fiscal Year: 2004
  4. DATABASES AND DATA MODELS ENABLING NEUROINFORMATICS
    Daniel Gardner; Fiscal Year: 2004
  5. GKB: An Integrative Resource for Genome Biology
    Lincoln Stein; Fiscal Year: 2006
  6. Automatic Literature-based Protein Annotation
    Xinghua Lu; Fiscal Year: 2009
  7. A Framework Based Clinical Documentation Evaluation Method
    SAMUEL ROSENBLOOM; Fiscal Year: 2009
  8. Computer Assisted Autism Care (CAAC)
    Stephen Downs; Fiscal Year: 2009
  9. Biosurveillance Utilizing SNOMED-CT Based Natural Language Processing
    Peter Elkin; Fiscal Year: 2007
  10. Interoperation of Genome Databases and Tools
    Kei Hoi Cheung; Fiscal Year: 2005

Publications

  1. Distributed modules for text annotation and IE applied to the biomedical domain
    Harald Kirsch
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Int J Med Inform 75:496-500
  2. Information extraction for enhanced access to disease outbreak reports
    Ralph Grishman
    Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY 10003 6806, USA
    J Biomed Inform 35:236-46
  3. BioRAT: extracting biological information from full-length papers
    David P A Corney
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    Bioinformatics 20:3206-13
  4. An architecture for biological information extraction and representation
    Aditya Vailaya
    Agilent Laboratories 3500 Deer Creek Road, MS 26U 16, Palo Alto, CA 94304, USA
    Bioinformatics 21:430-8
  5. Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques
    Ana L C Bazzan
    Instituto de Informática, Univ Fed do Rio Grande do Sul, Porto Alegre, Brazil
    Bioinformatics 18:S35-43
  6. 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
  7. OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networks
    Peter Mork
    Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
    J Biomed Inform 36:501-17
  8. Information extraction from biomedical text
    Jerry R Hobbs
    USC Information Sciences Institute, Marina del Rey, CA 90292, USA
    J Biomed Inform 35:260-4
  9. 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
  10. A hybrid method for relation extraction from biomedical literature
    Minlie Huang
    State Key Laboratory of Intelligent Technology and Systems (LITS, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
    Int J Med Inform 75:443-55

Detail Information

Research Grants63

  1. Patterned Gene Expression in Drosophila Development
    Susan Celniker; Fiscal Year: 2009
    ..and temporal embryonic expression patterns as well as annotations of the patterns using a standardized, controlled vocabulary, based on Gene Ontology (GO)...
  2. Development of a Cognitive Paradigm Ontology: BrainMap and BIRN Intergration
    Angela Laird; Fiscal Year: 2009
    ..This structured, well-defined, common and controlled vocabulary will be capable of representing the cognitive paradigms in the FBIRN Data Repository, which stores ..
  3. 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...
  4. DATABASES AND DATA MODELS ENABLING NEUROINFORMATICS
    Daniel Gardner; Fiscal Year: 2004
    ..Rather than maintaining distinct neuroscience and informatics components, the project fuses these so that each Aim represents a unified neuroinformatics entity. ..
  5. 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...
  6. 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 ..
  7. A Framework Based Clinical Documentation Evaluation Method
    SAMUEL ROSENBLOOM; Fiscal Year: 2009
    ..The proposed project will transition the PI from his current National Library of Medicine supported period of career development to an independent informatics investigator. ..
  8. Computer Assisted Autism Care (CAAC)
    Stephen Downs; Fiscal Year: 2009
    ..The primary outcome of interest for aim 3 is the number of guideline recommended activities/involvements that a child diagnosed with ASD receives. ..
  9. 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. ..
  10. 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. ..
  11. Biosurveillance/SNOMED-CT Natural Language Processing
    Peter Elkin; Fiscal Year: 2005
    ..9%. This proposal deals with practical issues that lead the way toward interoperable data. The fruits of this research will assist our national initiatives to pave the way toward a safe and effective BioSecure biosurveillance solution...
  12. 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. ..
  13. Innovative Methods for Function and Disability Assessment
    Alan Jette; Fiscal Year: 2007
    ..The public health research and clinical communities would be the likely markets interested in the CAT technology that would be developed and evaluated in this STTR. ..

Publications124 found, 100 most recent shown here

  1. Distributed modules for text annotation and IE applied to the biomedical domain
    Harald Kirsch
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Int J Med Inform 75:496-500
    ..The server and the underlying software are available to the public...
  2. Information extraction for enhanced access to disease outbreak reports
    Ralph Grishman
    Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY 10003 6806, USA
    J Biomed Inform 35:236-46
    ..A small study comparing the effectiveness of the tabular index with conventional Web search tools demonstrated that users can find substantially more documents in a given time period with Proteus-BIO...
  3. BioRAT: extracting biological information from full-length papers
    David P A Corney
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    Bioinformatics 20:3206-13
    ..Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers...
  4. An architecture for biological information extraction and representation
    Aditya Vailaya
    Agilent Laboratories 3500 Deer Creek Road, MS 26U 16, Palo Alto, CA 94304, USA
    Bioinformatics 21:430-8
    ..We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation. CONTACT: aditya_vailaya@agilent.com...
  5. Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques
    Ana L C Bazzan
    Instituto de Informática, Univ Fed do Rio Grande do Sul, Porto Alegre, Brazil
    Bioinformatics 18:S35-43
    ..Our preliminary results show that with a slightly different method, applied this method to data related to Mycoplasmataceae only, we are able to increase that rate of correct annotation...
  6. 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
    ....
  7. OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networks
    Peter Mork
    Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
    J Biomed Inform 36:501-17
    ....
  8. Information extraction from biomedical text
    Jerry R Hobbs
    USC Information Sciences Institute, Marina del Rey, CA 90292, USA
    J Biomed Inform 35:260-4
    ..In other domains, the technology plateaued at about 60% recall and precision. Even if applications to biomedical text do no better than this, they could still prove to be of immense help to curatorial activities...
  9. 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
    ..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...
  10. A hybrid method for relation extraction from biomedical literature
    Minlie Huang
    State Key Laboratory of Intelligent Technology and Systems (LITS, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
    Int J Med Inform 75:443-55
    ..In contrast to other systems, our approach achieves performance comparable to the best. A demo system has been available at http://spies.cs.tsinghua.edu.cn...
  11. 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
    ..We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework...
  12. 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
    ..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...
  13. Developing a corpus of clinical notes manually annotated for part-of-speech
    Serguei V Pakhomov
    Division of Biomedical Informatics, Mayo College of Medicine, Rochester, MN 55905, USA
    Int J Med Inform 75:418-29
    ..CONCLUSION: Our preliminary experimental results indicate the necessity for adapting state-of-the-art POS taggers to the sublanguage domain of clinical text...
  14. A unified framework for image retrieval using keyword and visual features
    Feng Jing
    Computer Science Department, Tsinghua University, Beijing 100084, China
    IEEE Trans Image Process 14:979-89
    ..It is shown to be more appropriate than two existing relevance feedback algorithms. Experimental results demonstrate the effectiveness of the proposed framework...
  15. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
    Iwei Yeh
    Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
    Bioinformatics 19:241-8
    ..AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu...
  16. Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts
    Hong Woo Chun
    Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
    BMC Bioinformatics 7:S4
    ....
  17. MaSTerClass: a case-based reasoning system for the classification of biomedical terms
    Irena Spasic
    School of Chemistry, The University of Manchester, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    Bioinformatics 21:2748-58
    ..RESULTS: The MaSTerClass system implements the case-based reasoning methodology for the classification of biomedical terms...
  18. Mapping data elements to terminological resources for integrating biomedical data sources
    Fleur Mougin
    EA 3888, IFR 140, Faculté de Médecine, Université de Rennes I, France
    BMC Bioinformatics 7:S6
    ..CONCLUSION: Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources...
  19. 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
    ..Metrics related to theta-criterion violations and to the distribution of arguments are able to detect flaws in semantic representations, given a set of predicate-argument structures and a relatively small corpus annotated with them...
  20. 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
    ..The high level of abstraction of the rules used by the system, which are considerably more powerful and versatile than finite-state approaches, allows speedy interactive development and validation...
  21. 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
    ..In the absence of such a resource, surface clues can provide remarkably good coverage and performance when tuned to the domain. The adapted parser is available under an open-source license...
  22. 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
    ..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...
  23. Discovering patterns to extract protein-protein interactions from the literature: Part II
    Yu Hao
    State Key Laboratory of Intelligent Technology and Systems, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
    Bioinformatics 21:3294-300
    ..This has significantly increased generalization power, and hence the recall and precision rates, as confirmed by our experiments. AVAILABILITY: http://spies.cs.tsinghua.edu.cn...
  24. Measures of semantic similarity and relatedness in the biomedical domain
    Ted Pedersen
    Department of Computer Science, 1114 Kirby Drive, University of Minnesota, Duluth, MN 55812, USA
    J Biomed Inform 40:288-99
    ..We conclude that there is a role both for more flexible measures of relatedness based on information derived from corpora, as well as for measures that rely on existing ontological structures...
  25. MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations
    Jing Ding
    Department of Electrical and Computer Engineering, Iowa State University Ames, IA 50011, USA
    Bioinformatics 21:694-5
    ..Text mining researchers and others may download and use the toolkit free for non-commercial purposes. AVAILABILITY: http://metnetdb.gdcb.iastate.edu/medkit CONTACT: ...
  26. Using argumentation to retrieve articles with similar citations: an inquiry into improving related articles search in the MEDLINE digital library
    Imad Tbahriti
    SIM, University and Hospitals of Geneva, 24 Micheli du Crest, 1211 Geneva, Switzerland
    Int J Med Inform 75:488-95
    ..A linear weighting combination of the moves is proposed, which significantly improves retrieval of related articles...
  27. 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
    ..AVAILABILITY: A demo system is available at http://textmining.i2r.a-star.edu.sg/NLS/demo.htm. Technology license is available upon the bilateral agreement...
  28. Gene symbol disambiguation using knowledge-based profiles
    Hua Xu
    Department of Biomedical Informatics, Columbia University, New York City, New York, USA
    Bioinformatics 23:1015-22
    ..The method achieved the highest precision of 93.9% for the mouse, 77.8% for the fly and 89.5% for the yeast. AVAILABILITY: The testing data sets and disambiguation programs are available at http://www.dbmi.columbia.edu/~hux7002/gsd2006..
  29. Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions
    Sampo Pyysalo
    Turku Centre for Computer Science TUCS, Department of Computer Science, University of Turku, Lemminkäisenkatu 14A, 20520 Turku, Finland
    Int J Med Inform 75:430-42
    ..While Connexor Machinese Syntax significantly outperforms Link Grammar, the failure analysis suggests specific ways in which the latter could be modified for better performance in the domain...
  30. 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
    ..GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information...
  31. FigSearch: a figure legend indexing and classification system
    Fang Liu
    Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
    Bioinformatics 20:2880-2
    ..AVAILABILITY: A searchable Web interface, FigSearch, is accessible via http://pubgeneserver.uio.no/figsearch/ for all figures from the available corpus...
  32. Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser
    Daniel M McDonald
    Artificial Intelligence Laboratory MIS Department, University of Arizona, 1130 E Helen St, Tucson, AZ 85721, USA
    Bioinformatics 20:3370-8
    ..AVAILABILITY: Relations extracted from over 600 000 PubMed abstracts are available for retrieval and visualization at http://econport.arizona.edu:8080/NetVis/index.html...
  33. GIS: a biomedical text-mining system for gene information discovery
    Jung Hsien Chiang
    Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan 701, Taiwan, ROC
    Bioinformatics 20:120-1
    ..The aim of this system is to provide researchers an easy-to-use bio-information service that will rapidly survey the rapidly burgeoning biomedical literature. AVAILABILITY: http://iir.csie.ncku.edu.tw/~yuhc/gis/..
  34. 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
    ..Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database...
  35. Font adaptive word indexing of modern printed documents
    Simone Marinai
    Dipartimento di Sistenmi e Informatica, Università di Firenze, via di S Marta, 50139 Firenze, Italy
    IEEE Trans Pattern Anal Mach Intell 28:1187-99
    ..Our experimental analysis addresses six data sets containing documents ranging from books of the 17th century to contemporary journals...
  36. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts
    A M Cohen
    Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health and Science University, 3181 S, Sam Jackson Park Road, Portland, Oregon 97239 3098, USA
    BMC Bioinformatics 6:103
    ..36% recall), with high efficiency in the use of seed pairs. CONCLUSION: The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge...
  37. Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information
    James W Cooper
    Text Analytics, IBM Thomas J Watson Research Center, PO Box 704, Yorktown Heights, NY 10598, USA
    BMC Bioinformatics 6:143
    ..74 (f = 0.83). CONCLUSION: This combination of linguistic and statistical approaches appears to provide the highest precision and recall thus far reported in detecting protein-protein relations using text analytic approaches...
  38. A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports
    Carol Friedman
    Department of Medical Informatics, Columbia University, 622 West 168 Street, VC 5 Bldg, New York, NY 10032, USA
    J Biomed Inform 36:189-201
    ..of occurrence, compositionality, relations to other terms (such as modifiers), and correspondence to a controlled vocabulary. This paper describes the method and discusses how it can be used as a tool to help vocabulary builders ..
  39. GPSDB: a new database for synonyms expansion of gene and protein names
    Violaine Pillet
    Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
    Bioinformatics 21:1743-4
    ..AVAILABILITY: GPSDB is freely available from http://biomint.oefai.at/ CONTACT: ...
  40. Text similarity: an alternative way to search MEDLINE
    James Lewis
    University of Texas Southwestern Medical Center, Eugene McDermott Center for Human Growth and Development, Division for Translational Research 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Bioinformatics 22:2298-304
    ..swmed.edu. A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities. CONTACT: ...
  41. Semantic search among heterogeneous biological databases based on gene ontology
    Shun-Liang Cao
    Department of Computing and Information Technology, Fudan University, Shanghai, China
    Acta Biochim Biophys Sin (Shanghai) 36:365-70
    ..Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched...
  42. Utilizing weakly controlled vocabulary for sentence segmentation in biomedical literature
    Kenji Satou
    School of Knowledge Science, Japan Advanced Institute of Science and Technology
    In Silico Biol 5:67-79
    ..It should be remarked that although we have not used term cost, connectivity cost, or syntactic information, reasonable segmentation and dictionary lookup were performed in most cases...
  43. Substring selection for biomedical document classification
    Bo Han
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    Bioinformatics 22:2136-42
    ..92-0.97] when using the proposed attribute selection than when using attributes obtained by the Porter stemmer algorithm (AUC in 0.86-0.93 range). The proposed approach is particularly useful when labeled datasets are small...
  44. Extracting human protein interactions from MEDLINE using a full-sentence parser
    Nikolai Daraselia
    Ariadne Genomics, Inc, 9700 Great Seneca Hwy, Rockville, MD 20850, USA
    Bioinformatics 20:604-11
    ..Further directions of the MedScan technology improvement are discussed. AVAILABILITY: MedScan is available for commercial licensing from Ariadne Genomics, Inc...
  45. Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature
    Jung Jae Kim
    Computer Science Division and AITrc, Korea Advanced Institute of Science and Technology, 373 1, Guseong Dong, Yuseong Gu, Daejeon 305 701, South Korea
    J Bioinform Comput Biol 2:551-68
    ..grammar, and by annotating the results with the terms of Gene Ontology, which provides a common and controlled vocabulary. BioIE deals with complex linguistic phenomena such as coordination, relative structures, acronyms, ..
  46. Literature mining and database annotation of protein phosphorylation using a rule-based system
    Z Z Hu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
    Bioinformatics 21:2759-65
    ..9 and 88.0% for extraction of substrates and sites. Coupling the high recall for paper retrieval and high precision for information extraction, RLIMS-P facilitates literature mining and database annotation of protein phosphorylation...
  47. 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
    ..AVAILABILITY: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/...
  48. AliBaba: PubMed as a graph
    Conrad Plake
    Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin Unter den Linden 6, 10099 Berlin, Germany
    Bioinformatics 22:2444-5
    ..Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. AVAILABILITY: http://alibaba.informatik.hu-berlin.de/..
  49. 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
    ..It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora...
  50. GOurmet: a tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
    Jason M Doherty
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
    BMC Bioinformatics 7:151
    ..The clustering analysis features a dynamic targetoid plot that is generalizable for use with any clustering application...
  51. 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
    ..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)...
  52. Using the biological taxonomy to access biological literature with PathBinderH
    J Ding
    Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
    Bioinformatics 21:2560-2
    ..Although the current project requires this function only for plant taxa, the principle is extensible to the entire taxonomy. AVAILABILITY: www.plantgenomics.iastate.edu/PathBinderH. Source code and databases on request...
  53. Building a semantic Web for securing the homeland
    Nicolas J Guzman
    School of Medicine and Health Sciences, Center for Emergency Preparedness, George Washington University, Washington, D.C, USA
    IEEE Eng Med Biol Mag 23:71-80
  54. A survey of current work in biomedical text mining
    Aaron M Cohen
    Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health and Science University, 3181 S W Sam Jackson Park Road, Portland, OR 97239 309, USA
    Brief Bioinform 6:57-71
    ....
  55. Paraphrasing for condensation in journal abstracting
    Richard Kittredge
    Department of Linguistics and Translation, University of Montreal, CP 6128, Succ A, Montréal, Que, Canada H3C 3J7
    J Biomed Inform 35:265-77
    ..The descriptive framework is computable and utilizes existing linguistic resources...
  56. uBioRSS: tracking taxonomic literature using RSS
    Patrick R Leary
    MBL Informatics, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Bioinformatics 23:1434-6
    ..Such value-added enhancements can provide biologists with accelerated and improved access to current biological content. AVAILABILITY: http://names.ubio.org/rss/..
  57. 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
    ..AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl...
  58. AliasServer: a web server to handle multiple aliases used to refer to proteins
    Florian Iragne
    Centre de Bioinformatique Bordeaux, Université V. Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
    Bioinformatics 20:2331-2
    ..The complete tool, including sources and data, is available for local installations upon request. SUPPLEMENTARY INFORMATION: Technical documentation is available at http://cbi.labri.fr/outils/alias/asdoc.pdf..
  59. The MIPS mammalian protein-protein interaction database
    Philipp Pagel
    Institute for Bioinformatics/MIPS, GSF-National Research Center for Environment and Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
    Bioinformatics 21:832-4
    ..The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements...
  60. Elective single embryo transfer following in vitro fertilization
    Jason K Min
    Ottawa ON
    J Obstet Gynaecol Can 32:363-77
    ..was retrieved through searches of PubMed, Medline, and The Cochrane Library in 2009, using appropriate controlled vocabulary (e.g., elective single embryo transfer) and key words (e.g...
  61. Cytomegalovirus infection in pregnancy
    Yoav Yinon
    Toronto, ON
    J Obstet Gynaecol Can 32:348-54
    ..Evidence: Medline was searched for articles published in English from 1966 to 2009, using appropriate controlled vocabulary (congenital CMV infection) and key words (intrauterine growth restriction, microcephaly)...
  62. Guidelines for the management of vasa previa
    Robert Gagnon
    The Society of Obstetricians and Gynaecologists of Canada SOGC, Montreal, QC
    J Obstet Gynaecol Can 31:748-60
    ..was retrieved through searches of PubMed or Medline, CINAHL, and the Cochrane Library, using appropriate controlled vocabulary (e.g...
  63. Ovulation induction in polycystic ovary syndrome
    Tannys D R Vause
    Ottawa ON
    J Obstet Gynaecol Can 32:495-502
    ..Evidence: Published literature was retrieved through searches of Medline using appropriate controlled vocabulary and key words...
  64. Antibiotic therapy in preterm premature rupture of the membranes
    Mark H Yudin
    Toronto ON
    J Obstet Gynaecol Can 31:863-7, 868-74
    ..was retrieved through searches of Medline, EMBASE, CINAHL, and The Cochrane Library, using appropriate controlled vocabulary and key words (PPROM, infection, and antibiotics)...
  65. Evaluation of prenatally diagnosed structural congenital anomalies
    Alain Gagnon
    Vancouver BC
    J Obstet Gynaecol Can 31:875-81, 882-9
    ..searches of PubMed or Medline, CINAHL, and the Cochrane Library for relevant articles using appropriate controlled vocabulary (e.g...
  66. Searching biomedical databases on complementary medicine: the use of controlled vocabulary among authors, indexers and investigators
    Linda S Murphy
    Science Library Reference Department, University of California, Irvine 926233 9557, USA
    BMC Complement Altern Med 3:3
    ..for the diagnosis of neuromuscular dysfunction, we developed four search concepts with their respective controlled vocabulary and key terms...
  67. On the quality of tree-based protein classification
    Betty Lazareva Ulitsky
    Computational Biology Department, Applied Biosystems, Foster City, CA 94404, USA
    Bioinformatics 21:1876-90
    ..In addition, the recent increase in the number of protein sequence entries with controlled vocabulary terms describing function (e.g...
  68. GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms
    Saurin D Jani
    Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
    BMC Bioinformatics 11:166
    ..experiment) to descriptors making up the hierarchical structure of the National Library of Medicine controlled vocabulary thesaurus, MeSH...
  69. Enhancing evidence-based practice--a controlled vocabulary for nursing practice and research
    Kaija Saranto
    Department of Health Policy and Management, University of Kuopio, P O Box 1627, FIN 70211 Kuopio, Finland
    Int J Med Inform 70:249-53
    ..The vocabulary will be added as an independent theme to the Finnish thesaurus the FinMeSH...
  70. 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
    ..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 ..
  71. Searching the MEDLINE literature database through PubMed: a short guide
    Edith Motschall
    Institut für Medizinische Biometrie und Medizinische Informatik, Universität Freiburg, Germany
    Onkologie 28:517-22
    ..This example will show how the application of Medline search tools and how the use of the controlled vocabulary of 'Medical Subject Headings' (MeSH) will influence the results in comparison with the fast and simple ..
  72. 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
    ..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...
  73. A case study: using social tagging to engage students in learning Medical Subject Headings
    Lauren A Maggio
    Alumni Medical Library, Boston University Medical Center, 715 Albany Street L 12, Boston, MA 02118, USA
    J Med Libr Assoc 97:77-83
    ..Hands-on assignments and in-class exercises enabled librarians to present MeSH and the concept of a controlled vocabulary in a familiar and relevant context for the course's Generation Y student population and provided students ..
  74. Endoscopy information online: can endoscopists close the gap between what is known and what they do?
    J Krabshuis
    Highland Data, Argyll, Scotland
    Endoscopy 29:871-82
    ..such as hosts, online databases such as MEDLINE and EMBASE, search engines, retrieval and query languages, and thesauri. The focus is on two specific thesaurus issues: the use (or absence of) complex hierarchical thesauri such as ..
  75. An evaluation of SNOMED CT(R) in the domain of complex chronic conditions
    Tara Sampalli
    Dalhousie University and Health Services Manager, Nova Scotia Environmental Health Centre, Capital District Health Authority, Fall River, Nova Scotia, Canada
    Int J Integr Care 10:e038
    ..retrospective audit of patient charts and feedback from multidisciplinary clinicians in the creation of a controlled vocabulary used in the generation of patient profiles for MCS...
  76. The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank
    Sambit K Mohanty
    Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
    BMC Cancer 8:91
    ..RESULTS: Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology...
  77. Building an ontology of pulmonary diseases with natural language processing tools using textual corpora
    Audrey Baneyx
    INSERM U729, Laboratoire SPIM, Faculté de Médecine Broussais, Hôtel Dieu, 15 rue de l Ecole de Médecine, Paris, France
    Int J Med Inform 76:208-15
    Pathologies and acts are classified in thesauri to help physicians to code their activity. In practice, the use of thesauri is not sufficient to reduce variability in coding and thesauri are not suitable for computer processing...
  78. 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
    ..OBJECTIVES: To evaluate the potential of controlled vocabulary resources for supporting the development of consumer entry vocabulary for diabetes...
  79. The brain atlas concordance problem: quantitative comparison of anatomical parcellations
    Jason W Bohland
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
    PLoS ONE 4:e7200
    ..attempts to reconcile neuroanatomical nomenclatures have been largely qualitative, focusing on the development of thesauri or simple semantic mappings between terms...
  80. Racial discrimination and health: a systematic review of scales with a focus on their psychometric properties
    Joao Luiz Bastos
    Federal University of Pelotas, Department of Social Medicine, Rua Marechal Deodoro, 1160, 96020 220 Pelotas, Rio Grande do Sul, Brazil
    Soc Sci Med 70:1091-9
    ..and Web of Science was conducted without any type of restriction, using search queries containing free and controlled vocabulary. After initially identifying 3060 references, 24 scales were included in the review...
  81. Developing the ontological foundations of a terminological system for end-stage diseases, organ failure, dialysis and transplantation
    Christian Jacquelinet
    Département Medical et Scientifique, Etablissement français des Greffes, rue Lacuée, Paris 75012, France
    Int J Med Inform 70:317-28
    ..with other local, national or international registries, a specific work has been conducted on the thesauri to integrate within the EfG-TS...
  82. Evaluating CD-ROM versions of the MEDLINE database: a checklist
    N S Hewison
    Life Sciences Library, Purdue University, West Lafayette, Indiana 47907
    Bull Med Libr Assoc 77:332-6
    ..g., the MeSH controlled vocabulary, the designation of major and minor MeSH emphasis, and the use of subheadings...
  83. 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
    ..This variance may ultimately impact the search results. These differences should be considered when choosing a MEDLINE interface and when instructing end users...
  84. Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets
    Peter B McGarvey
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
    PLoS ONE 4:e7162
    ..Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the ..
  85. Golf-related stress fractures: a structured review of the literature
    Alexander D Lee
    Sports Sciences Resident Year II, Graduate Education and Research Programs, Canadian Memorial Chiropractic College, 6100 Leslie Street, Toronto, Ontario, Canada M2H 3J1 Tel 1 416 482 2340 Email
    J Can Chiropr Assoc 53:290-9
    ..METHODS: A literature search of MEDLINE, CINAHL, and SPORTDiscus was conducted using a combination of controlled vocabulary and truncated text words to capture all articles relevant to golf-related stress fractures...
  86. Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice
    Marco Masseroli
    BioMedical Informatics Laboratory, Dipartimento di Bioingegneria, Politecnico di Milano, 1 20133 Milan, Italy
    IEEE Trans Inf Technol Biomed 11:376-85
    ..A controlled vocabulary of inherited disorder phenotypes was obtained by normalizing and hierarchically structuring disease ..
  87. Dynamic publication model for neurophysiology databases
    D Gardner
    Department of Physiology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021 48 05, USA
    Philos Trans R Soc Lond B Biol Sci 356:1229-47
    ..Copyright is retained by submitters; viewer displays are dynamic and do not violate copyright of related journal figures. Panels of neurophysiologists view and test schemas and tools, enhancing community support...
  88. An internet database for the classification and dissemination of information about hazardous chemicals and occupational diseases
    J A Brown
    Specialized Information Services, National Library of Medicine, Bethesda, Maryland, USA
    Am J Ind Med 51:428-35
    ..The information was indexed with a controlled vocabulary and documented with references to the scientific literature...
  89. The value of an in-domain lexicon in genomics QA
    Yutaka Sasaki
    National Centre for Text Mining, School of Computer Science, University of Manchester, MIB, 131 Princess Street, Manchester M17DN, United Kingdom
    J Bioinform Comput Biol 8:147-61
    ..While conventional genomics QA systems provide query expansion based on thesauri and dictionaries, it is not clear to what extent a biology-oriented lexical resource is effective for question ..
  90. Galen-In-Use: using artificial intelligence terminology tools to improve the linguistic coherence of a national coding system for surgical procedures
    J M Rodrigues
    Department of Public Health and Medical Informatics University of Saint Etienne Jean Monnet, France
    Stud Health Technol Inform 52:623-7
    ..of concepts, to compare the professional language proposed by expert clinicians to the French generated controlled vocabulary and to finalize the linguistic labels of the coding system in relation with the meanings of the conceptual ..
  91. Graph theoretic modeling of large-scale semantic networks
    Michael E Bales
    Department of Biomedical Informatics, Columbia University, New York, NY, USA
    J Biomed Inform 39:451-64
    ..The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the ..
  92. Euroethics--a database network on biomedical ethics
    Ylva Gavel
    KI University Library, Karolinska Institutet, Stockholm, Sweden
    Health Info Libr J 23:169-78
    ..The indexing terms derive from two thesauri, Thesaurus Ethics in the Life Sciences (TELS) and Medical Subject Headings (MeSH)...
  93. Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets
    Marc Aubry
    CNRS UMR 6061 Génétique et Développement, Université de Rennes 1, Groupe Oncogénomique, IFR140 GFAS, Faculté de Médecine, 2 avenue du Pr, Léon Bernard, CS 34317, 35043 Rennes Cedex, France
    BMC Bioinformatics 7:241
    ..The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes...
  94. Planned NLM/AHCPR large-scale vocabulary test: using UMLS technology to determine the extent to which controlled vocabularies cover terminology needed for health care and public health
    B L Humphreys
    National Library of Medicine, Bethesda, MD 20894, USA
    J Am Med Inform Assoc 3:281-7
    ..The test will determine the ability of the test vocabularies to serve as a source of controlled vocabulary for health data systems and applications...
  95. How to write a scholarly book review for publication in a peer-reviewed journal: a review of the literature
    Alexander D Lee
    Canadian Memorial Chiropractic College
    J Chiropr Educ 24:57-69
    ..EMBASE, CINAHL, and the Index to Chiropractic Literature was conducted in June 2009 using a combination of controlled vocabulary and truncated text words to capture articles relevant to writing scholarly book reviews for publication in ..
  96. Automatic assignment of biomedical categories: toward a generic approach
    Patrick Ruch
    University Hospitals of Geneva, Medical Informatics Service CH 1201, Geneva
    Bioinformatics 22:658-64
    ..for both GO and MeSH categorization, but we observe the categorization power of the tool depends on the controlled vocabulary: precision at high ranks ranges from above 90% for MeSH to <20% for GO, establishing a new baseline for ..
  97. Regulatory pathway analysis by high-throughput in situ hybridization
    Axel Visel
    Department of Genes and Behavior, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
    PLoS Genet 3:1867-83
    ..Patterns were textually annotated using a controlled vocabulary comprising >90 anatomical features...