Literature DB >> 19154797

The caBIG terminology review process.

James J Cimino1, Terry F Hayamizu, Olivier Bodenreider, Brian Davis, Grace A Stafford, Martin Ringwald.   

Abstract

The National Cancer Institute (NCI) is developing an integrated biomedical informatics infrastructure, the cancer Biomedical Informatics Grid (caBIG), to support collaboration within the cancer research community. A key part of the caBIG architecture is the establishment of terminology standards for representing data. In order to evaluate the suitability of existing controlled terminologies, the caBIG Vocabulary and Data Elements Workspace (VCDE WS) working group has developed a set of criteria that serve to assess a terminology's structure, content, documentation, and editorial process. This paper describes the evolution of these criteria and the results of their use in evaluating four standard terminologies: the Gene Ontology (GO), the NCI Thesaurus (NCIt), the Common Terminology for Adverse Events (known as CTCAE), and the laboratory portion of the Logical Objects, Identifiers, Names and Codes (LOINC). The resulting caBIG criteria are presented as a matrix that may be applicable to any terminology standardization effort.

Entities:  

Mesh:

Year:  2008        PMID: 19154797      PMCID: PMC2729758          DOI: 10.1016/j.jbi.2008.12.003

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  18 in total

1.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

2.  Guideline for health informatics: controlled health vocabularies--vocabulary structure and high-level indicators.

Authors:  P L Elkin; S H Brown; C G Chute
Journal:  Stud Health Technol Inform       Date:  2001

3.  SNOMED CT milestones: endorsements are added to already-impressive standards credentials.

Authors:  Kent A Spackman
Journal:  Healthc Inform       Date:  2004-09

4.  Terminological system maintenance: a procedures framework and an exploration of current practice.

Authors:  Ferishta Raiez; Danielle Arts; Ronald Cornet
Journal:  Stud Health Technol Inform       Date:  2005

5.  A terminological and ontological analysis of the NCI Thesaurus.

Authors:  W Ceusters; B Smith; L Goldberg
Journal:  Methods Inf Med       Date:  2005       Impact factor: 2.176

6.  Exchange of computable patient data between the Department of Veterans Affairs (VA) and the Department of Defense (DoD): terminology mediation strategy.

Authors:  Omar Bouhaddou; Pradnya Warnekar; Fola Parrish; Nhan Do; Jack Mandel; John Kilbourne; Michael J Lincoln
Journal:  J Am Med Inform Assoc       Date:  2007-12-20       Impact factor: 4.497

7.  caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability.

Authors:  George A Komatsoulis; Denise B Warzel; Francis W Hartel; Krishnakant Shanbhag; Ram Chilukuri; Gilberto Fragoso; Sherri de Coronado; Dianne M Reeves; Jillaine B Hadfield; Christophe Ludet; Peter A Covitz
Journal:  J Biomed Inform       Date:  2007-04-02       Impact factor: 6.317

8.  NCI Thesaurus: using science-based terminology to integrate cancer research results.

Authors:  Sherri de Coronado; Margaret W Haber; Nicholas Sioutos; Mark S Tuttle; Lawrence W Wright
Journal:  Stud Health Technol Inform       Date:  2004

9.  Cancer informatics vision: caBIG.

Authors:  Andrew C von Eschenbach; Kenneth Buetow
Journal:  Cancer Inform       Date:  2007-02-06

10.  Overview and utilization of the NCI thesaurus.

Authors:  Gilberto Fragoso; Sherri de Coronado; Margaret Haber; Frank Hartel; Larry Wright
Journal:  Comp Funct Genomics       Date:  2004
View more
  10 in total

1.  Enabling international adoption of LOINC through translation.

Authors:  Daniel J Vreeman; Maria Teresa Chiaravalloti; John Hook; Clement J McDonald
Journal:  J Biomed Inform       Date:  2012-01-21       Impact factor: 6.317

2.  CanProVar: a human cancer proteome variation database.

Authors:  Jing Li; Dexter T Duncan; Bing Zhang
Journal:  Hum Mutat       Date:  2010-03       Impact factor: 4.878

Review 3.  Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers.

Authors:  Andrew J Buckler; Tiffany Ting Liu; Erica Savig; Baris E Suzek; M Ouellette; J Danagoulian; G Wernsing; Daniel L Rubin; David Paik
Journal:  J Digit Imaging       Date:  2013-08       Impact factor: 4.056

4.  CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.

Authors:  Menghuan Zhang; Bo Wang; Jia Xu; Xiaojing Wang; Lu Xie; Bing Zhang; Yixue Li; Jing Li
Journal:  J Proteome Res       Date:  2016-12-15       Impact factor: 4.466

5.  Exposing the cancer genome atlas as a SPARQL endpoint.

Authors:  Helena F Deus; Diogo F Veiga; Pablo R Freire; John N Weinstein; Gordon B Mills; Jonas S Almeida
Journal:  J Biomed Inform       Date:  2010-12       Impact factor: 6.317

6.  Building a biomedical cyberinfrastructure for collaborative research.

Authors:  Peter A Schad; Lee Rivers Mobley; Carol M Hamilton
Journal:  Am J Prev Med       Date:  2011-05       Impact factor: 5.043

7.  Knowledge-based data analysis comes of age.

Authors:  Michael F Ochs
Journal:  Brief Bioinform       Date:  2009-10-23       Impact factor: 11.622

8.  The Cardiac Atlas Project--an imaging database for computational modeling and statistical atlases of the heart.

Authors:  Carissa G Fonseca; Michael Backhaus; David A Bluemke; Randall D Britten; Jae Do Chung; Brett R Cowan; Ivo D Dinov; J Paul Finn; Peter J Hunter; Alan H Kadish; Daniel C Lee; Joao A C Lima; Pau Medrano-Gracia; Kalyanam Shivkumar; Avan Suinesiaputra; Wenchao Tao; Alistair A Young
Journal:  Bioinformatics       Date:  2011-07-06       Impact factor: 6.937

9.  The PhenX Toolkit: get the most from your measures.

Authors:  Carol M Hamilton; Lisa C Strader; Joseph G Pratt; Deborah Maiese; Tabitha Hendershot; Richard K Kwok; Jane A Hammond; Wayne Huggins; Dean Jackman; Huaqin Pan; Destiney S Nettles; Terri H Beaty; Lindsay A Farrer; Peter Kraft; Mary L Marazita; Jose M Ordovas; Carlos N Pato; Margaret R Spitz; Diane Wagener; Michelle Williams; Heather A Junkins; William R Harlan; Erin M Ramos; Jonathan Haines
Journal:  Am J Epidemiol       Date:  2011-07-11       Impact factor: 4.897

10.  Measuring the evolution of ontology complexity: the gene ontology case study.

Authors:  Olivier Dameron; Charles Bettembourg; Nolwenn Le Meur
Journal:  PLoS One       Date:  2013-10-11       Impact factor: 3.240

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.