title: caCORE: a common infrastructure for cancer informatics.
abstract: BACKGROUND
  Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. 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.
  
  
  RESULTS
  We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources.
  
  
  BACKGROUND
  caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads.
  
  
  BACKGROUND
  http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).
authors.affiliation: 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. covitzp@mail.nih.gov
authors.forename: Peter A
authors.initials: PA
authors.lastname: Covitz
authors.forename: Frank
authors.initials: F
authors.lastname: Hartel
authors.forename: Carl
authors.initials: C
authors.lastname: Schaefer
authors.forename: Sherri
authors.initials: S
authors.lastname: De Coronado
authors.forename: Gilberto
authors.initials: G
authors.lastname: Fragoso
authors.forename: Himanso
authors.initials: H
authors.lastname: Sahni
authors.forename: Scott
authors.initials: S
authors.lastname: Gustafson
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Buetow
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods / Q000592:standards; D016208:Databases, Factual / Q000592:standards*; D004018:Dictionaries, Medical as Topic; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods* / Q000592:standards*; D020407:Internet; D009316:National Institutes of Health (U.S.); D009323:Natural Language Processing; D009369:Neoplasms / Q000145:classification*; D014481:United States; D014584:User-Computer Interface; D018875:Vocabulary, Controlled