Treffer: caCORE: a common infrastructure for cancer informatics.

Title:
caCORE: a common infrastructure for cancer informatics.
Authors:
Covitz PA; 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, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S, Buetow KH
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2003 Dec 12; Vol. 19 (18), pp. 2404-12.
Publication Type:
Journal Article; Research Support, U.S. Gov't, P.H.S.
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Print ISSN: 1367-4803 (Print) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Natural Language Processing* , User-Computer Interface*, Databases, Factual/*standards , Information Storage and Retrieval/*methods , Information Storage and Retrieval/*standards , Neoplasms/*classification, Animals ; Computational Biology/methods ; Computational Biology/standards ; Dictionaries, Medical as Topic ; Humans ; Internet ; National Institutes of Health (U.S.) ; United States ; Vocabulary, Controlled
Entry Date(s):
Date Created: 20031212 Date Completed: 20040817 Latest Revision: 20221104
Update Code:
20250114
DOI:
10.1093/bioinformatics/btg335
PMID:
14668224
Database:
MEDLINE

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Motivation: 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.
Availability: 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.
Supplementary Information: 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).