caCORE: A common infrastructure for cancer informatics

Peter A. Covitz, Frank Hartel, Carl Schaefer, Sherri De Coronado, Gilberto Fragoso, Himanso Sahni, Scott Gustafson, Kenneth H. Buetow

Research output: Contribution to journalArticlepeer-review

121 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2404-2412
Number of pages9
JournalBioinformatics
Volume19
Issue number18
DOIs
StatePublished - Dec 12 2003
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint Dive into the research topics of 'caCORE: A common infrastructure for cancer informatics'. Together they form a unique fingerprint.

Cite this