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Related Experiment Videos

eVOC: a controlled vocabulary for unifying gene expression data.

Janet Kelso1, Johann Visagie, Gregory Theiler

  • 1South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.

Genome Research
|June 12, 2003
PubMed
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eVOC is a new system that standardizes human gene expression data. It uses controlled vocabularies to link gene transcripts and libraries, enabling easier large-scale expression mining.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Gene expression data is crucial for understanding the human genome.
  • Existing data from ESTs, SAGE, and microarrays are vast but difficult to mine due to disparate storage and semantic ambiguity.
  • Human expert knowledge is often required to reconcile data from different sources.

Purpose of the Study:

  • To develop a system, eVOC, for large-scale expression mining of human gene expression data.
  • To associate labeled target cDNAs and cDNA libraries with controlled hierarchical vocabularies.
  • To provide an integrated, public resource for unifying transcript expression information.

Main Methods:

  • Developed eVOC, a system with four orthogonal controlled vocabularies (Anatomical System, Cell Type, Pathology, Developmental Stage).

Related Experiment Videos

  • Curated and annotated 7016 cDNA libraries from dbEST and 104 SAGE libraries with expression information.
  • Linked transcripts and libraries with controlled expression terms.

    • Main Results:

    • Created eVOC, a system that standardizes human gene expression data.
    • Annotated thousands of cDNA and SAGE libraries with standardized terms.
    • Established a public resource for unified transcript expression information.

    Conclusions:

    • eVOC facilitates large-scale expression mining by resolving semantic differences in gene expression data.
    • The system provides a unified approach to accessing and analyzing transcript expression information.
    • eVOC is available as a public resource to support biological research.