eVOC: a controlled vocabulary for unifying gene expression data.
Expression data contribute significantly to the biological value of the sequenced human genome, providing extensive information about gene structure and the pattern of gene expression. ESTs, together with SAGE libraries and microarray experiment information, provide a broad and rich view of the transcriptome. However, it is difficult to perform large-scale expression mining of the data generated by these diverse experimental approaches. Not only is the data stored in disparate locations, but there is frequent ambiguity in the meaning of terms used to describe the source of the material used in the experiment. Untangling semantic differences between the data provided by different resources is therefore largely reliant on the domain knowledge of a human expert. We present here eVOC, a system which associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. We have curated and annotated 7016 cDNA libraries represented in dbEST, as well as 104 SAGE libraries,with expression information,and provide this as an integrated, public resource that allows the linking of transcripts and libraries with expression terms. Both the vocabularies and the vocabulary-annotated libraries can be retrieved from http://www.sanbi.ac.za/evoc/. Several groups are involved in developing this resource with the aim of unifying transcript expression information.
Kelso
Janet
J
South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
Visagie
Johann
J
Theiler
Gregory
G
Christoffels
Alan
A
Bardien
Soraya
S
Smedley
Damian
D
Otgaar
Darren
D
Greyling
Gary
G
Jongeneel
C Victor
CV
McCarthy
Mark I
MI
Hide
Tania
T
Hide
Winston
W
D000818:Animals; D018076:DNA, Complementary / Q000145:classification; D020869:Gene Expression Profiling / Q000145:classification* / Q000639:trends; D005786:Gene Expression Regulation / Q000235:genetics; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D051379:Mice; D010336:Pathology / Q000145:classification / Q000379:methods / Q000639:trends; D013045:Species Specificity; D009626:Terminology as Topic
D018076:DNA, Complementary