TY - JOUR
T1 - The SOFG Anatomy Entry List (SAEL)
T2 - An annotation tool for functional genomics data
AU - Parkinson, Helen
AU - Aitken, Stuart
AU - Baldock, Richard A.
AU - Bard, J. B L
AU - Burger, Albert
AU - Hayamizu, Terry F.
AU - Rector, Alan
AU - Ringwald, Martin
AU - Rogers, Jeremy
AU - Rosse, Cornelius
AU - Stoeckert, Christian J.
AU - Davidson, Duncan
PY - 2004/8
Y1 - 2004/8
N2 - A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies. Copyright © 2004 John Wiley & Sons, Ltd.
AB - A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies. Copyright © 2004 John Wiley & Sons, Ltd.
KW - Anatomy
KW - Annotation
KW - Bibliographic keywords
KW - High-throughput
KW - Microarray
KW - Ontology
KW - Phenotype description
U2 - 10.1002/cfg.434
DO - 10.1002/cfg.434
M3 - Article
C2 - 18629134
SN - 1531-6912
VL - 5
SP - 521
EP - 527
JO - Comparative and Functional Genomics
JF - Comparative and Functional Genomics
IS - 6-7
ER -