The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data
2004
Parkinson, Helen(European Bioinformatics Institute, Wellcome Trust Genome Campus) | Aitken, Stuart(Artificial Intelligence Applications Institute, School of Informatics) | Baldock, Richard A.(MRC Human Genetics Unit, Western General Hospital) | Bard, Jonathan B. L.(Wolfson Laboratory, Medical School) | Burger, Albert(MRC Human Genetics Unit, Western General Hospital) | Hayamizu, Terry F.(The Jackson Laboratory, 600 Main Street) | Rector, Alan(Kilburn Building, University of Manchester) | Ringwald, Martin(The Jackson Laboratory, 600 Main Street) | Rogers, Jeremy(Kilburn Building, University of Manchester) | Rosse, Cornelius(Department of Biological Structure and Department of Medical Education and Biomedical Informatics, School of Medicine) | Stoeckert, Christian J.Jr.(Department of Genetics, Center for Bioinformatics) | Davidson, Duncan(MRC Human Genetics Unit, Western General Hospital)
A great deal of data in functional genomics studies needs to be annotated withlow-resolution anatomical terms. For example, gene expression assays based onmanually dissected samples (microarray, SAGE, etc.) need high-level anatomicalterms to describe sample origin. First-pass annotation in high-throughput assays (e.g.large-scale in situ gene expression screens or phenotype screens) and bibliographicapplications, such as selection of keywords, would also benefit from a minimumset of standard anatomical terms. Although only simple terms are required, theresearcher faces serious practical problems of inconsistency and confusion, giventhe different aims and the range of complexity of existing anatomy ontologies. AStandards and Ontologies for Functional Genomics (SOFG) group therefore initiateddiscussions between several of the major anatomical ontologies for higher vertebrates.As we report here, one result of these discussions is a simple, accessible, controlledvocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL).The SAEL is available from http://www.sofg.org and is intended as a resourcefor biologists, curators, bioinformaticians and developers of software supportingfunctional genomics. It can be used directly for annotation in the contexts describedabove. Importantly, each term is linked to the corresponding term in each of themajor anatomy ontologies. Where the simple list does not provide enough detail orsophistication, therefore, the researcher can use the SAEL to choose the appropriateontology and move directly to the relevant term as an entry point. The SAEL links willalso be used to support computational access to the respective ontologies.
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