Comparative and Functional Genomics
Volume 5 (2004), Issue 6-7, Pages 521-527
doi:10.1002/cfg.434
Conference paper

The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data

Helen Parkinson,1 Stuart Aitken,2 Richard A. Baldock,3 Jonathan B. L. Bard,4 Albert Burger,3,5 Terry F. Hayamizu,6 Alan Rector,7 Martin Ringwald,6 Jeremy Rogers,7 Cornelius Rosse,8 Christian J. Stoeckert Jr.,9 and Duncan Davidson3

1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
2Artificial Intelligence Applications Institute, School of Informatics, University of Edinburgh, Crichton Street, Edinburgh EH8 9LE, UK
3MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
4Wolfson Laboratory, Medical School, University of Edinburgh, Edinburgh EH8 9XD, UK
5School of Mathematics and Computer Sciences, Heriot–Watt University, Riccarton, Edinburgh EH14 4AS, UK
6The Jackson Laboratory, 600 Main Street, Bar Harbor 04609, ME, USA
7Kilburn Building, University of Manchester, Oxford Road, Manchester M13 9PL, UK
8Department of Biological Structure and Department of Medical Education and Biomedical Informatics, School of Medicine, University of Washington, Seattle, WA, USA
9Department of Genetics, Center for Bioinformatics, University of Pennsylvania, 423 Guardian Drive, Philadelphia 19104, PA, USA

Received 23 October 2004; Revised 1 November 2004; Accepted 2 November 2004

Copyright © 2004 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.