International Journal of Genomics

International Journal of Genomics / 2004 / Article

Conference paper | Open Access

Volume 5 |Article ID 453476 | https://doi.org/10.1002/cfg.434

Helen Parkinson, Stuart Aitken, Richard A. Baldock, Jonathan B. L. Bard, Albert Burger, Terry F. Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert, Duncan Davidson, "The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data", International Journal of Genomics, vol. 5, Article ID 453476, 7 pages, 2004. https://doi.org/10.1002/cfg.434

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

Received23 Oct 2004
Revised01 Nov 2004
Accepted02 Nov 2004

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.

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.


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