The SOFG Anatomy Entry List (SAEL) for functional genomics applications and as an entry point to existing anatomy ontologies
Stuart Aitken1, Richard Baldock2, Jonathan Bard, Albert Burger, Duncan Davidson, Terry Hayamizu, Helen Parkinson, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert
1stuart@inf.ed.ac.uk, University of Edinburgh; 2Richard.Baldock@hgu.mrc.ac.uk, MRC-HGU
Sample-based microarray, and other functional genomics, experiments produce large quantities of data. Detailed meta data about the samples are critical for analyses. Meta data can be controlled by the use of ontologies. However, in some domains, such as vertebrate anatomy, several alternative ontology resources exist. This presents a problem for those developing annotation and query applications for functional genomic data. Users are often not expert anatomists and are unable to make an educated choice between different resources. The practical result is that annotation is often incomplete or inconsistent. This limits further analyses and often means that the data cannot be usefully compared.
In order to address this problem, a recent Standards and Ontologies for Functional Genomics (SOFG) Workshop (www.sofg.org/integration/) investigated the needs of the functional genomics community in the light of available anatomy ontologies. Representatives of the FMA (1), Open Galen (2), the EMAP Mouse Anatomical Dictionary (3), the Adult Mouse Anatomy (4) and the MGED Ontology (5) considered two questions:
1. Can a Core Anatomy list be produced for in functional genomics applications, specifically those used in microarray experiments and will this be useful?
2. If construction of a Core Anatomy list is possible what are the use cases, limitations and build criteria?
The result is the SOFG Anatomy Entry List (SAEL) (6), a freely available selection of cross-species anatomical terms relevant to functional genomics. The SAEL has two functions. On its own, the SAEL can immediately be used as a controlled vocabulary for annotation. It also provides an entry point to existing anatomical resources via mapping to concepts in those resources. The implementation of the SAEL will also provide an entry mechanism for computational access to anatomy resources to facilitate automated information retrieval. We considered implementation of the SAEL as a web service and determined attributes that might be returned from target ontologies in response to a SAEL-based query. These attributes together may constitute a WSDL for anatomy ontologies. The SAEL is therefore a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics.
The SAEL currently consists of a list of anatomical terms for human and mouse organised by organ, body part, body substances, dissectable organ, organ part, and organ system. We are also exploring extension to other species. We envisage that this list will be revised and extended on the basis of requirements. The SAEL is not intended to replace existing ontologies and where more detailed terms are required the mapping of SAEL terms to ontology resources will allow users to navigate easily to relevant resources.
References
1. Rosse C., Mejino J.L.V. Jr. 2003. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J Biomed Inform 2003 Dec;36(6):478-500/uri
2. www.opengalen.org/
3. EMAP http://genex.hgu.mrc.ac.uk/Databases/Anatomy/ see also: Bard, J.B.L., Kaufman, M.H., Dubreuil, C., Brune, R.M., Burger, A., Baldock, R.A and Davidson, D.R. An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature, Mechanisms of Development 1998, 74. 111-20.
4. http://www.informatics.jax.org/mgihome/GXD/aboutGXD.shtml#adult_dict
5. MGED (http://mged.sourceforge.net/ontologies/index.php
We would like to thank the MRC-HGU for helping to fund this Workshop.