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Bioinformatics Advance Access published online on March 29, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti409
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 17, 2004
Revised January 3, 2005
Accepted March 22, 2005

Article

Formalising concepts of species, sex and developmental stage in anatomical ontologies

Stuart Aitken 1*

1 School of Informatics, The University of Edinburgh, Edinburgh EH8 9LE, UK

* To whom correspondence should be addressed.
Stuart Aitken, E-mail: stuart{at}aiai.ed.ac.uk


  Abstract

Motivation: Anatomy ontologies have a growing role in bioinformatics - for example, in indexing gene expression data in model organisms. To relate or draw conclusions from data so indexed, anatomy ontologies must be equipped with the formal vocabulary that would allow statements about meronomy to be qualified by constraints such as part of the male or part at the embryonic stage. Lacking such a vocabulary, anatomists have built this information into the structure of the ontology or into anatomical terms. For example, in the FlyBase anatomy for drosophila, the term larval abdominal segment encodes the stage in the term, while the terms male genital disc and female genital disc encode the sex. It remains implicit that a fly has one and only one of these parts during its larval stage. Such indicators of context can and should be represented explicitly in the ontology.

Results: The framework we have defined for anatomical ontologies allows the canonical anatomy structures of a given species to be those common to all sexes, and to have either male, female or hermaphrodite parts - but not combinations of the latter. Temporal aspects of development are addressed by associating a stage with organism parts and requiring a connected anatomy to have parts that exist at a common stage. Both sex and anatomical stage are represented by attributes. This formalisation clarifies ontological structure and meaning and increases the capacity for formal reasoning about anatomy. The framework also supports generalisations such as vertebrate and invertebrate, thereby allowing the representation of anatomical structures that are common across a sub-phylum.

Availability: http://www.aiai.ed.ac.uk/resources/bioinf/.


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