Abstract
BackgroundAnatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmatically accessible forms. They are also frequently used to group annotations in biologically meaningful ways. Accurate annotation requires clear textual definitions for terms, ideally accompanied by images. Accurate grouping and fruitful programmatic usage requires high-quality formal definitions that can be used to automate classification and check for errors. The Drosophila anatomy ontology (DAO) consists of over 8000 classes with broad coverage of Drosophila anatomy. It has been used extensively for annotation by a range of resources, but until recently it was poorly formalised and had few textual definitions.ResultsWe have transformed the DAO into an ontology rich in formal and textual definitions in which the majority of classifications are automated and extensive error checking ensures quality. Here we present an overview of the content of the DAO, the patterns used in its formalisation, and the various uses it has been put to.ConclusionsAs a result of the work described here, the DAO provides a high-quality, queryable reference for the wild-type anatomy of Drosophila melanogaster and a set of terms to annotate data related to that anatomy. Extensive, well referenced textual definitions make it both a reliable and useful reference and ensure accurate use in annotation. Wide use of formal axioms allows a large proportion of classification to be automated and the use of consistency checking to eliminate errors. This increased formalisation has resulted in significant improvements to the completeness and accuracy of classification. The broad use of both formal and informal definitions make further development of the ontology sustainable and scalable. The patterns of formalisation used in the DAO are likely to be useful to developers of other anatomy ontologies.
Highlights
Anatomy ontologies are query-able classifications of anatomical structures
We only include named classes where there is good scientific evidence for the presence in wild-type animals of structures with the properties described in both formal and informal components of the class definitiona. Access to this evidence is provided by links to the relevant literature and sometimes in the form of free text summaries provided as a comment separate from the class definition
In order to conform to this inclusion criterion, we have occasionally obsoleted mistakenly added classes that refer to structures not present in wild-type Drosophila
Summary
Anatomy ontologies are query-able classifications of anatomical structures They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmatically accessible forms. They are frequently used to group annotations in biologically meaningful ways. A query for genes expressed in the Drosophila leg would return gene expression annotated with the term middle leg (a subclass of leg) and claw (a part of the leg) as well as with the term leg The usefulness of such grouping depends on the accuracy of classification and of assertions about partonomy. Virtual Fly Brain (VFB) groups annotations based on inference of overlap between neurons and gross neuro-anatomical structures as well as using partonomy and classification [5,6]
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