The Drosophila anatomy ontology

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.

Using FlyBase, a Database of Drosophila Genes and Genomes

“…2), and are described in full in separate Allele Reports (not shown). FlyBase makes extensive use of controlled vocabularies (CVs or ‘ontologies’) in recording allelic and phenotypic data (13,14). These are collections of related terms (e.g., ‘allele class’, ‘phenotypic class’, ‘fly anatomy’) arranged into parent-child hierarchies.…”

“…The phenotype CV comprises ∼190 terms that are commonly used to describe Drosophila phenotypes, such as ‘lethal’, ‘sterile’, ‘homeotic’ or ‘Minute’ (13). The anatomy CV is much larger, comprising >8,800 terms that can be used to comprehensively describe Drosophila anatomy (14). Both types of CV term can be refined through the use of ‘qualifier’ terms that restrict the meaning of the term to a specific developmental stage, sex or other experimental/genetic condition – these appear after a ‘pipe’ symbol on the website, for example ‘small body | larval stage’.…”

FlyBase at 25: looking to the future

“…Recent years have seen the addition of Gene Group Reports (1), the design of multiple tools to access RNA-Seq data, improvements to FlyBase ontologies (15,16), the incorporation of the Disease Ontology (17,18), the addition of the user–curation tool Fast-Track Your Paper (19) and enhancements to our major search interface, QuickSearch.…”

Exploring FlyBase Data Using QuickSearch

“…Expression data may be searched by developmental stage, gross anatomical structure or subcellular location, or any combination of these. The allowed input terms are from the fly developmental stage and anatomy CVs (Costa et al, 2013) and the cellular component aspect of the GO. The lower panel of the Expression tab allows access to different options for querying or browsing high-throughput RNA-Seq expression data – click the ‘RNA-Seq overview page’ link in that section for further details.…”

“…There is also the option of restricting each search to a particular developmental stage. The allowed input terms are from the CVs used by FlyBase to describe phenotypic class, anatomy and developmental stage (Costa et al, 2013; Osumi-Sutherland et al, 2013). …”