Drosophila anatomy ontology
This work is licensed under a Creative Commons Attribution 4.0 International License.
The Drosophila anatomy ontology is a query-able reference source for information on Drosophila anatomy. It also provides controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotypes and images. It was originally developed by FlyBase, who continue to maintain it. A number of other projects use this ontology for annotation and to drive their query systems, including Virtual Fly Brain (VFB), FlyProt and RedFly. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature.
This ontology is developed in the web ontology language OWL2. Its extensive formalisation in OWL can be used to drive sophisticated query systems. This is well illustrated by the query system on VFB. Direct queries of anatomy on this site can be used to search for neurons by their innervation or fasciculation patterns. For more details please see references 1 and 2 below. For examples of OWL-DL queries, please see our query guide.
This ontology is freely available under a CC BY 4.0 license. Please see our download guide for details of the various available versions. Please see our attributions page for details of how to acknowledge us for its use.
The Drosophila developmental ontology was previously also maintained in this repository, but has been officially released as a separate project since 25 July 2019 and can now be found here.
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We encourage anybody who uses this ontology, either directly or via the resources that use it, to help improve it by requesting additions or changes. Simply make a new issue on our tracker to request new terms or to report synonyms, references or problems with definitions or relationships.
Publications
- Costa M., Reeve S., Grumbling G., Osumi-Sutherland D. (2013) The Drosophila anatomy ontology. Journal of Biomedical Semantics 4(32).
- Osumi-Sutherland D., Reeve S., Mungall C., Ruttenberg A. Neuhaus F, Jefferis G.S.X.E, Armstrong J.D. (2012) A strategy for building neuroanatomy ontologies. Bioinformatics 28(9): 1262-1269.
- Milyaev N., Osumi-Sutherland D., Reeve S., Burton N., Baldock R.A., Armstrong J.D. (2012) The Virtual Fly Brain Browser and Query Interface. Bioinformatics 28(3): 411-415
- Grumbling G., Strelets V., The FlyBase Consortium (2006) FlyBase: anatomical data, images and queries Nucleic Acids Res. 34(Database issue): D484–D488
Funding
Development of the Drosophila anatomy and development ontologies has been funded by:
- A series of grants to FlyBase from the National Human Genome Research Institute at the U.S. National Institutes of Health, the most recent of which is #U41 HG000739.
- An Isaac Newton Trust grant to Michael Ashburner to fund the work of David Osumi-Sutherland, awarded in 2007: Standardising the representation of Drosophila anatomy and development for databases.
- BBBSRC:BB/G02233X/1, awarded in 2009 to J.Douglas Armstrong, Michael Ashburner and David Osumi-Sutherland: Structured and graphical queries for Drosophila neuroscience data.
- An Isaac Newton Trust grant to Cahir O'Kane to fund the work of Marta Costa, awarded in 2012: Neuroinformatic identification of new types of neuron in the Drosophila brain.
- Wellcome Trust: Virtual Fly Brain: a global informatics hub for Drosophila neurobiology (WT105023MA) 2014-2017; Virtual Fly Brain (Grant ref: 208379/Z/17/Z) (October 2017 to September 2021)