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Developer Guide
Uberon is represented using the Web Ontology Language (OWL), so any API that works with OWL will work for Uberon. In practical terms, this usually means the java OWLAPI or some API layered on top of this such as OWLTools, The Brain or Scowl.
OWL has a representation in RDF, so any RDF API will work, as will the query language SPARQL. However, for certain kinds of operations on Uberon, RDF can be quite a low level means of access
Often, knowing OWL or RDF is not enough in itself; it's necessary to know how Uberon models anatomy and corresponding metadata in OWL. For the most part, Uberon uses standard patterns as seen throughout the whole OBO Library, and in anatomical ontologies in particular. However, Uberon incorporates a number of advanced features not seen in other ontologies, the documentation on the Uberon site is intended to cover these cases, but documentation may not be complete so please contact us with any information.
If there is sufficient demand, we will also release Uberon in more developer-friendly formats such as JSON. We provide obo dumps of most artefacts as that is what many bioinformatics developers are used to.
Note that it is useful to draw a distinction between APIs that provide access to the ontology itself vs those that allow access to the ontology plus some associated data.
Note that in many cases, the API may only provide access to some subset of the ontology - to ensure complete access, use the OWL from the Uberon site and a fully functioning OWL-DL Application Programmer Interface.
TBD
TBD
Please use the Uberon tracker for any issues or questions.
Uberon is a multi-species anatomy ontology and knowledge base, find out more on the home page