Phenoscape visits Xenbase for Anatomy Ontology Update

Last month I visited Xenbase and Aaron Zorn’s lab at the Cincinnati Children’s Hospital for a couple of days (August 21-23, 2011) to work with Xenbase curators in preparing the Xenopus Anatomy Ontology (XAO) for its next big release.  Xenbase curators Christina James Zorn and VG Ponferrada have been leading the effort, and Erik Segerdell, the ontology development coordinator for the Phenotype RCN and former Xenbase curator, was also visiting for the week and helping with the update. Erik and I provided training in ontology editing and synchronization tools.

We used the Synchronization Tool (an Obo-Edit plugin) to compare XAO to several external ontologies. The tool made it efficient to find and add missing cross-references and terms, and to resolve conflicting data (e.g., differing definitions). By the end of the week, we updated XAO with all relevant terms from the Amphibian Anatomy Ontology (AAO), Vertebrate Anatomy Ontology (VAO), Uber Ontology (UBERON), and Common Anatomy Reference Ontology (CARO).

Erik, VG, and Christina worked hard the rest of the week to make XAO is_a complete and to update definitions, relationships, and synonyms for existing terms. With XAO’s new release, the ontology is now 25% larger than before. The newest version of XAO will be available for downloaded soon from the OBO Foundry.

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