Tool support for Instances
Instances in Phenoscape Ontologies/Vocabularies
Several Phenoscape ontologies, particularly the TTO and the Fish Collection Ontology, might more appropriately represent their contents as instances or individuals. Unfortunately, the current versions of OBO-Edit (either 1.1 or 2.0Beta) do not support creating, editing, or viewing OBO Instance Stanzas. Additionally, current OWL/OBO conversion tools ignore instances when converting. Hopefully, a future version of OBO-Edit will support editing and reasoning with OBO Instances. However, at present (21 August 2008), adding such support to OBO Edit 2.0 would further delay the release process and providing this support as an OBO-Edit plugin would likely be buggy. Therefore, the interim solution to this problem will consist of a user defined instance_of relation (which should xref to OBO_REL:instance_of). This relation will allow creation of OBO child terms related to parents by instance_of. An outboard conversion utility will convert terms that are linked as children of instance_of relations back and forth between Instance and Term stanzas in the OBO file. To view an OBO file with instances, a user would run the tool to convert instances to terms, creating a new OBO file which OBO-Edit could display fully. Any changes to this file would require running the tool to convert in the opposite direction to restore the instance stanzas.
Since the OBO backend supports instance round-tripping, making modified versions of existing generation tools (e.g., TTOUpdate) that use instances when appropriate should not be unnecessarily difficult.