The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

We defend the fundamental ontological-pragmatic principle that where there are continua in reality science is often forced to make partly fiat terminological delimitations. In particular, this principle applies when it comes to describing biological organisms, their parts, properties, and relations. Human-made fiat delimitations are indispensable at the level of both individuals and the natural kinds which they instantiate. The kinds of pragmatically based ‘fiatness’ that we describe can create incompatibilities and lack of interoperability even between properly designed ontologies, if not (...) appropriately handled. (shrink)