Taxonomy as ontology: opening up the debate

We have created a new mailing list, obo-taxonomy, under the OBO (Open Biomedical Ontologies) umbrella. Our motivation for this new forum is to really open up the discussion surrounding the issues of what should be a proper ontological representation of taxonomy and phylogeny, for example proper semantics of the relationship between taxonomic groups, and between specimens and species. If you care about or have thoughts or opinions on these and related questions, we encourage you to subscribe to this new list.

One of the key components in our efforts to code the evolutionary diversity of phenotypes in a semantically rich and explicit manner is to have species or higher-level taxa be terms from a logically consistent ontology. Eventually we will want to reason over taxonomy ontologies and entity-quality statements to infer the evolutionary change of phenotypes between different clades of fishes, and hence the semantics of a particular ontological representation of a taxonomy or phylogeny will have bearing on the kind of inferences we will be able to make. It will probably come as no surprise that we have since found ourselves discussing the issues and what they might mean for us in quite some depth (see for example Peter’s previous post on how we built the first version of the TTO, and our work in progress on the Taxonomic Rank Ontology).

It turns out that questions of using a hierarchical controlled vocabulary or ontology to denote the taxonomic species is coming up on an increasing basis in the contexts of annotating biological experiments, observations, comparative analyses, and results, and probably elsewhere too. In fact, creating this group was instigated by a conversation about the NCBI taxon ontology within the OBI (Ontology of Biomedical Investigations) Biomaterials group.

As an aside, for those of you who dislike the SourceForge.Net mailing list interface, the list is mirrored as a Google Group, and you are welcome to use the Google Group interface to subscribe or post. 

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