We have also improved our software and data release processes so that the public Knowledgebase can easily keep up with new developments and the latest data updates from our curators. Looking forward, the next major feature to be added to the Knowledgebase is a faceted browsing interface which is currently under development. This interface should help provide an overview of how the data are organized within the various ontologies used in the Knowledgebase.

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. 

You might wonder why this has taken almost a year since we launched Phenoscape in June 2007.  The reason is that until just recently our software as well as ontology development activities have built on existing projects (such as Phenote on the software side or PATO on the ontology side) that already had their community infrastructure, or given rise to new community ontologies (such as the TAO and TTO) that each received their infrastructure within the OBO umbrella.

However, as we start shifting our focus this summer to developing the database and web-based user interface for the EQ data our curators will soon be generating in increasing amounts, our own code repository will be the natural home for much of the code we’ll develop.