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Two related articles in the December 2005 issue of Plos Computational Biology describe the state of the art in biomedical ontologies and where they might be going in 2006. The first is a report from the Eighth Annual Bio-Ontologies Meeting at ISMB 2005 which reviews current uses of biomedical ontologies while the second is a plea stating its Time to Organise the Bioinformatics "Resourceome" using ontologies. In the second of these papers, the authors Nicola Cannata, Emanuela Merelli and Russ B. Altman boldly state that the three "initial steps toward a bioinformatics resourceome are clear". These three steps are:

First, an overall ontology with the high-level concepts (algorithms, databases, organisations, papers, people, etc.) must be created,

This is important, but probably non-trivial to achieve. At least some if it has already been done, e.g. the Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers and the The Molecular Biology Database Collection: 2006 update have already classified resources available. Semantic Webheads would probably argue that the world would be a better place if these classifications of databases and web servers were expressed using the Web Ontology Language (OWL) or its poor cousin RDF... Following that, the next step is:

Second, a mechanism for people to extend this ontology with subconcepts in order to describe their own resources should be designed.

Most ontology languages allow you to do this in various ways. Getting people to use existing ontologies is much more difficult though...perhaps more of a social problem than a technical one? The final step is:

Third, the formats for the ontologies and the resource descriptions should be published so enterprising software engineers can create interfaces for surfing, searching, and viewing the resources.

It sounds deceptively simple. Lets hope 2006 will see significant progress towards this goal, it looks like the (Inter?) National Centre for Biomedical Ontology will play an important role in achieving this.