Monday, July 20, 2009

Towards HAO 0.1

One central premise we're following is to release early, release often. Given this we're planning to release a very early draft of the ontology within the next week or two. We hope that releasing an early draft will drive feedback early on in the projects lifespan. The first releases will undoubtedly contain errors and glaring omissions, but it will also let people start to use the real meat of our project, the ontology itself. The first draft will only include two relationship types (is_a, part_of). As the project continues we'll consider and adopt others (has_part?), there is much talk of integrating spacial relationships (in_contact_with, adjacent_to), but these will have to be carefully reviewed.

To accommodate the editing, review, and tweaking of the ontology we're also starting to ramp up the patches to mx, the underlying editor that we're using to build the ontology. These changes are posted immediately to our SVN repository on Sourceforge (yes, we're considering a move to git). In the future, we plan to split the ontology code out of mx and turn it into a gem (plugin) that any Rails project can easily use.

Curation of the ontology is currently focused on updating all the present definitions to a genus-differentia style, and cross referencing terms to other ontologies. One stumbling point we're hitting is what to do with accented characters, since the OBO specs don't presently permit them.


  1. Hi there,

    Looking forward to seeing this ontology. Would be good to compare methods for structuring insect anatomy ontologies. BTW, are you doing any development in OWL?

    David OS (Ontologist for FlyBase anatomy and Virtual Fly Brain)

  2. Looks like we overlooked your comment here. We haven't done any development in OWL, though we will be exploring this in the future. Our ontology is completely built in mx now, and the OBO syntax is a somewhat easier target to output to. For someone in the know it should be quite easy to write a OWL style dump of our present data for mx, of course this would only include very minimal support for OWL features. Because our ontology is relatively straightforward in its present format I think the OWL2OBO translators should do fairly well if you want to explore it in OWL tools.

    As mentioned elsewhere we will have a post doc, Matt Bertone, assigned full time to aligning the HAO with other insect/arthropod ontologies. Since we're relatively new at this we'll definitely be in touch with you regarding how best to approach this.