Wednesday, September 23, 2009

visualizing the HAO

A sneak preview of a HAO and protovis mashup. This is the "is_a" tree.

Friday, September 18, 2009


A short update on the status of the HAO - Our progress since has largely been technical, with some major improvements to how we manage getting new versions of the HAO out of mx. These changes allow us to more confidently generate new versions, with less fear of there being logical problems with the output. In addition, a new version of the HAO has been committed and should appear shortly, thanks to those of you who caught problems with it and notified us of them.

Another important update includes handling "obsolete" tags, which are required when we make a term that has an HAO id a synonym of another term. We're already confronted with questions like like these - How do you determine which term is the right one? Why is this term obsolete? - from our colleagues.

Synonyms and obsolete status, from our perspective at least, are not quite as big a deal as our users might feel, largely because they are meant to indicate a particular status to parsers reading the ontology (i.e., machines) rather than acting as decisions or recommendations to our users. The HAO has to be a logically consistent entity that is largely focused on defining and capturing anatomical classes. The particular labels we give to these classes are not necessarily as important as how we define the class. I.e., if a bunch of hymenopterists can agree on what that their colleague means by "that little point bit over there," then well over half the battle is won. By obsoleting or synonymizing a term in the HAO we are saying that two or more classes in the ontology are really the same thing, i.e. "that little pointy bit over there". It just happens that we need at least one label for a given class, this is often called the "preferred term" in ontology-speak, but we have to be careful to not worry about this semantic. We're not saying "You, hymenoptera taxonomist, don't use that word!" We're saying if you use that word, we're going to redirect you to more information about the "little pointy bit" others are talking about.

Several other cosmetic, and work flow related changes have been made to mx. We've made it easier to navigate back and forth across synonym tags. We've also formalized the Tag object in anticipation of creating links to external resources, including on data to the BHL and HOL digital literature databases.