Friday, August 7, 2009

iterating through the low hanging fruit

Perhaps a little behind schedule with the blog post, but we've been busy!

After several weeks of concentrated editing the first "version" of the HAO is in the hands of the folks at the OBO Foundry, to be included as a candidate (it should appear in the next several daysit's here). It was interesting to learn during this process (not process sensu HAO:0000822, but process sensu evo-devo) that no ontology is actually included in the foundry, they are all candidates.

The HAO is indeed a candidate in many senses of the word, this first effort is largely to get the editing team comfortable with the steps it takes to release versions of the HAO, and the basic skeleton logic into the hands of those who can start to provide us feedback. That said, we feel pretty good about this initial effort, even though we have perhaps been gathering the low hanging fruit. We have a full fledged ontology output from a web-based application (albeit with a hack here or two), and around 90% of the terms contain definitions in human-written genus differentia formats. We've also generated HAO ids for over 1000 terms, which is an important first step towards allowing others to reference fixed points in the ontology in meaningful ways. Perhaps most importantly, we have a product that people can begin to provide critical feedback on, like "where's the nervous system" (our first comment from a non-project member, it's not in there...yet). We're depending on this feedback, both from experts on ontologies in the broader sense, and from morphologists with much more experience than us.

Along with work on the HAO itself has come some feature development for handling the ontology. We're using tags to comment and annotate the HAO. Tags in mx contain a keyword, and an optional pointer to a reference, and option comment or "value". To make tags more useful on a day to day basis we hacked up a tag browser (see above) which lets us quickly return sets and then navigate to the results.

We also generated a quick tree viewer to browse through the ontology. Watch for a public version of the viewer to appear on the glossary in the following months. The tree gives us context, allows us to quickly edit the definitions, and we can drag terms to add relationships.


  1. Glad you started a blog about the project.

    For those biologists with little understanding about the basics of ontologies (e.g., how does one gets to use one for taxonomic or morphological work), would you consider including some educational posts here and there?

  2. Absolutely. We have a long queue of fun morphological problems that continue to emerge from this process, examples of ontologies in action, and ideas for products that will result from our collective synthesis of multiple domains. We'll use this space for at least some of those discussions, and we'd love to get feedback from potential users, like you (we need to involve more ant experts!)