Playing with ELK (the reasoner)

It’s been a long slog the past few weeks.  I’ve been pulling IRI’s for taxon, anatomy, substrates (entities that aren’t part_of an actor) that are associated with participants in a behavior, as well as IRIs for behavior and publication for assertions.  Yesterday, I finally had all (at least most) of the pieces together – I was now ready to start matching term IRIs against the support ontologies and copying OWL ‘entities’ from the support ontologies into the target ontology that will become the OWL file that’s loaded onto the server.

The first step was to merge all the support ontologies and run a classifier over them – primary to determine the class hierarchy.   The merging went smoothly and didn’t take too long, but trying the OWLAPI’s structural reasoner on the 7436381 assertions that resulted from merging the 8 support ontologies seemed a bit too much for it.  After 45 minutes on a 4-core i7, I decided it was time to try something else.

ELK  has been attracting some interest in the biological ontologies community in the past couple of years as a very fast way to do reasoning for ontologies that can stay within the limits of the OWL-EL language profile.  As it turns out, the current version of ELK currently implements only a subset, but that subset is more than sufficient my very limited immediate needs.

The first task for the reasoner was simply to extract the superclass closure (all the classes above) Arachnida in the NCBI taxonomy hierarch, followed by all subclasses of the same taxon.  Those, along with Arachnida itself (which is a taxonomic class as well as a OWL class) are copied into the target ontology, along with the axioms specifying their super/sub class relations and their labels (= Linnean names).

It all works – owlbuilder is generating an owl file that loads in Protege (after making sure the DOI cleanup was getting called in the right place), and contains a couple of other classes pertaining to an as yet incomplete representation of a posture in Tetragnatha straminea.  Nothing special about this behavior or species (surprised the first species wasn’t a jumping spider?), just the first publication that came up in the literature search all those years ago was about a couple of Tetragnatha species.  You’ll be hearing more about this behavior and a couple of other behaviors in this species and some congeners as I fill in the pieces and start pushing real data to the server.

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2 thoughts on “Playing with ELK (the reasoner)

    • Thanks Pavel – ELK is working fine for me, though my present use case doesn’t require any difficult reasoning (mostly extracting asserted superclasses).

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