A Beginning

This really isn’t the beginning.  Arachnolingua came out of a discussion at the February 2011 Phenotype RCN which lead to me proposing to collect a set of terms describing spider behavior so that existing behavior ontologies (at that time only the ABO core, NBO was not initiated until later that spring).  Since then, I constructed a (non-functional) front page and built a OWL file with Protege that used Ontofox to mireot terms out of several ontologies (especially NCBItaxon, Spider anatomy, IAO, as well as NBO as it developed).  I presented a lightning talk about this first stage at the 2012 iEvoBio meeting in Ottawa.

The slides for that talk made their way on to slideshare, and and were subsequently cited in an overview chapter by Melissa Haendel and Elissa Chelser.  If you go to the site front page today (June 2013), little has changed, just a few spelling corrections, and a new page for status queries on the backend triple store.

Of course there was no backend triple store last year.  All the semantic content on the site consisted of a collection of owl files, the most important of which was a first pass at representing behavior descriptions in OWL using vocabulary primarily from the OBO Information Artifact Ontology.  There were also 6 import files that I generated using the Mireot capabilities of the OntoFox tool.  Unfortunately, due to DNS issues, you couldn’t even load the complete ontology into Protege from the site (that has been subsequently fixed with the addition of the arachb.org alternate domain).

Meanwhile, I’ve also been collecting target papers mentioning spider behavior (currently about 500).  Some of these are complete ethograms, some are on other topics that contain brief mentions of a spider behavior pattern in passing.  Although the former are more immediately interesting, including the others are potentially more valuable just because of their obscurity.

The list (originally a spreadsheet) is now mostly moved to a mysql database, which isn’t visible from the site, but is used to generate the ‘new’ version of the semantics.  Some of the papers in the collection have made their way on to the Mendeley Spider Behavior group (after some vetting).   I just noticed that I am rather behind on this push process.

Meanwhile the real curation work consists of extracting assertions about spider behavior (more about those later) and putting those in the database.  These are coming more slowly and the design of the ‘assertion’ table is, unsurprisingly, driven by what the generated OWL will look like.

After an abortive attempt to build a java tool to maintain the database (I’m rather tired of swing and building new java desktop applications at this point) I was introduced to web2py as part of my new assignment with phylografter within the OpenTree of Life project.  I’ve built a tool called arachadmin for entering and editing the database.   I am using java for the generation part, primarily because the OWLAPI and associated tools still seem to be the best option for these sort of things.

That’s enough for now.  Next post I’ll describe what is happening behind the scenes in the site.


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s