RCN summit and some updates

I haven’t posted in a while because I was at the Phenotype RCN summit the week before last.  The week started with two workshops covering the Population and Community Ecology Ontology (PCO) and the Biological Collections Ontology (BCO).  I have been interested in the PCO for several years, both because my PhD project involved population level processes (‘culture’ in a population of birds) as well as population related processes in spiders (social spiders, but also predation and predator defense which, by involving multiple individuals are at the boundary of behavior and population/community processes).

One of the high points of the RCN summit was seeing Martin Ramirez again.   He has been continuing to work with the spider anatomy ontology and showed an interesting comparative analysis of complexity of reproductive structures using derived species-level anatomy ontologies.  I also showed him a bit of arachnolingua and we left open the possibility of more collaboration in the coming year.

I also got to have some brief discussions with Chris Mungall about NCBI taxonomy and the possibility of more frequent updates to the generated OWL from the source.  I expect that other projects would benefit from more frequent updates since not many projects are in the position to support a separate taxonomy ontology.

There has also been progress on followup workshops for the NBO.  More here and in the other blog as updates warrant.

Since I returned, I’ve had a couple of hours to clean up a number of issues on the web page: most significantly, I’ve added javascript code to turn the urls in the ethogram results table (currently just the publications) into links.  I’ve also generated simple publication labels (author list + publication year) so tracking the results doesn’t require decoding a doi.  The publication column now shows the label and links to the doi (which works for both publications with annotations in the KB).  Eventually I will change the link to point to a publication summary page which will link to the doi when it is available, but that will remain a low priority until I start annotating publications without doi’s.

An unexpected, but reasonable side effect is the change in behavior of the display of taxa without annotations.  They now treat the purls as links, which unfortunately don’t resolve.  This doesn’t seem to be something to fight, so I’ll convert them into links back to the NCBI taxon page on the fly (just extract the taxon id and generate a new URL).

A more immediate issue is getting the descriptions of the behavior to display.  This isn’t hard, but I’m taking a day or two to give some thought to the best way to model this (the simplest would be an rdfs:label or rdfs:comment on the annotation, but it would be better to use some IAO vocabulary to attach it to the node that represents the individual part of the publication being annotated).

I’ve pulled out the hardcopies of publications I made a year or so back; getting ready for some more sustained curation activity (as well as more changes to arachadmin).