It’s Darwin Day – I’ll celebrate by updating the site

I’ve spent a couple of hours cleaning up the arachnolingua site.  In particular, the link to the old ontology file is gone from the top menu bar – that file hasn’t been valid in nearly a year and even the current file doesn’t deserve that level of billing.  If you want to see the OWL file, there is a link on the project page (available from the ‘about’ menu item).  The new OWL file is, I’m happy to announce, a reasoned over version, with inferred axioms covering  inferences of subclass, equivalent class, and class assertion being added to the ontology.   ELK didn’t complain (unlike when it reasons over the mashup of supporting ontologies) and a quick inspection in Protege showed no apparent changes when the resulting ontology was re-reasoned with FACT++ (unlike when the unreasoned ontology was loaded – several top level classes disappeared after reasoning).  The lack of improvement resulting from reasoning in Protege doesn’t say much about FACT++ vs. ELK, simply that the KB is expressively simple enough that it is covered by the portion of OWL-EL that ELK reasons over.  It’s also still quite small, so the speed advantage of ELK isn’t very obvious in the second pass.  Hopefully arachb will keep growing past the point where this is no longer the case.

The project page has also been updated to link to the source ontologies directly rather than the MIREOT’ed owl files that went with the old KB file.  Perhaps these and other questionable links have something to do with all the hits on the projects page (and only the projects page) from Russian sources that my logs the past week or so have been showing.

The other big change is the attention I’ve given to the taxonomy status page.  First, a word of explanation: the taxonomy status page is a list of taxa I’ve encountered during curation (so the publications listed on this page have undergone some review and behavior annotation and will likely be the next ones to appear in the KB) that do not appear in the NCBI taxonomy.  The list here is over a year old, but none of the names listed here have appeared in the intervening months.  In some cases (e.g., synonymy) this is to be expected.  In any case, I’m using the World Spider Catalog as my authority for cases where names don’t appear in NCBI.  Because the WSC text pages don’t contain full species names and lists of genera are split by family, I’ve used wikipedia and EoL to get family names for these taxa.  Looks like this may trigger some EoL contributions on my part.

In any case, enjoy and feel free to comment on what you see, suggest papers to review (or bump up the queue) or any other suggestions.

 

 

 

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A couple of new papers

I haven’t been as active in adding papers recently – I collected a fair number during my time at NESCent, and I’ve been more focused on getting something to work and starting to work through the curation backlog.  Nevertheless, I added a couple of papers on spontaneous male death in different groups of spiders today (Schwartz et al. 2013 and Foellmer and Fairbairn 2003).  At least in the Fishing spiders studied by Schwartz, the situation is more a case of self incapacitation which facilitates post-mating cannibalism than immediate death as a result of copulation.  I went ahead and pushed these to the Mendeley group – apparently the first update to the group in over a year.  I need to do something about that.

On the software side, updated database query methods so the existing unit tests will work (mostly related to the schema change from term_usage to assertion).