Lots of little things

The pace of Arachnolingua development has picked up a bit.  After adding the first set of annotations for a non-NCBI taxon (Leucauge mariana in a courtship description in Eberhard and Huber (1998) – a rich source of annotatable material), the need to support these curator added taxa more completely became obvious.   The curation side was filling in the details for such taxa – the hook was already there to make a term, but it was not identified as to being a taxonomic name or its source authority (in this case the World Spider Catalog).  That would suffice to make it available as a taxonomy term, but I also needed to add a mechanism to add one or more levels of parentage to connect the term to something already in NCBI.   Fortunately in the case of L. mariana, the parent genus was in NCBI so chaining wasn’t required.  Actually linking via parents was not strictly necessary for the curation process – it just needs to capture the parentage to pass to the OWL generation tool.  Before I finished those changes, the OWL generator created a number of knowledge base files that attached L. mariana to the root OWL term.  This has been finished and L. mariana and a small subset of the behavior patterns documented by Eberhard and Huber are now annotated in Arachnolingua.

I also followed through on a long overdue change that rippled throughout the implementation.  I have been using the term ‘assertion’ throughout the code to refer to a conjunction of taxon, behavior, body part, publication, and eventually evidence.  The problem with calling these ‘assertions’ is simply that the OWL specification talks about assertions that are much smaller – an Arachnolingua assertion can be decomposed into about a dozen OWL assertions or RDF triples (formally an RDF triple is one (probably the most common) way of implementing an OWL assertion.  So, to avoid confusion with assertion (and likewise OWL has a subset of assertions referred to as annotation, so switching the Arachnolingua terminology to annotation would merely change the problem), I started looking for synonyms.

The best synonym for ‘assertion’ that I found seemed to be ‘claim’ – it has the advantage of not sounding definitive and suggesting the need for provenance (taking about a claim leads easily to the question ‘who’s making this claim?’).  Observation was a tempting second choice – most of the ‘assertions’ in arachnolingua are observations, but not all and if I were to use the term observation in Arachnolingua, I would prefer it to refer to claims at the level of individuals – individual spiders doing a particular something on a particular substrate.  So, the software taxonomy, I could look at observations as a subclass of claims – though I haven’t yet seen the need to implement such a subclass.

After going back and forth on whether the switch made sense, I went ahead and implemented it everywhere – curation, database, and owl generator now refer to claims.   In the curation screen, it seemed worthwhile to include observation as that was such a strong alternative:

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Changes like this are ugly, but only get uglier the longer they are put off.

Finally, I’ve spend some time on the query component of the website.  As I’ve described before, I’ve implemented an API that supports queries for the implemented search pages (currently just taxon and behavior).  The API generates SPARQL to query the in-memory Sesame triple store and returns the unprocessed JSON that Sesame generates.  Turning this JSON to results tables is pretty straightforward (though it represents the only ‘production’ JavaScript I’ve written to this point).  The SPARQL query is rather slow, particularly for queries to higher taxonomic groups: queries to Tetragnatha straminea are fast, queries to Arachnida are much slower and definitely not recommended at this time.  I took a long hard look at the SPARQL I had written and found a couple of things I thought would really speed it up – net result was only a 20% speedup for the API call (measured on the browser side using firebug).  I’m pretty sure I need to be traversing the taxonomy more intelligently, maybe using some server side inference.

I also added lexical filtering to terms from NCBI.  There are a lot of ‘taxa’ in NCBI that reflect either samples or unidentified species.   As samples are individuals (or collections of individuals) their identifiers don’t belong in the taxonomy for Arachnolingua’s purposes.  This is completely aside from whether any behavior data was ever collected from these individuals – I tracked down some underlying Genbank submissions and some were from old collaborators and friends in the Maddison lab so there might be some video data for some of these submissions.  The worst offender in sheer quantity was the Barcode of Life and its BOLD submissions.  I know NCBI is planning to move samples to a separate database, I don’t know if this only applies to new records or if existing records are moved, how quickly this will happen.  So best to filter these out consistently in both curation and OWL generation.  Removing these terms did provide some query speedup for the worst cases.

Lots of interesting spider behavior posted to the web in the past few weeks, but this post is already long enough.  I hope my northern hemisphere readers are enjoying the spring as I have.

 

 

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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.

 

 

 

Assertions, participants, and other artifacts

I’ve been quiet for over a month now, though not inactive with Arachnolingua.  I spent the first couple of weeks working through the forms chapter in the web2py book which was helpful both in the context of Arachadmin as well as a couple of issues that came up with the day job.  This was all in support of making a reasonably useful page for entering assertions, which are the primary records for generating behavior instances in arachnolingua.  Along with the web2py review, there was a fair amount of database redesign as I worked through the relation between participants (animals, their parts, and environmental substrates).  Participants might be individuals or quantified (e.g., some Habronattus californicus, portion of substance granite).  While animal and term terms come easily from existing taxonomy and anatomy ontologies, environmental participants will require pulling terms from one or more environment related ontologies.  Since it looks like I have an invite to the next Phenotype RCN in February, which will focus on environment, I should have an opportunity to size up the options.

Once I had a basic version of the assertion page up (no screenshots yet, it’s very much a work in progress), I started realizing just how long the drop down list for taxa would be.  I’ve not doing anything fancy with text completion (haven’t had any success with the text completion widget in web2py), so making taxon selection more manageable has focused on reducing the length of the list by filtering out irrelevant terms.  NCBI taxonomy, as anyone who has worked with term exports knows, contains, in addition to Linnean terms, identifiers for incompletely identified samples (e.g., Lycosidae sp.) which will often include lab identifiers.  Since these deposits are very unlikely to form the basis of any behavior observations, I’ve implemented filtering, currently just removing any children of nodes with labels of the form ‘unclassified x’.  This does not remove all the problem terms, the messier stage of filtering out terms by regex matching against labels will wait for another day.