Slow spell

Not as much to report recently, though there has been some Arachnolingua work.  The promised update of NCBI taxonomy hasn’t made it to release yet, so I’ve been concentrating on supporting non-NCBI taxa on both the curation side as well as the OWL generation side.  This will probably also be the mechanism I use for introducing taxa that aren’t Arachnids but relevant to Arachnid behavior (predator, prey, substrate, etc.) since I don’t really want to manage all of NCBI (or even NCBI pruned of all the non-organismal taxonomic terms).  The changes to Arachadmin are partially done and working, though merging these into the set of available terms at least needs some testing with actual curation of behavior.

I’ve also added the Environmental Ontology (EnvO) and the Population and Community Ontology (PCO) to the set of support ontologies.  The former will, hopefully provide some substrates as well as conditions that might affect behavior.  The PCO provides terms for populations (and groups of e.g., social spiders) and will provide a link between population level processes (e.g, juvenile dispersal) and individual behaviors (e.g., ballooning).  I have been somewhat involved in the later, and had the pleasure of meeting the main developer of EnvO, Pier Luigi Buttigieg, at the February RCN summit.

The other task I’ve been working on is getting the OwlTools incorporated into the OwlBuilder generator.  I seem to have resolved my maven issue, at least for local builds.  I still need to figure out if I can define the project to allow maven to find the OwlBuilder repository somewhere when I try building on Travis.  That still remains, as does integrating the ontology release tool with my own code.  Although arachb will never actually be an OBO ontology, many of the OBO foundry standards are relevant and appropriate and if I can automate compliance with as many of their standards as possible, it will be a good thing.

Finally not much progress on the annotation semantics work.

Arachnolingua was not affected by the HeartBleed bug we all heard so much about this past week.  Arguably this is for all the wrong reasons.   Arachnolingua doesn’t use SSL directly or even have certificates;  if the resource were actually authoritative about something, it would be worthwhile to support secure communications to prevent man-in-the-middle spoofing.  Likewise, Arachadmin could be set up as a real web tool with authorized curators and the like, but the need for such has not presented itself, though if the right people were interested…  So, because SSL isn’t used, Arachnolingua wasn’t affected.  Nevertheless, I did update the server to the patched version of the SSL library.  Meanwhile, it looks like I should update my other passwords (AWS, Namecheap, here, etc.).  Some of these have already been fixed.

I’m already looking forward to the summer – Evolution2014/iEvoBio and Animal Behavior 2014.  Plan is definitely to do a lightning talk for iEvoBio and either a different lightning talk (different audience and emphesis) for Animal Behavior, or maybe a poster.  Arachnolingua is alive and well, even if the last few weeks have been a bit of hibernation.

 

 

 

 

 

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