Thinking Clearly .

Two articles for Monkey Monday.

Science Daily summarizes an interesting study which compares the frequency of positive Darwinian selection in the development of the human and chimpanzee genomes since we diverged from a common ancestor 6-7 million years ago. One could interpret this to mean that chimpanzees are more advanced (or at least are more evolved) than their naked ape cousins. Full text of the journal article is made available by one of the authors.

This article appearing in the American Naturalist sates my interests in both great apes and infectious disease outbreaks. The report details observations of potential ape to ape (sometimes inter-species) transmission of Ebola, based on exchange of bodily fluids and the primate habit of inspecting carcasses of peers and rivals. Fascinating stuff, also available in a much abridged form.

And before someone points out that apes aren’t monkeys and don’t satisfy the requirements of Monkey Monday, here’s a bonus link, a beautiful male diademed sifaka, courtesy of the Duke University Lemur Center. The species is native to eastern Madagascar and is endangered.

In our work for NCI, I had the distinct “pleasure” of being the UI guy for the project, a role I find myself in more often these days.  Despite the vagaries and headaches that come with writing Java UI’s, I got the easy part of the deal.  I got to write Swing code while Mike and Evren did some amazing, but difficult work on Pellet.  And while I’m thinking of it, they should be applauded, they did a fantastic job on Pellet.  Anyway, the catch was the UI had to come in the form of Protege tab plug-in.  In the past I’ve done my best to not use Protege, but I was interested in finally using and dissecting a tool that many people use on a regular basis, including the folks at NCI.

Without going into extreme gory details of the work, I have a few thoughts on the ordeal.  I was dismayed by the lack of documentation on how to write your own Protege plug-ins and how to work with the Protege core in general.  There was a short blurb on their site, and some javadocs, but not much else.  Fortunately, coding from javadocs is not a foriegn concept, so I was able to piece together what needed to happen.  And the source is publicly available which was really invaluable.  I unfortunately recieved no support from the mailing list.  I guess perhaps it’s geared more toward users than developers.  So much of the first few days of work were spent fumbling in the dark.  But I eventually pushed through it and got things working.

I was surprised by how many default widgets were supplied with Protege.  Once I got up to speed and figured out how to get a tab installed, I was actually able to drop in a class tree and some list boxes populated from the tree without a whole lot of trouble.  However, the widgets did not seem designed for developers to be able to customize easily.  I could not find a trivially easy way to make the class tree just a plain tree.  I did not want any of the editing functions normally associated with the class trees in other tabs.  Same for the list boxes.  I just needed them to show a list of elements and respond to selection events, I did not need any of the editing features.  Also frustrating was some of what I would consider key functionalities where not present, or no-ops in the default implementation, such as the clearSelection function on the list boxes.  Again, more time spent customizing stuff.  Later in the process, once I had a working draft, I did try some of the widgets from the OWL plugin, which I had a little more success with, but not much.

All in all, the experience was less painful than I expected it to be.  The code definately came together quicker that I originally thought.  But if I was going to do it again, I’d definately consider coding bits of it from scratch rather than using widgets from the core codebase.  I struggled at times for too long trying to overcome some of the over-engineered bits of Protege.  All of this work has made me interested in the Protege 4 effort at Manchester.  I have yet to play with their beta, but I’ve heard some good things about it already, and I look forward to mucking about in their code and fiddling with the tool.

Until next time, stay classy cyberspace.

NASA has an inconceivably annoying amount and diversity of data (these are good problems to have; but, damn, they’re hard); and the Agency is likely to have more management obligations that it has to satisfy with less budget. But at least it’s only nearly everyone in the world who’s interested in NASA’s core data!

Ouch. Ouch!

This week I’m spending most of my time at a NASA Enterprise Architecture meeting out at UMD; imagine: lots of smart people in a room trying to figure out how to do more—in some cases, a lot more—with less, sometimes a lot less. That sucks in the small, but it’s exciting in the large.

SemWeb mavens will be happy to know that ontologies are playing a growing role in efforts to manage NASA’s information, particularly around the Data Reference Model part of the Federal Enterprise Architecture. That’s a lot of syllables that come down to how the Agency manages its data across its core lines of business. C&P cares about all of this; but especially the integration and policy management pieces.

There are other technologies in use, of course, it’s not an OWL clean sweep; but it should be happy making to see OWL being used for real problems in the federal space that have everything to do with cool stuff like science (aeronautics, cosmology, physics).

So at least two C&P people have something of an obsession with the great apes and lesser monkeys; I’m ready to grant them semi-legal rights, in fact. They’re as smart as very young human children and there’s little reason beyond mere speciesism to not treat them as at least quasi-persons. (But, eh, I’ll leave the rest of the lecture about the rights of the great apes for another, more appropriate time.)

That being said, I also love nothing more than a commercial featuring a chimpanzee in a business suit with a laser pointer…Oh, the irony.

I’m hereby inaugurating a new C&P weblog feature: Monkey Monday—one of us ape obsessifs will post something of interest about monkeys or apes every (okay, most) Mondays.

This week it’s a nice article about chimps hunting with spears and living in caves.

Please register. Sooner is easier on your poor beleaguered general chair. Also, prices will go up after May 26th, so don’t hesitate.

Through the generosity of KnowledgeWeb, there are student support grants available. There are a limited number, so apply soon.

As I’ve often said, I think OWLED is the best venue for influencing the future of OWL. This is, of course, by design. It’s not perfect, obviously, and it’s not the only way, but everyone there is a committed stakeholder in the success of OWL, many are able to immediately change the state of the infrastructure, and everyone is interested in effecting (beneficial) change. So, come make your experiences and voices heard.

(And register early so I know how many people I have to feed.)