My Evolution 2009 Highlights Saturday

Well, time to write this up before it gets too stale. First, what I missed: I heard about the talk on snakes that are specialized snail predators, but not until the next day. It has been covered elsewhere (e.g., Denim and Tweed) , so enough said.

I spent Saturday morning jumping around - caught David Wilson's opening talk and part of Peter Richerson's talk on gene culture evolution in the EvoS symposium. As someone doing a thesis project on social learning and culture in the 1990's the Boyd and Richerson book was required reading, so I wanted to hear what Richerson had to say. Sadly, he seemed to still equate culture with information passed by social learning, a view that the mainstream passed by a while ago. Social learning is an important component of culture, but is certainly not sufficient, either for chimpanzees or scrub-jays to be considered cultural creatures. Speaking of scrub-jays, I left the Richerson talk to catch the Aphelocoma divergence and speciation talk by John McCormack, a post-doc in Lacey Knowles lab. The only talk I remember from the later Phylogenetic methods section was the SATe talk, maybe because Jiaye Yu, in the Holder lab, has spent some time recently with it, even though he wasn't involved in this particular talk.

Saturday afternoon I spent in the Diversification symposium. Since I have been involved with BiSSE, I figured I should catch up a bit on the field. Of course, the Rich Fitz-John talk at the end (not listed in the program) was the most relevant. Rich has developed an implementation of BiSSE in his R package Diversitree, which besides the likelihood approach that we implemented in Mesquite, also includes an MCMC estimator, as well as his forward simulation method for dealing with missing tree structure (in press in Syst. Biol.) Rich also has a BiSSE-like method for continuous traits from which he showed some preliminary results in his talk. Very cool stuff.

All the talks in the Diversification symposium were good, and seeing the range of approaches was useful for me. I knew something of Dan Rabosky and Mike Alfaro were up to, since I had met them at the NESCent R-hackathon in December 2007. I am gradually getting more comfortable with R, I just keep telling myself that behind all those arrays and vectors, there's a Scheme dialect, but it hasn't gelled just yet.

I talked with Rich FitzJohn after the session, mostly about optimization issues and his continuous method.

This summer

I'll be attending two meetings this summer: Evolution 2009 (Moscow ID) 12-16 June and ICBO (International Conference on Biomedical Ontologies - Buffalo NY) 24-26 July. I'll be presenting some of my recent work with BiSSE at the Evolution meeting (my first non-ontology talk for a while) and representing Phenoscape at ICBO with a poster. Of course the rest of Phenoscape will be at ASIH in Portland while I'm in Buffalo, but it made sense to have Phenoscape represented both places. I'll miss Portland, but Evolution is there next year.

I'm mentoring another Google summer of code project - my student will be developing a Mesquite package that will read and display Phenex annotations to character matrices. Getting Phenex to talk to Mesquite is an important, relatively low-hanging fruit for Nexml to enable, and just the sort of thing I've been trying to do with Nexml for a while now.

I will be leaving Kansas at the end of August and headed (indirectly) to NESCent to start an ontology alignment project. I'm hoping to develop something that might be useful as a prototype both to Phenoscape as well as a core component to EthoOntos, the comparative method backend to OwlWatcher.

Minor Ethotools updates

I've put up in-progress versions of the updated OwlWatcher manuals (both pdf and html). There are also some minor site updates. Nothing profound, but perhaps useful if you're trying the release candidate.

It is (sort of) done

I've posted Windows and OSX versions of a release candidate for OwlWatcher 0.040. Despite the small version number bump, this release does represent substantial changes and, I hope, improvements. In addition to switching over to the Manchester OWLAPI, there are improvements to project management and video playback. I made this a release candidate because there seem to be people using OwlWatcher and I'm dubious about backward compatibility, so by making this a release candidate I hope people will approach this with more caution and make backups of their work before trying this.


New Project Tab View

New Watch Tab View

OwlWatcher and Mesquite releases coming soon

Wayne Maddison has released a beta of Mesquite 2.6 and I think I have finished the transition of OwlWatcher to the OWLAPI. I will be adding a bit of functionality to OwlWatcher before I release, so except the official release of Mesquite 2.6 and OwlWatcher 0.04 about the same time.

I'll have some comments on Mesquite 2.6 later this week. The existing PDAP:PDTREE seems to work fine with the beta of Mesquite 2.6 so there won't be any immediate PDTREE update.

OwlWatcher and Individuals

I've been poking away at a new version of OwlWatcher that uses the University of Manchester OWLAPI as a replacement for Jena. I have had discussions with several people who suggest that Description Logic (DL) based languages are inappropriate for representing processes, such as behavior. Although I think I understand those concerns, I am pressing forward with OWL as the representation language because the issues that lead me to choose OWL haven't really been resolved:

1. General availability and a large user community
2. Support for individuals

OWL, augmented, either with custom reasoners or a rule-based extension such as SWRL, still seem to be the best choice. The alternatives, that I have considered are:

• OBO
• Common Logic (CL) or similar
• CYCL
  

Let's review the alternatives:

OBO - This is the serious competitor, and it maybe that the backend (aka EthOntos) will be based on the OBD platform that BBOP is developing. Actually part of my reason for moving from Jena to OWLAPI is the built-in support for exporting to OBO. I hope they continue to support this - the only existing outboard translators seem to only support OBO Format v 1.0, which doesn't support individuals at all.

This brings me to the other problem with OBO - weak support for individuals. Although version 2 of the OBO Format includes a stanza type for individuals, no version of OBOEdit does anything more than roundtrip them at this point. Furthermore, OBD seems to be moving toward a 'T-box in the A-box' approach. This is a fancy way of saying that classes and class-level relations will be the 'individuals' in the OBD representation. Of course this is consistent with the history of OBO, for example look at how individual-level relations are introduced for the purpose of defining class-level relations.

I am not meaning to criticize the OBO approach - it has proven successful for its central use case of annotating publications. Indeed, I expect this approach will, more or less, be taken in the EthOntos backend, where the focus will, like OBO, be more on the tree-like and lattice-like networks of relations among classes.

However, OwlWatcher is different - the data comes in as observations of individual events, which are used in the construction a class hierarchy. In fact, the primary operation is more a type of induction or abduction, where classes are proposed, based on the observed properties of their observed individuals. Ideally, OwlWatcher will provide tools for assisting the user in adding restriction definitions to classes that were originally erected as undefined primitives.
I expect OwlWatcher will support a standard Description Logic (DL) reasoner, such as Pellet, and one or more special purpose reasoners, in particular one for temporal reasoning at the object level.

Common Logic - This ought to be a strong contender. Common Logic (CL) is a full, first order language, so there aren't any of the expressiveness issues that OWL and OBO ontologists have struggled with. The very first ontologies I ever constructed for behavior (before Protege) were done with a web-based tool called ontolingua, which used KIF as its serialization language. CL is in someways an extension of KIF, though its native syntax is not lisp-based, as KIF was. The main problem is the lack of tool support, either for the user (editors, preferably with access to some sort of reasoning support) or developers (backends with support for large data stores and reasoner interfaces). The main web presence for CL seem to be the pages left over from the (successful) ISO standardization effort, which ended in 2007. I hope support improves for this in the future.

CYCL - Cycorp has released two versions of Cyc to the outside world: OpenCyc and Research Cyc. The former is available on sourceforge, whereas the research version requires a special license from Cycorp. CYCL is a very expressive (n-th order) logic-based language, and the OpenCyc package includes an integrated reasoner and a substantial subset of the Cyc commonsense knowledgebase. CYCL's expressiveness and the inclusiveness of the packages also underlie some of the difficulties I have considered in evaluating them for this project: although CYC has excellent support for Java, the packages are large and only run on recent versions of Windows and particular Linux distributions. I have been able to install and run OpenCyc on a Windows-XP bootcamp partition on a MacBook Pro, so Mac users wouldn't be categorically excluded. However, the package is large enough and difficult enough to install, that I haven't considered using it for the OwlWatcher distribution or the initial version of EthOntos. There may come a time, however, when I will consider trying Cyc in a backend version. Honestly, that will probably have to wait until I have a stable academic position.

Report from ISBE

I spent last week at ISBE (International Society for Behavioral Ecology), which was held at Cornell this year. I've never been to this meeting before, I usually go to Animal Behavior, which returned to Snowbird for the third time this year. I have to acknowledge Anne Clark's role in getting me up there - we had a meeting of the advisory board to Ethosource and heard an update to the Ethosearch project.

Ethosearch is a database of ethograms that Anne and Sue Margulis have been overseeing development of. They demonstrated the web interface for searching (not publicly available yet) and have started soliciting for people to submit ethograms for the database in the near future (I'd guess toward the end of the year). They are also busy writing text definitions and doing some revision of the ABO Core ontology. I won't update the OWL version I have made available with OwlWatcher until they are ready and OwlWatcher knows how to deal with updates to included ontologies. I will keep you updated when Ethosource goes live.

Anne and Sue each brought students who have been entering ethograms from the published literature. Their method is simply to break up published ontologies into pieces and use the ABO core ontology as a pair of term taxonomies for classifying the pieces from each ethogram. There will be some text search and matching tools in a release at some point.

Besides Anne and Sue and some students they brought along, Cynthia Parr and Ed Scholes also attended. Cynthia, who recently took a position with Encylopedia of Life, was involved at the Cornell workshops and has acquired a substantial expertise in semantic web ontologies. Ed, who has published a couple of papers using a methodology very similar to ontologies to code ethograms of Bird of Paradise courtship has been the video curator at Cornell's Macaulay library for the past six months. Getting Ed and Cynthia talking about sharing between EoL and Macaulay may actually have been the most important outcome of the board meeting. Getting to meet Ed, though I didn't have any time to talk comparative methods, was a high point for me as well.

On to the meeting: there were a lot of papers on social learning and animal cognition. There were also lots of spider papers, though not much overlap between the two. The meeting was substantially larger than Animal Behavior, with 1006 registered for the full scientific program. Most of the time there were six concurrent tracks. Among the plenery talks, certainly Nico Michiels talk on Hermaphroditic invertebrates was memorably lurid - many cases of partners trying to manipulate the other into the female role with the manipulator taking the male role, with no reciprication. The Hamilton lecture, given by Alasdair Houston and John McNamara at the end of the conference program, included a predication of the return of ethology - certainly something that I and others that focus on the comparative study of behavior would welcome.

I also enjoyed talks that related to my social learning work with the Scrub-jays: Steve Scheoch has been continuing his endocrine studies of the jays, and has developed some field methods for assessing personality in fledgling jays. One of them involves a brightly colored ring (though it's bigger than an Aerobie). I also heard about a field experiment by Sarah Benson-Amram which involved placing puzzle boxes in the range of free-living spotted hyenas. Very cool, her data might have something to say about social learning, innovation or both - using a population that has been under long-term study.

I got to discuss Habronattus with Damian Elias, whom I had only briefly met before. I also discussed comparative methods for data sets that include intraspecific variation with Terry Ord, both the method I was involved with (Ives, Midford, Garland 2007) as well as Felsenstein's recent paper (Felsenstein 2008). He has also run into Ed Schole's work with some interest, as Terry works on a range of lizard visual displays. I also briefly spoke with someone from Louis Lefebvre's lab about the use of ontologies in the study of animal innovation

I'll discuss my poster in another post.