The Ontological Ethologist

PDAP and OwlWatcher

2010-08-03T08:55:00.000-07:00

I put up a new version of the PDAP:PDTREE Mesquite package last night. Nothing big in this one, mostly a couple of messages regarding the resolution of polytomies (it's arbitrary so the details of individual contrasts will differ). The most important change is that PDAP now supports Mesquite's new install system so you should no long need to manually download archives and drag folders of class files around. It also gives you control of where the PDAP examples (misc PDI files and the guided tour wind up). Previously you were told where to put the class files, but I'd imagine the examples would languish in the archive fold until forgotten or deleted.

I have a request pending that might yield another PDAP release in the next week or so.

OwlWatcher is making progress. The player is more or less done - there are two small issues that I know of (specifically related to audio buffering and 'rocking' single frames back and forth), but happily I can go back to more interesting things such as finishing the integration with version 3 of the OWLAPI. When the release finally comes, it will be a two step process, first installing Xuggler, followed by OwlWatcher itself. If there are other java API's for video that you would like to see supported in OwlWatcher, feel free to request in the comments. I don't have much time to devote to OwlWatcher these days, but now that I've gone through the process of building a player up from a decoder library, it should be easier the second time (Quicktime provided a player that was adequate, but I think this solution will be more flexible as OwlWatcher continues to develop).

Back from Portland

2010-07-07T10:55:00.000-07:00

Several interesting talks from the Evolution and iEvoBio meetings in Portland last week. Probably most relevant here were several comparative methods talks, and several ontology related talks at iEvoBio. Among the latter, I'll mention Nico Franz's talk on taxonomic ontologies, as well as a lightning talk by Suzi Lewis on a phylogenetically based ontology annotation tool (PAINT). The later is focused on protein orthologs, so it isn't directly relevant to Phylontal, but was nonetheless interesting. Franz's talk was a broad-ranging overview of some important issues in taxonomic ontologies, including the proposal of Schulz et al. (2008).

I presented a poster on Phylontal, as well as a lightning talk on the taxonomic ontology I developed and maintain for Phenoscape. The later was a brief summary and update (NCBI xrefs, common names, and updates to the collections vocabulary). The Phylontal poster is mostly a cleaned up version of the second half of my NESCent talk, but should give an idea of what it is about.

Recently I've been working on adding 'matrix' support to the Phylontal library, to eventually add alignment of character states as well as the possibility of 'unpacking' the homologies underlying a matrix (e.g., using data when you disagree with the homology judgments of the author).

Of course, if people archived their raw data or observations, there would be less need for unpacking matrices.

Coming this summer plus Phenoscape in Chicago last week

2010-03-27T12:06:00.000-07:00

I've registered for the Evolution and iEvoBio meetings this summer. I agree with the desire of the iEvoBio organizers to make a place for informatics approaches at the Evolution meetings - I've certainly given both talks and posters where I got the strong sense that I wasn't speaking to the right audience. There are several presentation plans I could have followed. What I have chosen to do is to present Phylontal as a poster at Evolution, explaining the need and approach in detail, something like the brown bag I gave at NESCent in December. Although it may not be the best venue, a poster seems the best format for Phylontal at this time and it helps justify my going to Evolution as well as iEvoBio. At iEvoBio, I'll give a lighting talk on pipelining OwlWatcher and Phylontal. The third player in this chain - a character constructor - I'll leave for later.

I have made an 'in-progress' release of Phylontal at Google code, but there's no rush. It loads up NeXML and OWL files, allows the user to assign ontologies to tips, then allows the user to lexically match terms from two sister taxa. It's as much a proof of concept for the frontend, operating as OWL + per taxon ontologies. There is another potential use case for phylontal - starting with annotated matrices, extract taxon+anatomy term pairs from annotated NeXML matrices with OBO ontology support and a separate NeXML file for the tree. This would approximate the usage in Phenoscape, and the desired output would be Phenoscape's multi-column homology table.

Chris Mungall gave two interesting presentations on reasoning with homologies at a Phenoscape meeting at the Field Museum in Chicago last week. He brought up some interesting cases involving '2 taxon' versus '3 taxon' homology relations, and an important discussion of the interaction of homology statements and is_a hierarchies. People were most impressed with Chris' approach being extensible to serial homologies, the most important point being that serial homologies strictly exist only within an individual. I think that is an important insight and it lead to a simple taxonomy of homology relationships that actually make sense for anatomical reasoning. The corresponding treatment for behavior classes is worth looking into (e.g., distinguishing similar actions by an individual animal vs. homologous behavior patterns).

There was also some discussion of individuals and inferring classes by abduction or generalization over dinner at some point. I'm beginning to think this may be an important new growth area for biological ontologies, and it was good to hear that several people were thinking in this direction.

Finally, after several experiments, I think the OwlWatcher player is settling down towards a usable configuration using only two threads, rather than the initial four. Still need to deal with the packaging issue, and I fear the first post-Quicktime release won't be an easy install.

I didn't submit a proposal for a phyloinformatics summer of code project this year; I'll help out if it's appropriate for someone else's project, but I didn't have any brainstorms this year. None the less, if you're a student reading this, you will probably find one or more projects of interest there.

OwlWatcher update

2010-01-29T09:57:00.000-08:00

Since the beginning of the year, I've been poking away at the new video support that uses Xuggler, a java wrapper for FFmpeg. When I get this worked out, OwlWatcher will not only potentially work under Linux, but be open source compliant as well (LGPL).

At the moment, playing at normal speed and stop works, and stepping forward is sort of working, but I haven't taken a crack at seeking arbitrary frames. The biggest issue so far has been getting audio and video streams to play together. Admittedly audio isn't the highest priority, but it would be nice to get it right so OwlWatcher could support multi-modal behaviors, at least in principle.

The rest of OwlWatcher will be similar to the 0.040 release candidate I posted last May. I'll worry about forward compatibility from 0.035 closer to the release, along with coming up with a reasonable installation process, though I'm sure it won't be as simple as the previous release, at least for a few iterations.

Ontology matching and Phylogenies

2009-12-13T11:24:00.000-08:00

As many will know, I've been spending the autumn at NESCent, working on two projects: a continuing effort in Phenoscape, and a new project to develop and implement an algorithm to align multiple taxon-specific ontologies using a tree. The resulting tool, Phylontal is still aways from even an initial release, but I still gave a brown-bag talk on Friday that covered ontology matching as it relates to evolutionary biology, particular compartive methods. While there is ongoing interest in the general topic of ontology matching (e.g., the OntologyMatching site) there has been relatively little in either the model organism or evolutionary biology communities. This is starting to change, there are several approaches being tried by model organism projects (most notably Uberon and the Homontol tool and Homology ontology of the BGEE project).

Although Uberon and Homontol may represent viable approaches for linking model organism ontologies, I've been dubious from the start that any approach that ignores or minimizes the role of phylogeny would be appropriate for studies that combine ontologies to ask comparative questions. Phylontal extends some of the ideas introduced by Homonotol and its Homologous Organ Groups (HOG's) by attaching alignments (the results of matching operations) to specific nodes in a tree and by explicitly distinguishing homologous and non-homologous alignments. Homolonol could move in a similar direction, and their homology ontology suggests they have been thinking about other types of correspondences between anatomical terms, but their multispecies gene expression database is plenty to fill their plate I think. If nothing else, introducing phylogeneticists to these issues will get people thinking about this.

In the talk, the question of missing various absent terms came up, especially when I discussed how phylontal could deal with a missing term in an ingroup that was shared with an outgroup. I'm beginning to think that the OwlWatcher approach of reasoning up from a series of instances, each of which is a graph, might allow the distinction between absent and missing terms to appear. This is particularly true in behavior sequences: if in one clade the sequence A->B->C is observed, and in another C immediately follows A in all the observed instance, then B is absent where it would be expected to be observed. Likewise, if all the observations show no successor to A, and no predecessor to C, then B may just not have been observed. It's the combination of use of sequences (complete orderings) and the ability to refer back to observed instances that make the difference. In principle, you could do the same sort of thing with anatomy by building chains of connections, but these are not the sort of details that make it into character matrices, so it would require going back to drawings/photos/free text and probably putting it into the taxon-level phenotype statements rather than the multispecies ontologies.

Aligning phenotypes might be a new frontier for Phenoscape and similar projects.

There was also some discussion about whether a down-pass from tips to root was sufficient to match terms. If so, then Phylontal can avoid some work when phylogenies change by getting the tree nodes aligned first. If otherwise, as Dave Swafford pointed out, it may be necessary to align from scratch with a new tree. This is an open and potentially important question.

Ethosource meeting

2009-10-01T08:08:00.000-07:00

Last weekend I attended a meeting of the advisory board for the Ethosource project. This project was launched originally by Emilia Martins and Anne Clark and initially focused on repositories for behavior data and making it accessible in a controlled manner. Repositories lead to metadata which eventually lead to ontologies for behavior. Although my interest in behavior ontologies started from more of an analytic angle, behavior ontologies are part of the solution to both repository metadata and comparative analysis of descriptive data, so worthy of pursuit regardless.

Ethosource was funded early in the decade (not sure of the exact interval) and held meetings on both repository issues and ontology development. Most notably from my perspective were the two Cornell workshops that lead to the ABO. More recently, Anne Clark and Sue Margulis obtained a three-year grant from the Institute of Museum and Library Services to support development of an ethogram database, indexed by the ABO, called Ethosearch. Although the web interface is not yet publicly available (though close), the database is a substantial effort, which includes over 1,000 ethograms (if I remember correctly).

The board meeting was held at the University at Binghamton over 1-1/2 days. The first morning was overviews and presentations from attendees. Anne Clark started with a history of Ethosource, followed by Leah Melber discussing a k-12 outreach program that used behavior and ethograms at the Lincoln Park zoo. Mike Webster, the new head of the Macaulay Library discussed depositing data and how scientific repositories, as opposed to YouTube, need to be selective. Mike just started a few weeks ago, replacing Jack Bradbury - who co-chaired the Cornell workshops, and passed some of the questions to Ed Scholes, the Macaulay video curator and another fan of using ontologies as ethograms. Anne comments about a Japanese researcher who stopped by the Ethosource table at last year's ISBE meeting. He has established a sort of YouTube for animal behavior site with annotated clips but is relatively unselective in what he accepts as long as it is relevant to animal behavior.

Cyndy Parr, who has a history with Corvid behavior and the Cornell workshops has been director of species pages at the Encylopedia of Life for about a year. She discussed the role of EoL as a place where integration doesn't necessarily happen, but it helps people find other working on similar projects. She reviewed how EoL worked, including how images were harvested from Flickr and what the opportunities for behavioral contributions to species pages were. She gave an overview of EoL funding opportunities which we went over in more detail on Sunday.

After a brief lunch break, I followed with a presentation of Phenoscape, starting with an overview of the curation process and how we coded character matrices into EQ statements. After showing a few screen shots from Phenex and figures from my ICBO poster, I finished with a list of challenges for integrating behavior into OBO and showed a slide of the Biological Process Tree from GO. After describing the curation process, Emilia Martins, who I was very happy to see attend, asked about the getting the process of curating publications for Phenoscape out to individual authors. Emilia is concerned that not distributing the work might be the eventual kiss of death to any annotation process. Although that doesn't seem to be necessarily the case in other annotation projects, I have heard that ZFIN has recently had some difficulty keeping up with the rising flow of Zebrafish papers they selected to curate.

I've been trying to get OBO to acknowledge the existence of Ethosource and the ABO ontology for a while now. MGI sent Sue Bello, a mouse phenotype curator, to the meeting. This was an important step and her presentation gave everyone a sense of how ontologies are actually used in at least some model organism projects. I say some because, unlike the PATO phenotype ontology used by Phenoscape and ZFIN, MGI and (I believe RGD) use a precomposed trait ontology (Mammalian Phenotype Ontology), rather than building postcompositions of ontology terms.

Emilia discussed Ethobank's status; it was built from a collection of media material from an archive of lizard displays. It is no longer online due to some security issues. Although Indiana University has offered unlimited raw storage space, ongoing funding would still be required for database maintenance and curation. Emilia also observed that the behavior community lacks a tradition of combining data across investigations.

We then started discussing issues that could come out of the meeting. One of the first was the status of the ABO core ontology. There are currently at least four versions floating around: the one posted at ethodata.org, which is the official product of the Cornell workshops, the one edited by Anne and Sue for Ethosearch, the OWL conversion (but no additions) I have distributed with OwlWatcher and dropped in OwlWatcher's sourceforge site, and the version developed by David Shotton and his student, which includes independent revisions and term definitions. We discussed putting ABO on sourceforge and adopting a term tracking and curation approach like that adopted by several OBO projects.

We also thought of identifying several key projects that would serve as exemplars (case studies) for ethobank, and felt that these should include zoo projects, as zoo data may be more easily comparable than data across multiple wild populations.

The role of educational outreach, particularly at the K-12 level was discussed, both collection and analysis (e.g., bringing data together from multiple student observers). Traditional citizen science, as run by the Cornell Lab of Ornithology is more focused on collection than analysis, though the data is generally available, if members of the public knew what they wanted to do with it.

We discussed goals at various time scales, which were elaborated on Sunday morning.

Although the current entry tool does not support multiple parents from terms in the ontology, there was a consensus that many descriptions will require multiple parents to capture correctly. Although it might have been fun to introduce the notions of intersection and restriction from OWL at this point, Ethosearch and ABO have a ways to go before these would be meaningful.

We also saw demos of two search tools for ethosource database that were developed by Weiyi Meng and his student Jiang Yu. These are used both to assist contributors in categorizing their submissions and for clustering and mining in a way that suggests they would be applicable to comparative analysis, at least at the level of bringing relevant paragraphs from different ethograms together.

On Sunday, we went over our goals and what we would be doing. This involved continuing to serve as conduits to our respective projects, getting the word out to wider communities (e.g., ABS, ISBE, and the 2011 IEC). Likewise, there was discussion of K-12 outreach and stepping up the collaboration with Lincoln Park Zoo and the wider zoo community. The need for more work on the editoral review process was also discussed, both in terms of mechanics, but also whether there was a way to make it sustainable. Cyndy Parr gave us more details on EoL funding that might be relevant to supporting curation of material from existing collections. It was clear that continuing to build the bridge with Macaulay Library would be a near term priority.

After the formal break up of the meeting, Sue Bello gave Anne a brief walk through of OBO-Edit and the Mammalian Trait Ontology. There was interest on both sides in having Anne and her students review the behavior portion of this. I also passed on some material relating to the CARO anatomy ontology as an example of what a common phenotype (e.g., for behavior) might look like in OBO.

OwlWatcher is broken, and what will happen to fix it

2009-10-01T07:33:00.000-07:00

Summary

The video support in OwlWatcher for OSX is broken, in both Leopard and Snow Leopard. As far as I can tell, it still works in Windows. I am working on a fix for the problem which will require use of a different video player (Quicktime support in Java is gone and Apple seems to have no interest in bringing it back). I am investigating alternative player frameworks, some based on JMF, some on wrappers for FFMPEG, and some which are both. I expect the result of this will be a more complex installation process, at least for OSX, but it will also open up the possibility of using OwlWatcher on Linux (something I've been wanting for a while now).

Rant
Apple's support for Quicktime in java has always been rather spotty, and developers have been burned by Java upgrades which broke Quicktime before. I investigated alternative Quicktime bindings this week (Rococoa), but those seem to be broken in Snow Leopard as well. Although I expect the Rococoa developer(s) will eventually try to address this, there are alternatives to Quicktime, especially for this application, so it is time to finally make OwlWatcher independent of Quicktime.

I should have done this a while ago, and I apologize for anyone who has been inconvenienced by this. I do not blame Apple for OwlWatcher breaking, I was expecting something like this to happen. However, I should point out that there was apparently a Java update from Apple that also broke Quicktime support in 10.5 (Leopard) and I'm rather disappointed that things broke even without an upgrade to SnowLeopard.

It was suggested that I consider an alternative to Java. Unfortunately, I don't think reimplementing this in Python (which seems more to my taste than Perl, though I've written a bit more of the latter) would necessarily avoid this sort of breakage. Apple seemed to be promoting Python and Perl as having Cocoa support in 10.5, but, looking at the new X-code IDE for Snow Leopard, their enthusiasm for these languages has waned. Unfortunately, it seems at the moment that some of the most interesting work in scripting languages is going on with languages like Scala and Clojure, which are also jvm-based. So much the worse for Apple, though I'm sure it won't affect the sale of iPhones or the development of applications, which seems to be where Apple's focus increasingly lies.

My Evolution 2009 Highlights Saturday

2009-06-19T12:32:00.000-07:00

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

2009-05-28T20:45:00.000-07:00

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

2009-05-25T21:58:00.001-07:00

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

2009-05-20T21:32:00.000-07:00

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

2009-01-14T07:10:00.000-08:00

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

2008-12-06T18:32:00.000-08:00

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:

General availability and a large user community
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

2008-08-18T11:18:00.001-07:00

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.

Getting ready for Minneapolis

2008-06-15T21:53:00.000-07:00

The evolution meetings in Minneapolis start late this week. For me the meeting will start on Friday, with the Ontology workshop. I'll be giving a 20 minute talk on taxonomy ontologies. The workshop has been booked full for several months now. I am also associated with three posters: one from a comparative methods in R workshop I attended last December, another one from Phenoscape, which gives an update on the TTO, TAO and where we are headed with Phenote and the new workflow, and finally my single author poster on the behavior work. Part of this will be explaining the difference between annotating publications and behavior videos, and part will be an update, not so much on OwlWatcher, but a preliminary discussion of a toy implementation of the EthOntos-Lite alignment module. There is, as of today, running code, but I haven't given it anything more an a couple of trivial examples, which it seems to handle correctly. It would have been nice to have something I could feed OwlWatcher projects into, but that will have to wait - I've still got lots on my plate, despite a productive weekend.

This summer

2008-06-07T20:48:00.000-07:00

Besides the Evolution Meetings (less than two weeks away), I will also be attending the ISBE (International Behavioral Ecology Congress) in Ithaca this August (9-15). I will be presenting an ontology-related poster, and with any luck, I will have a demo-able version of OwlWatcher using the Manchester OWL-API. I have already started building this version. The Manchester OWL-API, although somewhat more experimental than Jena, is more OWL-centric than Jena, which has a larger RDF and semantic web focus. This is not to disparage either Jena or it's development team, both of which have been quite helpful in the process of developing the first versions of OwlWatcher.

I'll save the latest news of EO-Lite for another posting.

OwlWatcher 0.036

2008-05-05T14:43:00.000-07:00

This isn't a big deal, mostly a bug fix for a problem that apparently cropped up when with the OSX application during the release of 0.035. The work I've been doing with Phenoscape has had an influence on how the later tab views in OwlWatcher will work. I expect I'll have at least a mockup of a view for instance graphs for the Evolution meetings (which I will be attending) in Minneapolis.

OwlWatcher 0.035 released

2008-04-06T14:39:00.001-07:00

For what it's worth, I've released a new version of OwlWatcher, my ontology-based behavior scoring tool. By announcing it here, I avoid the possibility of this becoming a Mesquite blog, not that there would be anything wrong with a Mesquite blog, it just doesn't go with the title, and I do spend time with other projects.

You can find it here.

I write scripts...

2008-02-15T10:38:00.000-08:00

No, I haven't been on strike for the past few months; I write small programs in scripting languages. Many people in bioinformatics, even those with no formal programming background, learn enough to write a simple series of commands in some scripting language or another. The most popular language for this sort of coding is almost certainly Perl. Python is another popular language for doing this. I've written some Perl and a few one liners to play with Python, but those languages won't be the focus of these posts. I intend to provide some enlightenment on another, lesser known language - the scripting language used by the Mesquite package.

Mesquite, for those who haven't heard of it or read my introductory post, is a application environment for phylogenetics, focusing on doing things with trees rather than inferring them. It does have the ability to serve as a frontend to programs that do tree inference - either directly for MrBayes or indirectly using a bridge to the Cipres libraries - which support PAUP*, RAxML, and GARLI as well as MrBayes. Mesquite will also create trees using a variety of simulation methods, such as pure birth (aka Yule trees), birth-death, and the model that corresponds to the BiSSE method of estimation.

Many, if not most, users treat Mesquite as a GUI application without any knowledge of the scripting that Mesquite supports and uses when they save and then reload a project containing trees and character matrices. There are several ways to use Mesquite scripts - either by including them in a Mesquite block in the nexus file that represents the project, but they can also be used to send a series of commands to a window during a Mesquite session. If you use a command line to launch Mesquite you can also send commands or scripts via the terminal that you launched Mesquite from.

I'll finish this post with a simple "Hello World" style example of some Mesquite script that you can run within the Mesquite GUI.

Start Mequite and create a new project, call it scriptTest.nex. Accept the defaults in the dialog that comes up for creating the project. If you are running Mesquite 2.0 or later, you should see something to this in your Mesquite window.

Make sure that "Tree Window 1" is selected and from the Window menu select Scripting:Send Script. This will bring up a dialog where you can type a script command. Here's "Hello World" in Mesquite Script :
message 'Hello World'

So bring up the script window, type in the commands and press the OK button.

So where's my message?
After the script window disappears, you are probably wondering where the message went? It's not in the Tree Window - you actually didn't request the window to do anything. The message appeared in the Mesquite Log. The log contains a record of what Mesquite has done during a session. The easiest way to see the log is to go back to the window menu and select Log from the list. This will expose the log window. If you scroll down to the bottom, you will see your message, followed by the showWindow command you used to bring up the log.

The log appears in other places - the file Mesquite_Log that is created in Mesquite_Support files - a new file is created each time you start Mesquite. If you start Mesquite from a command line, logged information is also written to the terminal you launched from.

That's it for now. Next time, I'll discuss It and other important variables and the structure of scripts. In the meantime, there is a list of "Universal" Mesquite scripting commands available by choosing Scripting from the help menu and the selecting the 'universal commands' link near the top of the page.

A little bit about me

2007-12-02T16:00:00.000-08:00

My interests lie in the study of evolution and comparative methods, particularly as they relate to behavior. I subscribe to, and have helped develop, the unorthodox view that ontologies are appropriate data representations for studying behavior.

I'm currently a postdoc at the University of Kansas. I am currently funded from two projects:

Cipres - A large project devoted to developing algorithms and software for building phylogenetic trees. I work some on the infrastructure software and it also funds some of my ongoing work on Mesquite. I have been involved in several Mesquite packages, most notably the PDAP:PDTREE package, the Mesquite implementation of the correlation method of Pagel (1994), and the Bisse model (Maddison, Midford, and Otto 2007) of correlated speciation, extinction, and binary character change. I am also somewhat involved in the development of Nexml, an XML-based successor to the Nexus file format.
Phenoscape - A project to build a multispecies ontology of fish anatomy.

My current unfunded projects include an ontology based tool for scoring and analyzing behavior videos, called OwlWatcher, an implementation of a 'type-2' comparative method for ontologies, called EthOntos , and several improvements to the PDAP:PDTREE package.

A special, although not exclusive, area of interest in behavior is understanding how and what humans and other animals understand about the behavior of other animals. My doctoral project looked at social learning in Florida scrub-jays, training them under free-living conditions, and them allowing them to demonstrate to young hatched the following spring and in subsequent years. This works because Florida scrub-jays live on year-round territories and could be easily trained to perform a task on the ground. From social learning, I have been shifting my interest towards how animals (and humans) acquire information by watching the behavior of others.