We held a workshop...

Last month George Gkoutos and I ran a behavior ontologies workshop in association with the Phenotype Ontologies RCN.  We posted a detailed report here.  This meeting was an opportunity for Animal Behaviorists (I invited Anne Clark, Sue Margulis, and Cyndy Parr who were at the 2003-2004 Cornell workshops that developed ABO) with some of the top ontologists from the OBO community.  My only regret was that we didn't have enough space to invite a broader range of behavioral interests.

ABS 2012 - It's different this time

I've finally made it back to full attend an ABS meeting for the first time in five years (I last presented at the 2007ABS in Vermont).  I'm here in a different role this time though, not as a postdoc or an ontology contractor.  I'm attending talks for the first couple of days, then representing the Dryad repository at an exhibitor's table, which will extend into the first days of the following HBES meeting.

I haven't stopped doing ontologies or thinking about spider behavior (I caught talks on Black Widow sibling cannibalism and jumping spider vision this morning - the later talk included some courtship clips that looked very familiar).  And although I've stopped work on OWLWatcher, I have a more focussed project related to spider behavior and one more in keeping with NESCent's focus on synthesis.  More about that later.

For the moment, I will spend the time catching up with behavior people, making new contacts, and enjoying some talks.  You can catch me on twitter at @pmidford, or follow the tag #abshbes2012.

PDAP and OwlWatcher

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

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

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

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

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.