A Belated Summer Update

I’ve been quiet since April, but I’ve also been pretty busy.  I have been to one meeting this summer, the 20th International Congress of Arachnology.  I gave a talk about the progress on the spider behavior ontology I mentioned a few posts back.  The slides are here.   I have finished my initial pass for behavior terms in two recent works: Foelix's Biology of Spiders, a standard textbook, and an edited volume, Herberstein's Spider Behaviour.   Since returning from the meeting, I've nearly finished a first pass of data cleaning.  You can see the raw data here.  In the next week or so,  I'll put up a little landing page with more explanation and links to the raw data and the results of the cleaning pass.  Eventually there should be a CMAP or other visualization and possibly an OWL file.

I say possibly an OWL file because I'm not sure that an ontology will be the final outcome.  I may generate a set of terms and turn them into term requests for the NBO/ABO, the Spider Biology Ontology, and others (GO, ChEBI, PATO).  It's been clear to me (finally) that the database is where the interesting comparative work will come from and the ontology is just a necessary support for this.  It should also be useful as a standardized vocabulary for arachnologists, and there seems to be interest in this, based on the reaction to my talk.

obo-behavior is a thing

Yes, this is an update, not an ontological assertion.  Robert Hoehndorf has set up a new github project (obo-behavior) for the NBO and moved the NBO and the ABO associated material over.  So, the negotiation is over and we progress with the merging.  We hope to have the merge done this summer (at least so we can report back to our several funding supporters).

Why Arachnolingua needs a T-Box

It is common in knowledge representation to distinguish between statements about individuals (e.g., "John loves Mary") and statements about classes or universals ("Love is a emotion exhibited by humans").   The set of former statements are sometimes referred to as being the "A-box" (A for assertion), the latter set the 'T-box' (T for terminology).  Many ontology languages, such as OWL, allow both types of statements, though ontologies, strictly speaking, are terminology.

It's been nearly five years since I mentioned to Martin Ramirez at a Phenotype Ontology RCN meeting at NESCent that I thought it would be a good idea to test the NeuroBehavior Ontology (NBO) as a vocabulary for describing the behavior of spiders.  The NBO is organized as approximately parallel trees of terms for behavior processes and phenotypes, though with a bias toward the behavior of humans and model organisms.  So I gathered up a collection of papers on the behavior of spiders and some other arachnids and did some annotation of behavior.

Now the annotations in Arachnolingua turn out to be both assertions about (frequently anonymous) individuals as well as about classes.  For example, statements about the types of webs various families of spider produce, or don't produce, are at the level of terminology - statements relating a type of web to a type of spider.  Others, such as the sequence of acts in building a web are necessarily about individuals, because it is generally the same individual (or in some cases group of individuals) involved in each step in building a web.  Each step has an active participant, the same spider for each step.  So descriptions of process will consist of assertions about individuals, even if nothing else is known or stated about the individual.

Actually I was more successful at gathering papers and building some software infrastructure (python frontend, SQL database, Java backend and public website - more detail here).  However, in 2014, I presented a poster at the Animal Behavior Society describing the quality of annotation possible using the NBO process terms for a small set of papers.  Because I included relevant anatomy as part of the annotation I was able to do a little better than if I had just used the NBO terms, however, a lot of interesting behavior wound up as courtship behavior, or locomotion, or predatory behavior with reference to specific body parts.

My original hope was to build the T-box from the data and descriptions in the curated papers. However, it has become clear that the gap from the terminology in the descriptions to the available terms in NBO really is too great. The annotation process requires terms at an intermediate level to be useful. Thus the project to test NBO coverage using spider behavior is concluded.

Therefore, while I continue to tweak the frontend code, I have retreated to the approach recommended by Arp, Smith, and Spear and have started simply extracting behavior terms from two sources.  The first is the 3rd edition of Foelix's Biology of Spiders.  The second, Herberstein's Spider Behaviour, will be a followup to catch anything that Foelix missed.  The idea is to collect the terms, throw them against whatever results from merging NBO and the Animal Behavior Ontology (ABO) process terms and the Gene Ontology to identify synonyms and subsumption 'parents', and propose at least a taxonomy of terms at the World Arachnology Congress in Colorado this summer.  Ultimately these might wind up as a part of the existing spider biology ontology, which already has a small behavior branch, as well as contributing to whatever final vocabulary results from merging process terms from NBO and ABO.  Arp et al. recommend starting with a small set (~50) of terms, I'll grab every behavior related term for a while and pull the most general terms from the list.  The remainder can be added once the tree is in place.

There are deeper issues here, particularly about the relation of behavior phenotypes and their associated processes, but that's a topic for another post.

Behavior Ontologies workshop 2

Over the weekend we held the second workshop (funded by NSF and the Phenotype Ontologies RCN) to begin the process of merging the ABO (Animal Behavior Ontology, which came out of a series of workshops in 2004 and 2005) and the NBO (NeuroBehavior Ontology) which, as we learned at the workshop, had its roots in a phenotype vocabulary that started around 2001.  To be fair, the effort that led to ABO came out of a private discussion between two of the principals held at the 1999 ABS meeting.   The workshop was held at the Smithsonian Museum in Washington.

We aren't quite where I expected to be after the meeting.  We made good progress getting started on a use-case based paper for applications of a behavior ontology.  We also have a real home for the ABO - we deposited the OWL rendering I generated in 2006 as the initial commit here  (note that this is the same repository where NBO is maintained. The main use of the ABO was for indexing an ethogram repository called Ethosearch. Ethosearch enhanced the ABO by adding definitions to many of the original terms. We should shortly have those terms merged into the OWL version of the ABO.

We started the process of merging the ABO and NBO. One of ABO's strengths is a clear division between observable behavior (acts, events) and functional interpretations (for example, running vs. fleeing from a predator). The NBO is organized rather differently and we would like the division in ABO to appear at least somewhere in NBO. NBO does have a sizable number of terms that would apply to neither, but are more mechanism or 'mental function' related. The main challenge to reorganization is making changes in a way that would be acceptable to other NBO stakeholders. One of our tasks in this meeting was to identify at least some of the other stakeholders that might be affected by a merge and reorganization. I would say this goal was partially met, but I'm not sure we have identified everyone.  (Personal note: Arachnolingua does use NBO, but would only benefit from any ABO integration).

We have plans for sharing this work (besides the paper, there will be, at the very least, a poster at SICB-2016, and there were other ideas floated on Sunday).  I will have updates as things progress.

Workshop Organizers: Anne Clark, Sue Margulis, Cynthia Parr, Katja Schultz (Local Host), and myself

Participants: Elissa Chesler, George Gkoutos, David Osumi-Sutherland, and Reid Rumelt

Melissa Haendel participated remotely. 

A little more on morphological data

Apropos of last week's post on models and data, here is a preprint study on the amount of morphological data available for living mammal taxa.  The focus was on coverage in each order, where coverage was defined by the fraction of OTUs with available data, where available seems to be defined as appearing in a character matrix with more than 100 characters (which doesn't necessarily mean that >100 characters were scored for each OTU).  I can't judge whether the three databases and the literature search constitute a sufficient search, but their results aren't implausible.   Using their appearance in a sufficiently character-rich matrix, they counted 1074 mammalian OTUs in 126 matrices.  Without the matrix size filtering, there were 5228 OTUs in 286 matrices.  This is apparently less than the morphology data for fossil mammal taxa.

I expect there are very few character matrices for any group with more than 100 behavioral characters.  This is probably a combination of the difficulty of extracting a 100 behavioral characters in a study as well as the rarity of this sort of comparative/phylogenetic analysis in behavior.

Thanks for to everyone who responded to last week's post.

Models vs. Data - not a choice for behavior

These are some thoughts that have been rattling in my head since the SSB 2015 standalone meeting back in May.  They are somewhat depressing, so I'm open to suggestions of more positive ways to look at the situation in comparative studies of behavior.

The main part of the meeting was bracketed by two 'panel' discussions (I scare quote the word panel because the panel was two people in each case).  The first panel consisted of David Hillis and Antonis Rokas arguing whether models or data would be more important going forward.  Not surprisingly for this meeting, the focus was on molecular methods, particularly genomic comparative analysis. Interesting question, but of course both are viable research paths at this point - gathering and managing rapidly growing data sets and refining the models of molecular evolution to more realistically mimic the actual processes are both worth pursuing.

The question of data vs. models came up several times, including during another panel discussion of putting dates on time trees.  This seems to be a very fertile area for developing improved models and statistical methods at the moment, while the corresponding fossil data is accumulating at a steadier pace.

The second panel was Wayne Maddison and Cécile Ané discussing the limits of comparative methods.  The issues that Wayne raised are ones I know firsthand, mostly from my stint in his UBC lab.   The issue is that most or all comparative methods for discrete trait values suffer from phylogenetic non-independence, despite 25 year-old claims to the contrary.  I spent some time thinking about these issues, but the best discussion at this point is the Maddison and FitzJohn (2014;  doi:10.1093/sysbio/syu070) paper.  The situation is somewhat better for continuous traits, though there are always questions of model adequacy. I'll admit I don't remember a great deal of Ané 's discussion of limits of OU methods, though it seemed someone more optimistic for the continuous trait cases that OU applies to. Wayne did point out that tip data won't help answer the question of trends in evolution - you'll need fossil data for that.

Thinking about the situation after the meeting wrapped up, I was struck about the differences between different trait domains.  In molecular biology we have lots of data and a selection of models that are at least plausible representations of things that actually happen (not perfect by any means, but GTR is a reasonable stochastic approximation of what happens at a single site).  Lots of data allow a certain freedom to 'run about' the non-independence problems mentioned in the last paragraph - with enough sites, you could, in principle, assume independent changes.  Molecular data also provide a small, but real sampling of fossil data and useful amounts of molecular evolution can occur over experimental time-scales.  Thus, molecules provide lots of data, a solid starting point for models, and some temporal depth.  Morphology has fossils, a reasonable and slowly growing dataset and a mix of continuous and discrete trait models.  Are Brownian motion and OU models good stochastic approximations of morphological change for continuous characters?  Not necessarily, but they are definitely a start.  As noted above, the situation for discrete characters, even using model-based (Likelihood and Bayesian) methods is rather problematic.  However, you aren't limited in your ancestral reconstructions to using contemporary data.  This won't solve these problems, but they might give you confidence in your analysis.  There is room for optimism here, particularly the hope of better models and statistical methods to make the most of the data available, while new data trickle in.

Then we come to behavior: no fossil data and not a lot of data at all relative to molecular traits.  Behavior also has the problem of much of the data being transient - if not captured on a recording device, it's just an observer's memory.  Apart from the lost opportunities to capture data, the animal behavior community has been slow to embrace the culture of data sharing, as discussed in Caetano and Aisenberg's (2014; http://dx.doi.org/10.1016/j.anbehav.2014.09.025) Forgotten Treasures paper. Data sharing is, of course, more than just dumping your raw data in a repository - to be useful, the data require annotation, even if that is little more than plain text labels for columns and a glossary of observation codes.  So behavior researchers need to up their game to overcome the challenges of slow data accumulation dribbling into a leaky pipeline.

I became interested in ontologies and knowledge representation for behavior because I, rather optimistically, it turned out, thought a flood of behavior data would follow the flood of molecular data.  Ontologies have played an important role in making sense of genes and proteins, and are slowly starting to contribute to morphological studies, but behavior and especially behavioral ecology and ethology lag behind even other branches of ecology in making use of ontologies.   There is some motion towards an ontology (or sub-ontology) for behavioral ecology, follow me here for updates.

As challenging as the data situation is, I worry that the modeling side is in complete disarray.  Models of the evolution of behavior are frequently descriptive and of little use for inference.  For example, there is a sizable collection of models for the evolution of sexual signals, but I defy anyone to throw these models on branches of a tree and generate likelihood estimations of the history of signaling in any clade.  Note that this isn't the same as applying an Brownian or OU model of change to a particular measurement or set of measurements sampled from a signal and testing for the presence of selection - Brownian motion is not a model of sexual selection and it isn't clear (at least to me) that there is a way to go from a descriptive model of sexual selection to a something that would yield up a likelihood estimate.  

If there is work being done here, it is either well ahead of its time or not being recognized for what it is.  Please prove me wrong on this.  Meanwhile, I can only hope that the time for this theory to model link is not too far off.

Rather than end on such a pessimistic note, I will suggest two places to start looking for temporal depth.  These won't solve the model problem, but they may yield up data that could support some development and testing.  The first is the fossil traces of behavior - this means both behavior inferred from morphological fossils as well as, secondarily fossil artifacts and trace fossils.  I have some reservations about the later, simply because it is frequently hard to identify the organism(s) involved. 
The second is the study of cultural change, both human and animal.  There are a lot of interesting questions here, especially at the group/population level, though the link to heritable genetic change still has a long ways to go.

I know not everyone in the comparative methods community is going through the stages of grief that Wayne Maddison discussed in his SSB talk.  The community response to his questionnaire reflected optimism for new methods, though I don't know how many behaviorists were surveyed.  I did speak with Emilia Martins in the ABS meeting a few weeks later and she was more optimistic about the state of comparative methods.  I hope she's right and that the behavior community will find a welcome from the comparative methods community when we manage to shake off the fog of our data amnesia.

Summer meetings 2015

In recent years, the main thing I've been using this blog for is letting people know about meetings I'm attending and from time to time, meeting reports of varying quality.  So here are the meetings I'll be attending during Summer 2015:

Society for Systematic Biologists standalone meeting (Ann Arbor MI May 20-22) Not planning to present here, but will be around for face-to-face with other OpenTree of Life people and anyone else who wants to discuss or simply catch up.

Animal Behavior Society (Anchorage AK June 10-14).  I'm coming up to Anchorage a couple of days early, and currently have the 9th completely open. No sudden exits this year I promise. I have signed up to give a talk about Arachnolingua and I promise I'll keep the focus on the spiders (ontologies and reasoning will stay in the background).

American Arachnological Society (Mitchell SD June 19-23).  Not sure whether I'll do a poster here.  The plan is mostly to play sponge and catch up with some people.

I'm currently focussing on contributing to the OpenTree taxonomy effort (with Jonathan Rees) and reworking the Arachnolingua tools.  Nothing to report on the next Behavior Ontologies workshop at this time.

Finished up a Behavioral Ontology workshop, now at ABS2014

We finished up the first of our two workshops to followup the one-day session we held in conjunction with the 2013 phenotype RCN summit.  We gathered together a fairly diverse group of 15 behavior people at Princeton for a day and a half prior to the ABS 2014 meeting.  Our task was to compare the ABO (the ontology constructed over the course of two workshops in 2004 and 2005 at Cornell) and the NBO (the ontology for behavior processes and phenotypes developed within the OBO framework).  Despite some initial fears, it looks like we have a good chance of coming up with a proposed integration of these that will allow behavioral ecologists to make use of the NBO while not breaking things for the current users, mostly model organism genetics and phenotype investigators.

Thanks to all who attended, my three co-organizers (Anne Clark, Sue Margulis, Cyndy Parr) and also to George Gkoutos, developer and maintainer of the NBO, who listened through most of our friday session and took an hour to host a question and answer session over skype. 

I'll be at ABS2014 next week.

I’ll be presenting a poster at the Animal Behavior Society meeting next week in Princeton New Jersey. The poster is NE 116. If you aren’t attending, the poster and a supporting script file are now up on figshare. The poster looks at how well NBO serves as a vocabulary for spider behavior. It turned out to do a little better than I expected, and I omitted a couple of statistically non-significant tests I tried over the weekend (looking at term depth across NBO vs depth of NBO terms used in 40 arachnolingua claims).

Note: there is a small chance I may not be able to attend the poster on Tuesday evening. I’ll update this if it turns out I won’t be there.

This summer - 2014

I'll be attending Evolution/iEvoBio 2014 in Raleigh in June.  I am scheduled for another iEvoBio lightning talk on Arachnolingua, my semantic database of behavior of spiders and other arachnids.  I expect the talk will bring in some things I've learned while working with OpenTreeofLife.  I'm still blogging the development of Arachnolingua and its associated tools and web presence at the development blog.

At Animal Behavior 2014 I'll be presenting a poster that focuses more on the behavior (and the spiders).

ABS 2013 Wrap up

It's been two weeks since ABS 2013 finished up.  So, definitely need to get the rest of these out before I forget.

The theme of why so few comparative studies continued to pop in talks, from a brief mention in Patricia Gowaty's Tuesday morning plenary talk, to Daniel Caetano's plea for more data sharing, ironically comparing the data sharing situation to that in genomics and indirectly in phylogenetics - where the deposit situation isn't as rosy as in genomics, though certainly better than in behavior (shout out to Terry Ord and his growing collection of Dryad deposits).  One interesting comparative talk by Odom reconstructed that female song was present in the ancestry of songbirds, a conclusion that was dependent inclusion of a representative sample of taxa outside the northern temperate zone.

I missed a fair number of talks due to ongoing commitments, but managed to catch a number related to spiders, cognition, and a couple of the social learning talks on the final contributed session.  One of my favorite spider talks was Elizabeth Jakob's look at visual perception in jumping spiders - in particular a study of biological motion which used moving dot animations constructed by an undergraduate.  I spent some time looking at biological motion perception in pigeons a long time ago, so to see that jumping spiders can distinguish spider-like animations from scrambled dot animations was quite amusing. Another spider talk that caught my attention was Schwartz's Allee talk on spontaneous male death in the Dark Fishing Spider.  Although this work was published a few weeks before, the talk filled in a lot of details I missed in the paper.  Overall spiders were well represented, including Andrade's plenary talk on spider sociality.

There were also some good (and not so good) presentations in cognition and social learning.  A nice comparative study across 9 families of mammalian carnivora showed widespread (8 of 9 families, excluding Herpestidae) ability to solve a box opening task involving a latch (though not every species in the 8 families could solve the task).  The question being asked was whether sociality (as measured by group size) was predictive on performance in the task - it wasn't.  What did predict task performance was the size of the repertoire of actions used to manipulate the box and neophobia (negatively).  There was also a suggestion that brain size was predictive.  I'm very cautious about that last result - there have been too many poorly done brain size studies and this analysis seemed to be an after thought.  I saw a couple of cephalopod cognition talks that I didn't find convincing - I know cephalopods, especially free living, are hard to study, but that's all the more reason to throughly understand the issues involved before spending hundreds of hours of data that fail to address all the alternative explanations.

There were a number of good social learning talks on the last day - I unfortunately missed a good one on social learning in Drosophila, but did see Simon Reader's talk on conditions that influence choices of learning strategy, using guppies, which have become another good model system for social learning.  Ipek Kulahci looked at the role of social networks (both positive and negative relations) on demonstrator effectiveness in two Corvus species (C. corax and C. corone).  She looked at the effect of relationship on both attention to the demonstrator (observers were free to ignore demonstrators completing a box task designed to minimize scrounging) as well as learning effectiveness.  

Apart from the talks, this was a good meeting for socializing - being the 50th anniversary meeting of the ABS, lots senior and emeritus people were there, including my advisor Jack Hailman.  There was also more focused socializing, especially as several us continued our planning for next year's followups for the Behavior Ontologies workshop from last February.

ABS 2013 Part 1

It's been a productive, though at times frustrating, first 24 hours at the 2013 Animal Behavior Society meeting.  I met last night with one of my long time behavior ontology collaborators.  We are planning two NBO focussed events next year.  The second one will definitely be during the break between ISBE and ABS next summer.  The first, which will be more technically focussed will likely be around the time of the next Phenotype RCN summit though it might be at a different time or venue.

Before I arrived yesterday, they held a public outreach day and apparently the human habituated wolves they brought onto the U Colorado campus were a big hit.  Continuing the canine theme this morning, the plenary was on 'Why we love dogs' - discussing various behaviors dogs and their owners use to maintain their bonds.  After the Plenary and coffee (sort of, only decaf was left by the time I got through the line), I spent most of the morning in the predation session.  The primary talks of interest to me was one on ontogeny of newly hatched spiderlings, and one on resource patch decision making by slime molds.  The spider study (on a central american Pholcid species it turns out) demonstrated that the newly hatched spiderlings could respond appropriately with differing levels of attack intensity to differing prey (Drosophila vs. a local ant species), and that this flexibility was not the result of learning from previous experience (Escalante).  The slime mold talk (Reid) mentioned previous work that showed slime mold could find the minimum distance through a maze between two food sources through a type of 'distributed processing.'   Another talk of interest described a study of chunking and the limits of memory used by caching squirrels (Jacobs).  The ABS tweeters have settled on #2013ABS as several other groups have been using ABS2013.

My favorite tweet of the morning was certainly this one:

Animal behavior studies are rarely comparative. Need to gather data, store and make it available. Phylogenies are needed too! #2013ABS
— Daniel Caetano (@darkymoss) July 29, 2013

The phylogenies have gotten better and more comprehensive, but the gathering and sharing of comparative data still has a long way to go.

AAS 2013

Here's a belated report from the 2013 American Arachnological Society meeting last week.  While I was there I tweeted a couple of times and @nsandlin tweeted about nearly all the talks.  Time to get this off my plate before Animal Behavior next week.

I found several talks quite memorable, including Eileen Hebets talk that seems to represent a start at integrating all the multi-modal signaling data for Schizocosa she's accumulated over the past 15-20 years.  I also liked Igni Agnarsson's talk on the diversity of Malagasy Anelosimus - lots of related species in close proximity, and unlike their North American sister clade, all remain sub-social.

Another memorable talk, if for more personal reasons, was Angela DiDomenico's (student of Marshal Hedin) systematic work with the Opilione genus Sitalcina.  Turns out there is likely an undescribed species in a draw only a couple of miles from where I attended Junior High School in Palos Verdes.  I'm not really surprised - the ecology of Palos Verdes has been known to include endemics for a while now (remember the Palos Verdes Blue butterfly?).  Hopefully this (not so traditionally charismatic) arachnid will have a better future than the PV Blue butterfly.

I knew that George Uetz had done a lot with the Schizocosa system, but the shear number of Schizocosa talks, especially during the second Monday morning session, was a bit of a shock.  S. ocreata really is attaining model organism status.

Apart from the talks, I got to catch up with people I knew in the Tucson Maddison lab, particularly Greta Binford, who indicated that several spider genomes are either done or nearing completion.   Having the genome sequenced is not the same as the level of annotation we have in vertebrate model organisms, but it is a step towards the day we could do a Phenoscape like project for spiders.

I also briefly chatted with Eileen and with Jonathan Coddington, who I got to know a bit from some phenotype ontology activities prior to the launch of the RCN.

The meeting also offered several opportunities to add to my literature collection, and I took advantage of the honor system reprint table as well as a couple of items in the silent auction.

Arachnolingua

At last year's iEvoBio I gave a lightning talk about Arachnolingua, an informatics project for spider behavior.  I've been plugging away at it, but not saying much.  Not ready for a release yet, but I've decided to try blogging my progress on it.  I've also decided to do that in a separate blog, keeping this one for items of more general interest (e.g., trip reports, more general musings).  So, if you have any interest in semantic representation of spider behavior, take a peak at An Arachnolingua Blog.

This summer

After going to Evolution and iEvoBio for the past three years, it's time for a change. I'll be heading back to the Animal Behavior Society meeting this summer (representing myself this time), and, for the first time in 11 years, I'll be attending the American Arachnological Society meeting.  I'm not turning my back on Evolution or the interesting community developing in Evolutionary Informatics - I expect to be back in the Triangle for the Evolution Meetings next year.

Meanwhile, I'll hope to have some interesting reports, both here and on twitter (@pmidford) and looking forward to meeting old and new friends.

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.