Thursday, October 1, 2009

Ethosource meeting

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, 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


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).

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.