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. 

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. 

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.

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 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.