Apr 292013
 

Are you interested in describing and linking biological data? Apply by June 1, 2013, for the Ontologies for Evolutionary Biology course at the National Evolutionary Synthesis Center, July 29 – August 3 in Durham, NC:

https://academy.nescent.org/wiki/Ontologies_for_evolutionary_biology

Evolutionary research has been revolutionized by the explosion of genetic information available, and ontologies must play a central role in relating this knowledge to observable diversity. Ontologies provide scaffolding that interconnects many kinds of observations; across species, they provide evolutionary, developmental, and mechanistic insights. The theme for this year’s course is “enrichment”. We aim to help participants enrich their research through the use of ontologies, to enrich existing ontologies with new content, and to bring new domain expertise to the ontology community.

Aug 042012
 

We started the the last day of our course with presentation and discussion of group ontology exercises and issues facing the different domains, such as nomenclature and a nice example of linking taxon-specific anatomies with mineralized properties of tissues. We discussed an evolutionary time-analogy to developmental time for paleontology, which resulted in the question  “Is the big bang the first temporal boundary?”

We then moved on to discussion of what it takes to release an ontology in different flavors, and decided that a flavor is a slice of a version (!). Was it too early to think about discussion of ontology release processes? We felt not, because because these are end goals to keep in mind as we go about our work in developing anatomy ontologies.

We dealt with a number of additional technical issues, such as choosing a primary axis of classification and how this relates to properties (a nice realization). You CAN in fact, have structural and partonomy hierarchies exist in harmony. Next, we tackled the beforehand taboo topic of homology. The intentional delay in discussing homology until the last day paid off, as the presentation of how the community is currently representing homology hypotheses external to the anatomy ontologies seemed to go over without too much controversy.

We concluded the week with a gong show of 5 minute lightning talks of students discussing some problem, perspective, or plan. These turned out to be a great highlight of the week, and it was suggested that they should be emphasized in future years of the course (which the instructors think should be taught in Borneo).

An extra special thank you to the NESCent staff, in particular Jeff and Karen, who were flawless in helping make the week go super smoothly. Further thanks goes to the Phenotype RCN for suggesting and co-sponsoring the course. We are happy to announce a new graduating class of peer anatomy ontologists. We welcome your participation in our community in the years to come, and thank you for your enthusiasm.

Melissa Haendel, Matt Yoder, Carlo Torniai, Jim Balhoff, and Erik Segerdell

Ontologies can be released in multiple formats using the OBO Oort tool.

Aug 032012
 

Whew, just made it out of OWL hell (not really, we didn’t actually manually edit an OWL file, but we scared everyone enough not to do it) in time for a combined Wednesday/Thursday blog post.  Wednesday was completely devoted to an introduction to the Web Ontology Language, WOL, OWL.  After some morning theory, participants dug into (and finished!) a 41 page tutorial (not including 5 additional exercises) on the use of Protégé.  This was perhaps the trickiest day of the workshop with a lot of potential for confusion, but the relative silence and lack of gnashing of teeth foreshadowed a successful day.

Thursday, with OWL basics in hand, we moved on to a tutorial about importing other ontologies. Where to get them, how to get them, how to tell Protégé what to do with them. But of course, it is not always convenient to import a whole other ontology, so we learned the principles of “MIREOT”, or the minimum information required to reference an external ontology term. This required the complex navigation of the Ontofox tool to obtain bits and pieces of external ontologies. We then learned how to put them back together again (in Protégé).

We also had a lot of fun classifying the Balhoff family tree, as well as blue jeeps, as we learned to classify instances and use them for testing our anonymous classes. We learned to install Protégé plugins and link images within our ontology. Including pictures of Jim’s baby, hymenoptera heads, and blue jeeps.

At the end of the day, we broke into groups to brainstorm what would be needed to represent spatial relations and classes for the postcomposition of anatomy classes. This was done without peeking at the Spatial Ontology (we think!), in order to gain unbiased requirements for this ontology and get the participants thinking about spatial relationships.

On Thursday night some of the participants gathered in Robert’s room to listen to his daughter Leah’s music on the fabulous MTV show, Snooki and Jwoww. To everyone’s disappointment, her music was only on for around 10 seconds (although the show was fabulous). However, you can listen to her music here.

Matt Yoder, Melissa Haendel, Carlo Torniai, Jim Balhoff, and Erik Segerdell


Aug 012012
 

The second day began with participants a little more rested (if not a little more confused).  We started the day with an impromptu follow up to the SVN tutorial where we illustrated how repository conflicts can be resolved, and files can be moved/deleted and reverted using SVN.  And there was much understanding.  We followed up this discussion with a review of the previous days’ ontology design documents that were developed in CMAP.  This lead to some interesting give-and-take about some specific anatomical problems (nervous system), and ultimately helped to illustrate the point that use-cases and a-priori planning are critical to the developmental goals of an anatomical ontology.

The primary topic of the day was an introduction to the OBO world.  We started with the ‘evilness’ of an OBO file format (an inside joke, see the corresponding powerpoint), and then moved into a OBO tutorial focused on search, queries, and navigation.  This allowed course participants to have an introduction to some basic reasoning, as well as to learn some of hte visualization tools available in OBOEdit that are not available in Protege. Unfortunately we were using the latest version of OBOEdit, and were thus acting as beta testers–this resulted in a completely unstable platform for a few of our Windows-using participants.

Visualization in OBO-Edit

Following this healthy mix of relatively abstract thinking and pragmatic application, we moved to a lecture and demonstration lead by Jim Balhoff on phenotype annotation using the “EQ” syntax, and post-composition. Jim demonstrated the basics of Phenex configuration and use and also some examples derived from the HAO’s approach to instance and phenotype modelling with respect to semantic phenotypes.

For supper we returned to the previous evening’s locale (it was that good) for beverages and elevated-debate.

Matt Yoder, Melissa Haendel, Jim Balhoff, and Erik Segerdell

Jul 312012
 

Today was the first day of the RCN co-sponsored Anatomy Ontology Course. The course includes an introduction to ontology principles, including basic logical reasoning, version control, use of ontology editors, and community resources, standards and activities. The course has twelve students in attendance, ranging from experts in paleobiology and the fin to limb transition, to comparative vertebrate embryogenesis, cartilaginous fishes, weevils, gastropod and cephalopod molluscs, arthropod circulatory systems, taxonomic nomenclature, plant disease, electric fish morphology, mammalian feeding muscle systems, food web representation, and anatomy of model organisms such as zebrafish and mouse.

The morning started with a bit of a grind, with lots of lecturing to broadly cover the basic principles of ontology logic and anatomical ontology development.  In between lectures a breakout exercise focused on answering the question “Are ontologies for me?”.  This lead to a nice round of discussion as to the specific problems associated with instantiating an anatomy ontology.

In the afternoon participants learned the basics of SVN (http://subversion.tigris.org/), and important tool used throughout the anatomical ontology community for managing the ontology-related metadata.  As part of the exercise participants collaboratively built a “pass-it-on-story”: “ It was a dark and stormy nite. And I forgot an umbrella. Melissa’s cat Peanut is sleeping. The rain falling on your face…The roar of the tyrannosaur woke the cat up and it jumped off the sofa. The cat scratched my face on the way off the coutch, it hurt me. Your mother. That was a strange dream, must stop eating so late at night!” To conclude work-day we learned to develop design documents for ontologies using CMAP (http://cmap.ihmc.us/) and parts of the nervous system. It is amazing to see how the classification schemes compared to each other and to existing anatomy ontologies.

A collage of cmaps designed by Anatomy Course participants.

To polish off the evening, participants gathered at Geer Street Garden for some excellent food and a nice round of one-to-one conversations.  Not unsurprisingly, the topic of homology was almost instantly raised during the day (and somewhat quickly squashed- it’s a dangerous path), but over beverages became a welcome topic.

Matt Yoder, Melissa Haendel, and Erik Segerdell