Aug 062013

The final day of the course was presentation day, where we got to hear about everyone’s research questions and how they were going to use (or not!) ontologies for their work. We group brainstormed solutions and next steps for everyone’s projects. The group was very synergistic and we believe that we’ll see some nice contributions and connections being made in upcoming months in the ontology community. Highlights from the presentations are below:


Chris Sheil:

Developmental comparative morphology of the chondrocranium in turtles


Elise Larsen:

Developing a knowledge base of North American butterfly monitoring data


Ashleigh Smythe:

Comparative morphology of nematode anatomy and behavior


Mariangeles Arce:

Connectivity and function of cranial and ventral musculature in catfishes


Peter Uetz:

Representing diversity of form in The Reptile Database


Corrine Blank:

Phenomics of Prokaryota for Tree of Life


Jing Liu:

Use of CharaParser and ontologies to generate plant character matrices from publications


Maria Christina Diaz:

Development of the Porifera ontology to represent sponge comparative anatomy and biodiversity


Eric Chen:

Characterizing gene retention after whole genome duplication, triplication


John Wieczorek:

Semanticizing the Darwin Core


Laura Jackson:

Gene regulation of fin positioning in fishes


Steve Elliott:

Representing the semantic types in the Embryo Project


Anne Thessen:

Phenomics of Eukaryotic microbes


Aug 032013

We spent the entire Day 3 working on learning Protege and exploring the use of various OWL2 capabilities. The students worked at their own pace, but all made it to the light at the end of the tunnel. They are all now enlightened :-) (bearers_of some instance_of PATO:0001291). We had also converted the students VUE files into OWL, and some students were able to start work on their OWL files. Day 4 of the course was focused on developing skills around reuse of other ontologies and data interoperability. We learned techniques for performing OWL imports and the use of MIREOT (Minimum Information to Reference and External Ontology Term), which is basically a way to use a subset of another ontology in your own.

We saved a discussion of homology for the end of the last full day, knowing full well that a) the discussion would be vigorous, b) people would have to break for food at some time, and c) the conversation could continue into the evening. Kudos to our students, as they seemed to immediately understand our community’s general approach to this subject, to the degree that nobody even foamed at the mouth.

Jul 312013

Day two started with a “speed-dating” approach with instructors pairing off for short periods with participants to strategize and work on individual projects. VUE files representing participants’ projects continued to be formalized, some now contain many nodes and some are even very pretty. These visual representations will be translated into OWL files shortly, and further refined in Protege. The morning progressed into a presentation on annotations, where tools like Phenex and Phenote were outlined.

In the afternoon we had a great overview from Karen Kranston, PI on the OpenTreeOfLife project, and we discussed how ontologies may or may not be useful for projects like OToL. We continued with a survey of web-based resources related to evolutionary biology, with participants auditing well known websites for their use, or lack thereof of ontologies. The day concluded with the last bit of preparation prior to our big practical exercise on Protege on Wednesday, a nice overview of OWL, with specific reference to the (very nice) primer. We’re looking forward to the first real taste of formalization with the Protege tutorial, and the creation of individuals’ own ontologies.


Matt Yoder, Melissa Haendel, Erik Segerdell and Jim Balhoff

Jul 302013

The first day of the NESCent and Phenotype RCN sponsored Ontologies Course started with introductions. What a diverse group we have this year, with expertise in: phylogenetics and muscle anatomy of South American fishes, gene retention in plants, reptile limb development, microbiology, systematics of nematodes, natural history collections, sponge taxonomy and evolution, herpetology and turtle anatomy, biodiversity standards and Darwin Core, ecology and Lepidoptera traits, text mining species and character matrices, mathematical models in evolutionary biology, developmental biology of fishes and evolution of habitat and physiological traits in Cyanobacteria and Archaea. WOW!

The day was packed with a lot of lecturing about logic and how it can be your friend, true path violations, ontology best practices, and the community that we are convincing our students that they are now part of ;-). However, we promised that on Tuesday we’d get them using what they had been taught and it would all make more sense once they got their hands dirty. The students had homework last night – they started working on modeling their own ontology project for the course in VUE, and we plan to convert these files to OWL with Jim’s new script so that they can continue their work in OWL following Wednesday’s Protege tutorial. We also had a very interesting discussion about the differences between specimens and samples, intent to collect, and whether or not populations or tissues can be target populations for sample collection.


Erwin Mill Building, Durham, NC

Melissa Haendel, Matt Yoder, Erik Segerdell and Jim Balhoff