POC-TraitNet meeting 05-28-2010, NYBG

POC-TraitNet Meeting 05-28-2010, 9:00 am, EDT New York Botanical Garden

Under Construction

Present: Ramona Walls (POC, New York Botanical Garden), Dan Bunker (Traitnet, New Jersey Institute of Technology), Farshid Ahrestani (TraitNet, Columbia University and NJIT)

Discussion Summary

One of TraitNet's goals is to develop a sematic web application that would allow users to access ecological datasets on the web. To do this they are developing a "functional trait ontology." This is currently focusing on plants, because there are far more plant trait databases. Plant functional traits includes plant entities (the physical parts of the plant = plant structures in PO) and plant characteristics (direct or derived measurements of plant entities made by ecologists/biologists).

They are aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms in TO were too specific to crop organism or to specific experimental procedures, and they needed many new characteristics that would be appropriate for ecologists. The TraitNet plant characteristics ontology development is being headed by Eric Garnier at CNRS in France.

The PO (plant structure) had the terms they need for their plant entity ontology, but at when they began working on their ontology, PO's structure was not suitable for their needs. After consulting with several ecologists/plant experts, they began working on their own ontology, using terms from PO. They are more interested in part_of relationships than is_a relationships. They have run into many of the same problems the PO has been dealing with, like where to classify terms or how to define upper level terms.

Ramona gave them some background on the PO (how it originally united several individual species ontologies from model organisms and is currently being revised to include all plants; who were the people involved; our participation in the OBO Foundry), showed them how to access annotations, talked about how scientists might use the PO (primary uses being the the genetics/genomics field), showed them the current test ontology on the dev browser and explained how to access the PO on SVN. She also explained that the anatomy_test file is under active development and is constantly changing.

There was a discussion of whether TraitNet should use the PO outright (once a new release is published) or use terms from the PO, but with their own structure. It was agreed that it would add power to both TraitNet and PO if the ontology was shared, since then users would have access to both genetic and ecological annotations. They may be able to use the PO/GO annotation form. If they use PO terms with their own structure, they will probably need to create alternate IDs, to avoid issues of different parentage in the two ontologies. Since ecologists generally study a limited set of plant structures, and they would probably only need to use a subset of PO terms, and might consider making a PO-Slim (see GO slims) for TraitNet.

TraitNet would like to evaluate a newer version of the PO to see if the structure will work for them, and if so, they will probably just adopt the PO, rather than create their own ontology. Perhaps PO can complete one branch of the ontology from top level to leaf terms, so they can get a better idea of the structure. TraitNet could also provide a list of terms they anticipate needing, and PO could show them how the new PO structure would work for those terms.

PO and TraitNet will stay in contact, and Farshid or Dan will contact Pankaj or Laurel after returning from an NCEAS working group on their semantic web application.