GCP Crop Ontology
POC- Crop Ontology meeting, Webex Conference Call; Date: May 6th, 2010 1 pm (PDT)
In attendance: POC member: Laurel Cooper (OSU),Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico,
Agenda:
1.Introduction and overview of the Crop Ontology-
Rosemary showed an introduction to the GCP Crop ontology website and the layout of the Crop Ontology Domains:
010-089 General Germplasm Ontology Ontology
090-099 Taxonomic Ontology
100-299 Plant Anatomy & Development Ontology
300-499 Phenotype and Trait Ontology Ontology
500-699 Structural and Functional Genomic Ontology
700-799 Location and Environmental Ontology
800-899 General Science Ontology
900-999 Other (Sub-domain or Site-Specific) Ontology
The overall goals of the Crop Ontology are to unify and connect the many databases. There are different ontologies for each of the species of interest rice, wheat, maize, banana, chickpea, sorghum. Within these ontologies, there are species-specific descriptions of plant anatomy and growth and development terms that can be browsed on the GCP - Crop Ontology Lookup Service.
There is a listing for on the Ontology lookup service for PO_anatomy ontology CO_100:0000000, which lists terms from the PO, but with the CO_100: prefix. This is being phased out and replaced by the species specific ontologies. Within these, there are terms common to CO and PO, but in most cases, the definitions are more specific to refer to the individual plant species. In these cases, the PO term is listed as an xref.For example: Musa (banana) leaf CO_125:0000002.
2.Avenues of possible collaborative activity:
Addition of species-specific terms to the PO- corm seems to be missing from the PO although there is a PO ID PO:0004542 associated with it (analog xref).
Updating the PO files on the CO webpage is done automatically on a set schedule. Daily?
We are not sure about whether or not the xref links in the species-specific ontologies will be automatically updated.
Action Items:
Rosemary will continue to take part in the POC Conf calls as she is available,
We will meet at the Bio-Ontologies meeting in July in Boston
We will plan another call to discuss collaborations in ~ a month.
