Minutes POC Dec 2009
Report of the POC Meeting Dec 17th, 2009 Cornell University
Overall objectives were to create a set of top level reference terms (parents) that satisfy the needs for all the plants that are going included in the Plant Ontology (not just the Angiosperms). The new additions are Gymnosperms, ferns, mosses, lycopods and algae eventually. - The focus was on the Plant Anatomy ontology at this meeting- we did not touch the growth stages.
At the meeting: Maria Alejandra Gandolfo (Bailey Hortium, Cornell), Dennis Stevenson and Ramona Walls (NYBG), Barry Smith (OBO Foundry), Laurel Cooper (OSU) Pankaj Jaiswal (OSU) and Chris Mungall (LBNL)- over Webex
Objectives and Progress: 1) Introduce the changes discussed at the last meeting. See Appendix A-1 Implementation Timeline.
2) Define the top level parent terms- look over the ontologies and find the deficiencies. Progress: Barry defined the new organization of the ontology as “PARO”- Plant Anatomy Reference Ontology. There was much discussion about each of these and how to make them consistent with CARO (Common Anatomy Reference Ontology). The new top level reference terms (parents) in PARO were defined as: plant cell, plant organ, portion of plant tissue and whole plant. It was agreed that the term: in vitro cultured plant cell, tissue, and organ should be moved to a separate ontology root. Changes will be submitted for review to SourceForge.net > Projects > Open Biomedical Ontologies > Tracker > Plant Ontology (PO) TERM requests
3) Modify definitions for organ, tissue, cell and add new terms to accommodate non-angiosperms. There was much discussion about each of these as well and how to make them consistent with CARO. -Lol instituted the edits to the terms and definitions into a working version of the Plant Ontology file using OBO-Edit. The terms that were out of place or lacked the “is_a” term were moved to a new temporary root called “Problem Terms”. Changes will be submitted for review to SourceForge.net > Projects > Open Biomedical Ontologies > Tracker > Plant Ontology (PO) TERM requests
4) Review the missing and incomplete (~200) “is_a” terms. (Go through the SourceForge items that Chris Mungall submitted) -Reviewed the suggested new upper level terms: stalk, vein, margin that encompass about 20 of the terms with the missing 'is_a' relationships. Lol instituted the edits to the terms and definitions into a working version of the Plant Ontology file using OBO-Edit. The new or modified terms were moved from the “Problem Terms” and placed under the new parent terms.
5) Create a template on the PO Wiki for a few sample image files from MAG. How will these be annotated? Descriptors? The target is to map images to anatomy terms from various taxonomic clades. e.g. Ovules This is underway and in progress and will be facilitated by the redefinition of the PARO.
6) Sanity checks- Chris Mungall: cross reference products to GO and TO- in progress
7) Plans for Trends Paper: Spring 2010. This was discussed briefly, based on the diagram Pankaj had included.
8) Plans for outreach activities: Teachers and NYBG, Annotation Jamborees at ASPB, others? In progress- Tabled for discussion at the next conference call, as people's schedules were uncertain at this time
9) Schedule monthly conference calls for the group- This will be set up after the holidays, as people's schedules were uncertain at this time. Barry said he preferred to correspond by email.
10) Schedule weekly conference calls/webex between Lol and Ramona- This will be set up once Ramona officially joins the project in January.
11) Meeting at PAG 2010? Who is attending? Lol and Justin are presenting a Computer Demonstration. Lol will visit LBNL afterwards for OBO-Edit training with Chris and Amina.
