POC Conf. Call 12-15-10
POC meeting, Webex Conference Call; Date: Wednesday Dec 15th, 2010 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC Conf. Call 12-1-10?
Restructuring PGDSO for Occurents
Suggested New "working" Structure of the PGDSO:
- The root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent").
LC, BS and RW met on 11-30 to discuss this restructuring, and changed the upper level term from plant life cycle process to plant process, plus several other changes.
The top level structure would have three branches, as below
None of the old term names or definitions have been changed yet, except to put (phase) on the end of some term names that did not have stage in their names.
Most of the terms from PGDSO went under plant structure development phase, but a few went under plant structure development process. In the case of seedling development (which went under plant structure development process) we added a new phase called seedling phase. Something like imbibition is not a phase, but a developmental process, so it went under plant structure development process. Could add a germination phase that begins with imbibition and ends with emergence of the radicle.
From last meeting:
-Add corresponding phases for each of the developmental processes.
For example: gametophytic phase corresponds to gametophyte development and leaf development phase could correspond to leaf development.
Then it would be possible to move the developmental processes to GO, but keep the phases in PO.
At the POC meeting on 11-10-10, we reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms. Barry suggested that his goal was to have all PO terms in one of two branches: plant structures (plant anatomical entity = independent continuant) and plant processes (plant life cycle process = occurent)
Lol and Ramona will work on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit.
- Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser.
Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.
-Stage term names need to be rewritten as nouns, for example: "whole plant in the phase where 1 leaf is visible
-Complex terms could be rendered using post coordination; ie: 'on the fly' for users, but some may need to have actual PO IDs in order to accommodate annotations.
New: Barry has suggested we need a term like 'plant life' ('life of whole plant') of which all phases would form parts
Upcoming meetings 2010-2011:
- Plant and Animal Genome XIX Conference
January 15-19, 2011 PAG 2011
PO Activities at PAG: -PAG_2011_Collaborators_Workshop and meeting with collaborators
Laurel, Ramona, DWS and Justin Preece are attending. PJ may attend for the weekend only as he is teaching. Alejandra cannot attend.
Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)
Poster:
-Outreach booth being organized by MaizeGBD
-Plant Phenotypes workshop and panel discussion (Laurel):
-Laurel is organizing a mini-symposium for the PO on Sunday morning.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.
Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?
Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology, and abstracts have been submitted.
No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds. This means that as of now, only Ramona and Pankaj are giving talks (two of the six slots are filled). Dennis might be able to give a talk, and we are allowed to request other speakers (but they would have to be willing to travel to the meeting). Do we still want to go ahead with attending this meeting? Should we ask the organizers if we can use part of the time to do a computer demonstration of annotation workshop for the PO? Need an answer on this today.
PJ will contact two potential speakers from New Zealand, who should be able to attend. RW will send him recommendation forms (if possible) or PJ can send the contact info to RW so she can fill out the forms. DS can give the talk that Angelica was going to give. If we have an open slot, will ask the organizers if we can use it for a discussion session.
