POC Conf. Call 1-4-11
POC meeting, Webex Conference Call; Date: Tuesday Jan 4th, 2011 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC Conf. Call 12-28-10?
Completion of Changes for the Next Release:
Timeline and Plan for Upcoming Release:
- We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the Beta browser (Thanks Justin E!)
- Internal review before full release:
- Annotations that need to be moved:
- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)
-see also Jan 2011_Release_Page
List of things to fix:
Issues arising from last week's meeting:
inflorescence and infructescence branch orders, secondary inflorescence
There was some debate last week about whether or not to name the sub-inflorescences that arise from the main inflorescence axis primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders.
We don't have terms for different vegetative branching orders (outside the inflorescence), but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes.
We do have terms for inflorescence branch orders:
inflorescence axis (PO:0020122): A shoot axis that is part of an inflorescence. [describes any order axis in an inflorescence]
inflorescence branch (PO:0009081): Any branch forming from the primary or the higher order inflorescence axis.
second order inflorescence branch (PO:0006321): Any branch forming from the primary or first order inflorescence branch.
third order inflorescence branch (PO:0006322): Any branch forming from the second order inflorescence branch.
We don't have terms for first order inflorescence branch or primary inflorescence axis, so it is unclear if the use of the phrase "first order branch" in the definition of second order inflorescence branch refers to the main axis or a branch from this axis. This makes all of the definitions ambiguous, but since they have annotation attached to them, we cannot change them until it is clear what they mean.
All of the annotations for second order inflorescence branch are from QTL, and most of them are for genes called "primary branch" or "primary branch length" Most of the annotations for third order inflorescence branch are for a gene called "secondary branch."
- Also need to add terms for infructescence axis and branches (for next set of revisions?).
- Proposed term names and definitions (may change, depending on resolution of inflorescence branch order names):
secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower
secondary infructescence: A reproductive shoot system that is part of an infructescence and has as parts a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit
sensu terms
- RW replaced all of the ~80 term names that were structure (sensu Taxon) with Taxon structure. However, there were three terms that were obsoleted and replaced with new terms in November, rather than being renamed:
-floret (sensu Poaceae), floret meristem (sensu Poaceae) and gynoecium (sensu Poaceae)
Either we should unobsolete these terms and rename them or obsolete all the terms with sensu in their names. Not clear why they needed to be obsoleted for a renaming.
Action:
- Elizabeth Arnaud confirmed we should use "musa as their terms encompass banana and plantain
TIPS proposal
An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010. It was sent out to everyone by email.
Computer Demo for PAG:
Upcoming meetings 2011:
- Plant and Animal Genome XIX Conference January 15-19, 2011 PAG 2011
Laurel, Ramona, DWS and Justin Preece are attending. PJ will attend for the weekend only as he is teaching. Alejandra cannot attend.
PO Activities at PAG:
- Computer Demonstration: Ramona will present.
Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)
- Plant Phenotypes workshop and panel discussion: Laurel will present.
" The Plant Ontology: Linking phenotypes and genomics across plant taxa"
Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am
- PAG_2011_Collaborators_Workshop and meeting with collaborators
Sunday Late Morning:
Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)
PO Workshop Reg'n site and Survey
- Poster: PO Poster Monday 3:00 pm - 4:30 pm
- Outreach Booth being organized by MaizeGBD- More info TBA
- Phenotype Ontology RCN Summit
February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,
Laurel and Pankaj will be attending.
* 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.
Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. 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.
Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.
We received permission to use the 6th time slot for a discussion session, but need to have a commitment that someone will lead the discussion. PJ will do it.
