POC Conf. Call 6-26-12
POC meeting, Webex Conference Call; Date: Tuesday June 26th, 2012 10am PDT/1pm EDT
In attendance:
POC members:
Absent:
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_6-19-12?
Back to POC Meetings Minutes
Upcoming Release:
At the POC_Conf._Call_4-10-12 we decide that the next release would be in late June to early July, before the BSA meetings. We have a number of important changes that have taken place,
- 20 new PAE terms, including the new upper-level level terms for the PAE
For more information about the changes see: Summary of Changes to PO July 2012 and New terms and obsolete terms July 2012 Release
Only have obsoleted two terms:
consider flower meristem (PO:0000229) or floral structure primordium (PO:0025477) instead.
This has 27 annotations, mostly from TAIR, one Gramene and one SGN
- adventitious root primordium (PO:0008038) - consider basal root primordium (PO:0025479) and consider shoot-borne root primordium (PO:0025480)
LC has sent an email to TAIR and SGN to inform them of the upcoming changes.
- Propose we go ahead and do this release, so we have an updated version on the live site.
We will make the release asap, and update the manuscripts to match the upcoming release. It will not be in review before the release is out.
JE will look into whether or not he can make the changes to the website and server at the same time as the release.
What other things should be included in it- open trackers that need to be dealt with:
We will finish edits this week, so the ontology can be reviewed next week and preparations made for the release. Should try to have release out before the Botany meeting (before July 4th).
Only the changes on today's agenda will go into the next release. Other items (including ovary) can wait until the next release.
Ale will need a list of new terms (RW will send to her in the next few days).
To-do list for July 2012 Release
-new multi-tissue structures and CPS still say LC:test, change to POC:curators done
-fix definition hilum groove, open tracker -Done. Already on tracker for parts of seed.
-need icon for located_in, update on wiki page
-fix annotations on flower primordium
-caryopsis new child of fruit?
-pericarp on emergence terms RW: Maybe just add comment to seed emergence terms.
-update definitions and comments of upper level terms with PO ids and new names done
-fix comment on plant egg cell: see SF tracker RW: Looks like this is already done.
- Update the webpages- which ones are top priority?
-adventitious root nodule ?
- file naming and which variations of the file to create for each release - check with cjm, review SOP page
Things to fix
generative cell (PO:0020097) and related terms
We need to fix this definition, as it currently only includes angiosperms
Current def'n: generative cell (PO:0020097): A cell of the male gametophyte of angiosperms that divides to produce two male gametes or sperm cells. [source: APweb:Glossary]
Proposed def'n: A plant cell (PO:0009002) of the microgametophyte (PO:0025280) of seed plants that divides to produce two plant sperm cells (PO:0000084) in angiosperms and the the sterile cell (PO:xxxxxxx) and spermatogenous cell (PO:xxxxxxx) in gymnosperms.
Need to add to PO: sterile cell (PO:xxxxxxx) and spermatogenous cell (PO:xxxxxxx)
should be: part_of the microgametophyte (PO:0025280)
Definition from Raven 5th ed: generative cell: 1. In gymnosperms, the cell of the male gametophyte that divides to form the sterile and spermatogenous cells
2. In angiosperms, the cell of the male gametophyte that divides to form two sperm
Probably should also have the prothallial cell- part of the gymnosperm pollen grain: Definition from Raven 5th ed: The sterile cell or cells found in the male gametophytes, or microgametophytes of vascular plants other than angiosperms; believed to be the remnants of the vegetative tissue of the male gametophyte.
Upcoming meetings and Presentations 2012:
Botany 2012
July 7 - 11, 2012 - Columbus, Ohio
PO workshop on Sunday, July 8th, 9:00AM - 12:00PM
see: link on Botany 2012 workshops schedule to view the abstract.
Wiki page for workshop: Plant Ontology Workshop, Botany 2012
Goal of workshop: To teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices.
A desktop version of the image annotation software should be ready to demo at this meeting.
Announcement has been posted on the PO home page and FB page.
exhibitor's booth
We had considered hosting an outreach booth. (Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference)
We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth
RW will look into purchasing a TV/monitor (~22") that could display a rotating slideshow. Could also be used for future presentations
Bio-Ontologies SIG 2012
Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012
When: Submissions Due: April 13th, 2012 (Fri)
Three types of submissions.
- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page
Successful papers will be presented at the Bio-Ontologies SIG.
Poster abstracts: time will be allocated during the 2 days for at least one poster session.
Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.
ASPB Plant Biology 2012
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX
Link to meeting page: ASPB2012
Abstract was submitted for submission: Poster Number: P28002
Plant Informatics Workshop is planned with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 10:30 PM
LC and PJ are attending
ICBO 2012
International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria
co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)
RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on Plant Disease Ontology.
Relevant dates
- Feb. 28th, 2012: Notification of paper acceptance
- April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
- May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
- June 30th 2012: Deadline for all camera-ready copies for the proceedings
RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts
Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012
Link to: Anatomy Ontology course
from Paula Mabee: Opening are available the Anatomy Ontology course.
Link to Course materials
This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).
Apply here: [1]
Application deadline is April 4th, 2012 (extended through mid-April)
LM will be attending
Crop Ontology Workshop
For more information see the wiki page: Plant Ontology Crop Annotation Workshop at OSU, 2012
Dates: Sept. 13-15th
The focus of the workshop will be on mostly development stages and traits for the crop plants
