POC Conf. Call 6-26-12
POC meeting, Webex Conference Call; Date: Tuesday June 26th, 2012 10am PDT/1pm EDT
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
Absent: Chris Mungall (Lawrence Berkeley National Lab), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU)
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
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=66155882&rKey=029b3633d0018757
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=66155882&rKey=7cf456a12eba0306
Publications: AJB paper and PAE paper
- RW is ready to resubmit the AJB review paper, needs the letter from DWS as he is corresponding author.
- Draft of PAE paper has been circulated to PO-internal. Comments have been received by CM and BS
- Need to emphasis the focus on the PAE branch, revise the title
- Include near the beginning "this paper is designed to provide to more details on the anatomy portion of the PO to supplement the more general paper which was recently published in AJB- make it clear we are not trying to cover up the fact there are two related papers"
- Need a short write-up on the Inparanoid analysis from JE
- RW will send a merged copy to DWS and MAG again, along with her comments
- Collaborator groups TAIR, MaizeGDB and SGN are sending in a write up of how they use the PO
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- RW will do as PJ is away
-fix annotations on flower primordium- LC will do
-caryopsis new child of fruit? -Create SF tracker and work on for next release.
-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 We will eliminate the second part of the comment, and add "non-mobile gamete" (with a B) as a broad synonym.- Done
- Update the webpages- which ones are top priority? -Download page is top priority
-adventitious root nodule -Create SF tracker and work on for next release.
- file naming and which variations of the file to create for each release - check with cjm, review SOP page -We will stick with current SOPs for this release, and address this more fully for the next release.
Barry will send link to OBO Foundry doc with best practices for releases and versioning.
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.
Generative cells can occur in both angiosperms and gymnosperms. They are the same thing, even though they develop into something else. Need to look at Singh's book on gymnosperm embryology.
We will work on this more for the next release.
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
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.
Currently no one from the PO is planning to attend
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 - 9:00 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
- 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]
LM will be attending
Online Ontology Workshops at The University at Buffalo
The University at Buffalo is pleased to announce two on-line tutorials in ontology:
1. Introduction to Protégé for absolute beginners:
Saturday and Sunday, August 11-12, 2012.
Faculty: Ron Rudnicki (CUBRC, Buffalo), Alan Ruttenberg (University at Buffalo), Barry Smith (University at Buffalo)
This course will provide an introduction to the Protégé 4.2 ontology editor. It will begin with a brief introduction to ontology building, and to the use and importance of ontologies. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.
Saturday and Sunday, August 18-19, 2012
Faculty: Alan Ruttenberg and Barry Smith (University at Buffalo)
Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The tutorial will provide an introduction to the content and use of BFO in ontology development. Participants will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the new version 2.0 of the BFO ontology, including new formalizations of BFO in first-order logic and in OWL.
Both tutorials are also open for face-to-face participation.
PO/TO Crop Annotation Workshop at OSU
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
