POC Conf. Call 2-19-13
POC meeting, Webex Conference Call; Date: Tuesday Feb 19th, 2013 10am PST/1pm EST
In attendance: Laurel Cooper (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU).
Absent: Pankaj Jaiswal (OSU)
Defining the plant structure development stages
On last week's conf call Barry said we should not be defining the plant structure development stages as a stage that has as a primary participant a plant structure and also adding the has_participant (or participates_in) relation as well. That makes sense as it does seem to be somewhat circular,and if the definitions are ever formalized, then it would be redundant. The problem is that we already have a whole bunch of them defined this way, besides the new ones added for the shoot system.
Examples already in the Plant Ontology:
- collective plant organ structure development stage (PO:0025338)
- whole plant development stage (PO:0007033)
- fruit development stage (PO:0001002) (currently no has_participant relation to fruit)
- plant organ development stage (PO:0025339)
- plant tissue development stage (PO:0025423)
- seed development stage (PO:0001170)
- trichome development stage (PO:0025368)
- gametophyte development stage (PO:0028003)
- sporophyte development stage (PO:0028002)
For the terms I have recently added, I think the best solution is to change the definitions. These include most children of the shoot system development stage (new PO:0025527). I think I will to have to go back and revise the others at some point so that they are consistent.
- Current def'n: shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).
added relation: shoot system (PO:0009006) participates_in shoot system development stage
Proposed Revised def'n:
- shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that begins with the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage or death.
Notes:
Need to revise the definition of the shoot system to include all meristems, not just the the shoot apical meristems. Also we decided that the shoot system development stage begins with the development of the plant organs and ends when the plant undergoes senescence and or death.
current def'n: A collective plant organ structure (PO:0025007) that produces shoot apical meristems (PO:0020148) and the plant structures that arise from them.
What about the development of vegetative shoots??
Revised relation: shoot system (PO:0009006) shoot system development stage has_participant shoot system
This should be shoot system development stage has_participant shoot system. Can the shoot system ever exist outside of the shoot system development stage? yes
Also need to revise:
- bud development stage (new PO:0025528): A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).
added relations: bud (PO:0009006) participates_in bud development stage (PO:0025528).
revised def'n: A shoot system development stage (PO:0025527) that begins
- reproductive shoot system development stage (new PO:0025530)
Proposed def'n: A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).
add relation: reproductive shoot system (PO:0025082) participates_in reproductive shoot system development stage (PO:0025530).
- flower development stage (PO:0007615): A reproductive shoot system development stage (PO:0025530) that has as primary participant a flower (PO:0009046).
already has a cross product flower is participant, needs to be revised for the new parent term.
- inflorescence development stage (PO:0001083)
current def'n: A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
added relation: inflorescence (PO:0009049) participates_in reproductive shoot system development stage (PO:0025530)
All have DbxRef to OBO_SF_PO: 3595703
prothallial cell
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
prothallial cell (PO:0025533):
proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.
should add the PO id for microgametophyte (PO:0025280) to the definition
For reference about prothallial cells in gmnosperms see:
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
Available online: Coulter + Chamberlain, 1910
Upcoming meetings and Presentations 2013:
Phenotype Ontology RCN Annual Summit Meeting, Feb. 25th - 27th, 2013, Durham, NC
The workshop and meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, from Monday morning, February 25 through Wednesday noon, February 27th (you would arrive Sunday evening).
Overall goals: To introduce and establish communication and collaboration among scientists from different research backgrounds. The two primary themes: The use of text mining phenotypes and representing behavior in ontologies.
For more information: please contact Paula Mabee (pmabee@usd.edu)
Biocuration 2013 conference, Cambridge, 7-10th April 2013
submission deadline for abstracts for posters is Jan 31st.
website and registration are now open: Biocuration 2013
PRO-PO-GO meeting, May 15-16th 2013
Please see this page for more information: PRO-PO-GO_Meeting
Location: Buffalo, NY
Dates: May 15-16th, 2013.
Goals:
- To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
- To identify potentially fruitful applications which such enhanced coordination might bring
- To enhance the Protein Ontology treatment of plant-related proteins
- To address coordination issues between the GO and PO, for example as concerns treatment of development stages
- To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]
Tentative participant list:
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)
BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO
10th Extended Semantic Web Conference (ESWC) Montpellier, 26-30 May 2013
Extended Semantic Web Conference Montpellier
Location: Montpellier, 26-30 May 2013.
Semantics for Biodiversity (S4BIODIV)
Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.
Paraphrased from email exchange with EA (Bioversity):
Ontologies will be part of the workshop discussion. The latest development sent by Justin on AISO also raised interest of the organizing committee. So, we would you like that the Plant Ontology team be represented in the scientific committee of our workshop.
This is a very first draft of course but will provide you with the context, scientific objectives, and expected outputs. Would you accept in principle (if the workshop is accepted and funds raised) to join our committee and submit a a paper for a presentation and/or poster? Deadline will be March and April.
MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013
5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)
The New York Botanical Garden & Fordham University
Botanical Society Meeting July 27-31st New Orleans
- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract
