POC Conf. Call 1-29-13
POC meeting, Webex Conference Call; Date: Tuesday Jan 29th, 2013 10am PST/1pm EST
In attendance:
Updates
- Release #19 is out Dec 31st- Release_19
Highlights: Addition of 35 new terms, for both the Plant Anatomical Entity (20) and Plant Structure Development Stage (15) branches. It also includes new and updated annotation data for Oryza sativa, Vitis vinifera, Gossypium hirsutum and Arabidopsis thaliana.
This release also includes a new feature: Japanese translations displayed on the browser as synonyms for the Plant Anatomical Entity terms.
- Status of new hire at NYBG?
- Publications- met with RW in PAG about PSDS paper
- cROP proposal and ERA-CAPS- see below
Open trackers: To be addressed: PSDS Terms
shoot system development stage
Revisions and new terms needed for grape data set:
We are deficient in terms to describe the stages of development of the shoot system (PO:0009006).
We currently have collective plant organ structure development stage (PO:0025338) with two direct child terms: flower development stage (PO:0007615) and inflorescence development stage (PO:0001083).
I suggest we should have:
shoot system development stage (PO:0025527): A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).
added relations: shoot system (PO:0009006) participates_in shoot system development stage
bud development stage (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).
bud dormancy stage (PO:0025529): proposed def'n: A bud development stage (PO:0025528) during which a bud (PO:0009006) participates in a bud dormancy process (GO:0097207)
bud dormancy process GO:0097207
Definition: A dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a bud. Bud dormancy is a suspension of most physiological activity and growth that can be reactivated. It may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. The exit from bud dormancy is marked by the resumed growth of the bud.
Source: GOC:PO_curators, PO_REF:00009
Comment: Bud dormancy may precede dormancy of the whole plant.
Then we could add:
New term: bud swell stage PO:0025531
Synonyms: exact: E-L 2 Definition: A bud development stage (PO:0025528) during which a bud (PO:0009006) enlarges due to growth of the shoot system (PO:0009006).
New term: bud burst stage (PO:0025532):
A shoot system development stage (PO:0025527) during which a shoot system (PO:0009006) emerges from the bud (PO:0009006).
Synonyms: exact: E-L 4
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).
and revise the two existing child terms:
flower development stage (PO:0007615): A collective plant organ structure development stage (PO:0025338) that has as primary participant a flower (PO:0009046).
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
inflorescence development stage (PO:0001083)
current def'n: Stages of development of an inflorescence defined by characteristic morphological, structural, histological or other visible features.
Revised: 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
References for grape terms:
Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 link
Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 link
Open trackers: To be addressed: PAE terms
basal axillary shoot system (tiller) (PO:0005001)
Currently: An axillary shoot shoot system (PO:0006343) that develops from an axillary vegetative bud (PO:0004712) that is part of a stem base (PO:0008039).
Comment: Called a tiller in the Poaceae.
This should be revised to develop from an axillary bud rather than an axillary vegetative bud (PO:0004712), since tillers often become reproductive.
Proposed def'n: An axillary shoot system (PO:0006343) that develops from an axillary bud (PO:0004709) that is part of a stem base (PO:0008039).
also tillers occur in many grasses, not just the Poaceae
-add SF DBXref
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.
seta
seta (PO:0030032):
Currently: A plant axis that holds up a spore capsule. [source: ISBN:0962073342, POC:curators]
proposed def'n : A stalk (PO:0025066) that supports a spore capsule, the sporangium (PO:0025094). [source: ISBN:9780473067304]
Comment: Found in some bryophytes, especially mosses and liverworts.
Malcolm B, Malcolm N (2000) Mosses and other bryophytes: an illustrated glossary. Micro-Optics Press
Comments from SF:
"A stalk is a cardinal organ part, and should be part of the same organ as the thing it is holding up (e.g., a petiole is part of a leaf and holds up the lamina that is part of the same leaf). The seta and the capsule are not part of the same organ. The seta is like the stem of a moss sporophyte and is thus a plant axis. It could more specifically be a shoot axis." (RW)
stalk (PO:0025066): A cardinal organ part that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part. Comment: Some stalks may be ridged or grooved.
note: It does not say it has to be part of the same organ as the thing it is holding up.
- plant axis: An axial plant organ, narrow synonym= stalk
Other examples of stalks: filament of stamen, antheridium stalk (PO:0030035), archegonium stalk (PO:0030036), funicle (PO:0020006), petiolule (PO:0020050), petiole (PO:0020038), leaf rachis (PO:0020055)
antheridiophore (PO:0030033)
Def'n: A stalk (PO:0025066) that supports an antheridium head (PO:0030075). [source: ISBN:0962073342] Comment: Found in mosses and other bryophytes such as the liverwort Marchantiales.
archegoniophore (PO:0030034): Def'n: A stalk (PO:0025066) that supports an archegonium head (PO:0030034). [source: ISBN:0962073342]
Comment: Found in Marchantiales.
The seta is part of the sporophyte (not a PO term) and supports the moss capsule (synonym of sporangium)
Open tracker for moss capsule
Meeting Report
PAG 2013, San Diego, CA; January 12th - 16th, 2013
We hosted a workshop focusing on:
Applications of Ontologies for Plant and Animal Genomics
- Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6
Speakers: Eva Huala, Reinhard Simon, Elizabeth Arnaud, Chris Mungall, and Pankal presented the cROP Vision
posters:
LC presented a poster #P0936 "Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics".
JP presented an AISO Computer Demo: Date and Time: Sunday, January 13, 2013; 5:20 PM, California room
Update on planning for cROP proposal
EU consortium is moving ahead with the ERA-CAPs propsal- they will had a meeting last week in Paris to proceed with writing
See notes on gdocs
Schema: see 1-28-13 ppt
From EA: "As our project (ie:GCP) cannot be a BREAD idea and EAGER project, Diana suggested that The GCP/Bioversity entry point in the proposal can be through SAVI, Science Across Virtual Institutes, showing that the product we are all aiming at will be the glue between the centers. Particularly if our product is web based. We can also be partners in the PGRP proposal."
Components of cROP
Plant Ontology
Central reference for all the others
Reference Trait Ontology
- Ref-TO should be hosted and coordinated at OSU, but should solicit input on it from the EU partners- responsibility for various aspects
Plant Disease Ontology-PDO
- involvement of pathologist at OSU?
Environment Ontology
Group at Jurlich is interested in taking responsibility for it-
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.
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):
"We are finalizing a workshop proposal to be submitted in the 23rd to the conference organizing committee. In parallel, we are developing a proposal for raising some support funds.
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
