POC Conf. Call 2-14-12
POC meeting, Webex Conference Call; Date: Tuesday Feb 14th, 2012 10am (PST)
In attendance:
POC members:
Absent:
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12?
Back to POC Meetings Minutes
News and Report from the Wood Ontology Meeting
Upcoming PO Release:
In October, we had planned the next release for Feb 2012:
POC_Conf._Call_10-18-11#Next_PO_Release
Goals and Priorities:
- First major Revisions of PSDS (formerly PGDSO):
Status to 1-30-11:
-22 new terms added, many existing terms have been modified, eg changed all the 'phase' names to 'stage'
-most of the recent work has been on the whole plant development stage (PO:0007033) and its children
-will be working on wood development at the NYBG next week
- Complete old user requests/SF tracker items:
- This is an ongoing process, we have added about 50 new PAE terms recently
- New association files: Physcomitrella (released Jan 2012), small set of cotton annotations (TBA Feb 2012)
- Glossary of PO terms (see PO Glossary on dev)
This was discussed at the RCN meetings 2011, plan is to eventually replace APWeb Glossary. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.
what is the status of this?
Other Items from POC_Conf._Call_10-18-11
- Fix dbxrefs for Fragaria annotations
- ABRC annotations to PO and TO terms: These are descriptions of mutant phenotypes from Arabidopsis stock center, based on free text descriptions
- Links to images on PlantSystematics.org - Update?
Timeline:
- Target date for finishing edits:
- Target date for release:
Collaborative projects:
- Mapping of Flora of North America Glossary to PO terms:
RW: We now have id's for FNA terms. Can finish adding synonyms before this release, and probably mapping file for existing terms.
-What are the plans after this?
Once mappings are done, want to see how PO shows up in their data base. Show utility of PO for recovering descriptors from free text.
FNA is using natural language processing to map their descriptions to PO. We are starting with plant structures and later will add phenotype descriptors. We will start with leaf characters.
Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.
-Others (These may be longer term than the next release):
- Leaf character ontology for Phenotype RCN? see notes above
- Linking ontology terms to character matrices using Morphobank?
Also need to work on providing PO in glossary form, to eventually replace APWeb Glossary. PJ has hired new grad student who will be working on this. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.
Vascular tissues and cell types
leaf vein, primary vein, mid vein
These changes have been made to the obo file.
- leaf vein (PO:0020138)
Suggest: rename "leaf lamina vein"
revised def'n, leaf lamina vein (PO:0020138): A vascular bundle that is part of a leaf lamina vascular system.
part_of leaf lamina vascular system
synonym: leaf lamina vascular bundle
- primary leaf vein (new term)
proposed def'n: A leaf vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.
- midvein (PO:0020139)
revised def'n: A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).
broad synonyms: mid rib, midrib, mid-rib; exact synonym: vascular leaf midvein; related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128
We already have terms for secondary, tertiary, quaternary, and higher order veins.
Primary and secondary growth, etc.
request has been made to GO.
proposed terms for GO
primary growth (new term):
proposed definition: Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)
comment: Has its inception in the apical meristems (PO:0020144) and continues in their derivative meristems - protoderm (PO:0006210) and procambium (PO:0025275) - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.
is_a growth (GO:0040007)
secondary versus lateral growth
GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290
Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by Rudall et al. in Botanical Review (JSTOR:4354165).
I suggest that GO add a general term for lateral growth (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.
lateral growth (GO:new term): Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).
Comment: Includes thickening of plant axes (PO:0025004) due to the activity of a cambium (PO:0005597), known as secondary growth and found in most gymnosperms and dicotyledons, a primary thickening meristem (PO:0005039) as found in many monocotyledons, some ferns and some cycads, or secondary thickening meristem, (PO:0025414) as found in some monocotyledons.
proposed new def., secondary growth (GO:0080117): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)
Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium or phellogen (PO:0005599). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.
Add exact synonym "cambial secondary growth", which is makes the meaning clearer.
secondary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:0025414).
comment: Occurs in shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.
References: Fahn 1990, ISBN:0080374903; Rudall 1991, JSTOR:4354165
primary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)
comment: Occurs in shoot axes and rarely in roots in many monocotyledons.
Ref: JSTOR:4354165, Rudall 1991; and Esau ISBN:0471245208
diffuse secondary thickening (GO:new term): Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fiber cells of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.
comment: Occurs in the stems (PO:0009047) of some Arecaceae (palms).
Ref.: Fahn 1990, ISBN:0080374903
Upcoming meetings and Presentations 2012:
Phenotype RCN meeting, February 23rd-25th, 2012
The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.
It will be held again at NESCent (Durham, NC).
This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.
The projects of the Plant Working Group that we started in CO will be worked on during the next meeting, in the fall.
RW will attend, the RCN is covering her air travel.
Maize Genetics Meeting, March 15-18, 2012
The maize meetings are being held in Portland, OR this year.
For more info see: Maize Genetics Meeting 2012
Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.
Deadlines: Advance meeting registration is due by January 31, 2012.
LC submitted an abstract for consideration for a short talk
The PO and Gramene will most likely be co-hosting a workshop. Details TBA....
Katherine Esau Research Symposium
Integrating Plant Structure with Function, Development and Evolution
Thursday, March 29, 2012
1002 Giedt Hall, UC Davis
We will keep a track of this symposium and request if we can be invited for a short presentation. Esau's work has helped us build the ontology to a greater extent.
5th International Biocuration Conference
April 2-4, 2012, Washington DC
• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.
See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf
• Notification date: February 3, 2012
PJ is planning to attend, may do a talk. LC is planning to attend.
SPNHC 2012
Annual meeting of the Society for the Preservation of Natural History Collections
Yale University, New Haven Connecticut June 11-16, 2012
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).
From PJ: If we can show progress in the FNA work or Morphobank yes we should
Botany 2012
July 7 - 11, 2012 - Columbus, Ohio
Call for Symposia, Colloquia and Workshops:
RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.
Proposal was submitted, waiting for news.
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.
exhibitor's booth
We should also consider 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. (plus all the extras!)
• 2 months of Rotating Banner Ads in the online American Journal of Botany
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin
• A Rotating Banner Ad on the Botany 2012 abstract submission site
• A Rotating Banner Ad on the 2012 Conference Registration site.
PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.
- Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
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
Link to meeting page: ASPB2012
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX
Joint workshop is planned with PO, Gramene and TAIR
Registration scheduled to open first week in January.
Early Bird Registration: by May 11
Advance Discounted: May 12-June 15
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)
Relevant dates
- Paper submission deadline extended to...Feb. date?
- Feb. 28th, 2012: Notification of paper acceptance
- March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
- April 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
BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.
RW will circulate a draft of a manuscript for a plant disease extension of the Infectious Disease Ontology. Must be submitted by Jan. 31, 2012.
RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts
