POC Conf. Call 5-17-11
POC meeting, Webex Conference Call; Date: Tuesday May 17th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_5-10-11?
Status Report for Upcoming Release:
- See the List of changes on our wiki which is available from the May_2011_Release_Page. In progress...
- List of terms that have been obsoleted or merged: New_terms_and_obsolete_terms_for_May2011_release. In progress...
- Reviews of the new version for release and the associated webinar: Plant_Ontology_Webinar-_May_2011_release
New terms requested by Moss Ontology
leaflet
As a related synonym of non-vascular leaf (in the sense that it is a small leaf)
leaflet midrib
As a related synonym of costa (not as a new term for a midrib in a non-vascular leaflet).
amphithecium
We have the term exothecium (PO:0030073): A portion of epidermis that is the outermost layer of a sporangium. [Crum]
Sporangium epidermis, epithecium, and amphithecium are currently synonyms of exothecium.
However, "these two (amphithecium and exothecium) are not synonymes - exothecium may develop from the amphithecium but not necessarily" (from Stefan)
Moss Ontology defines ampithecium as "The outer layer of cells of the sporangium, cf. endothecium.[Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary]"
Campbell, p. 13: "the outer tissue (amphithecium) of the embryo"
and also p. 179: "The terms endothecium and amphithecium have been given respectively to these two primary parts of the young Moss sporangium." (the inner and outer parts)
This contrasts with a broader use of endothecium (PO:0030049) across land plants, which we define as: A portion of ground tissue that is the sub-epidermal layer of a sporangium wall. Comment: The outermost layer of a sporangium wall, internal to the exothecium.
Both Parihar and Smith say that the amphithecium gives rise to the sporangium jacket layer (which is equivalent to the sporangium wall).
Definitions from Crum (Definitions from Schofeld are similar):
amphithecium: tissue of the embryo external to the endothecium, giving rise to the capsul wall and the peristome of true mosses and, in hornworts and peat mosses, spores.
endothecium: in bryophyte capsule, the embryonic tissue internal to the amphitecium; in liverworts hte endothecium produces sporogenous tissue; in Sphagnum, Andreaea, and hornworts, it produces columella and sporogenous tissue.
exothecial cells: the outer layer of cells of a capsule wall.
Proposed definitions (new or modified):
A portion of plant tissue that is the outer layer of a sporangium early in sporangium development.
Comment: Term used for bryophytes. An amphithecium may give rise to an ex
New apical cells
Proposed definitions:
caulonema meristematic apical cell: A protonema meristematic apical cell that is part of a caulonema.
chloronema meristematic apical cell: A protonema meristematic apical cell that is part of a chloronema.
rhizoid meristematic apical cell: A gametophytic meristematic apical cell that is part of a rhizoid.
gametophore bud initial
Proposed definition: A protonemal side branch initial that gives rise to a gametophore bud.
Sibling of protonemal side branch rhizoid initial (PO:0030077)
Add gametophore bud develops_from gametophore bud initial.
Timeline for release:
* Week of May 9th to 13th:
*Completed required edits and changes?
-All edits as per minutes are done :-)
-All known errors are fixed (sure others will show up)
-LC, RW, JE and PJ met on 5-12 to make a decision about the translations and the nouns vs adjectives in names (see below)- done
-Need to assert implied relations (see below)- in progress...
-Reassigning annotations from terms that been obsoleted. in progress...
See the page: along with database groups TAIR, Gramene, SGN, MaizeGDB, etc
-JE ran the script to give LC a list of the annotations attached to the obsoleted terms- see below
* Week of May 16th to 20th:
-Load new file onto Beta browser to check for any issues with loading, annotations
- send link to reviewers- Physcomitrella group, po-internal, others??
- Schedule a Plant Ontology Webinar- May 2011 release to demonstrate the new plant anatomy terms that have been added to accommodate mosses and give reviewers a brief tutorial on how to use PO.
-prepare release notices, update on PO page, facebook
* Week of May 23-27th:
-fix any final issues that have come up
-Release on live browser
-Send out announcements
Items arising from previous meetings:
Adjective form vs Noun form in term names
Do we need to use the adjective form for some, e.g., antheridial wall versus antheridium wall?
The advantage of using adjectives is that they often seem more grammatically correct.
The advantage of using nouns is that if the differntia is another PO class, then the noun will match that class name (for example, antheridium wall automatically matches to the PO class antheridium).
At the POC meeting on 5-10-11, we agree to use the noun form for all primary term names, and add the adjective form as an exact synonym.
The obo file has been changed to reflect this. Terms that had antheridial, archegonial, floral,embryonic, gametophytic, and sporophytic have been changed to antheridium, archegonium, flower, embryo, gametophyte and sporophyte, and the adjective forms made exact synonyms.
Maybe this does not work for every case? For example, should be we change apical meristem to apex meristem or meristematic apical cell to meristem apex cell?
What about terminal bud to terminus bud or axillary bud to axil bud? Basal endosperm transfer cell to base endosperm transfer cell? Cultured plant cell to culture plant cell?
Others that are probably okay to change: cambial/procambial, epidermal
We decided the make it a policy to use the noun name when the term refers to another term in the ontology. In the other cases such as for descriptors "extrafloral", we will use the form of the word that is in common use and makes the most sense.
idioblast
We use the term idioblast in the comments for plant cell and plant organ. At an earlier meeting, we discussed adding a term for idioblast.
idioblast (PO:0000283) was in the PO before. Def.: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue. [ISBN:0471245208]
PO:0000283 is obsolete: "This term was made obsolete because its a kind of attribute for a cell type."
This term has be un-obsoleted. See SourceForge for definition and comment.
Upcoming meetings 2011:
Phenotype RCN Meeting: June 1-3rd, Boulder CO
Goals of the Plant Working Group at this meeting (from the Phenotype RCN webpage):
"Plants – Go through relevant parts of Plant Ontology in order to develop proofs of concept; explore how to make links to homology. Examine existing annotations and determine kinds of info can be extracted. Analyze quantitative data and look for ways to annotate them."
PJ will attend
More details TBA
2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
-JE and JP will be attending
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
For more Workshop details: Semantic web.
Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.
Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).
Anybody going??
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
Full-Day Workshops Schedule:
July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability
July 26 6.30pm-9pm Evening Workshop: Common Logic
July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium
- LC will attend and represent the PO. Invite other plant people?
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.
Gramene will be putting together a workshop again, focusing on pathways. LC and PJ will present a PO poster.
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
Scott Schuette from the Department of Plant Biology at Southern Illinois University has been added as the sixth speaker in our symposium. He will speak on "Predicted Protein-Protein Interactions in the Moss Physcomitrella patens: A New Bioinformatic Resource".
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
