Difference between revisions of "POC Conf. Call 4-5-11"
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=Issues arising from last week's meeting:= | =Issues arising from last week's meeting:= | ||
| − | =Sporangium and its parts= | + | =New Physcomitrella and related terms= |
| + | |||
| + | ==Sporangium and its parts== | ||
This is continued from our discussion at the [[POC_Conf._Call_3-8-11]] | This is continued from our discussion at the [[POC_Conf._Call_3-8-11]] | ||
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| + | |||
| + | ==Plant organs:== | ||
| + | |||
| + | ===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]=== | ||
| + | - This is the term used for the gametophore stem or axis. | ||
| + | |||
| + | Suggest using '''gametophore axis''' as primary name, cauloid as synonym. | ||
| + | |||
| + | Proposed def'n: A shoot axis that is part of a gametophore. | ||
| + | |||
| + | Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase. | ||
| + | |||
| + | intersection_of: is_a plant axis, intersection_of: part_of gametophore | ||
| + | |||
| + | -Also suggest adding terms for '''gametophore stem''' and '''gametophore branch'''. | ||
| + | |||
| + | |||
| + | '''gametophore stem''': A stem that is part of a gametophore. | ||
| + | |||
| + | is_a stem, part_of gametophore | ||
| + | |||
| + | |||
| + | '''gametophore branch''': A branch that is part of a gametophore. | ||
| + | |||
| + | is_a branch, part_of gametophore | ||
| + | |||
| + | |||
| + | -If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or branch). | ||
| + | |||
| + | ===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract]=== | ||
| + | |||
| + | - The specialized phyllids surrounding the antheridia. | ||
| + | |||
| + | Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition) | ||
| + | |||
| + | A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract. | ||
| + | |||
| + | Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase | ||
| + | |||
| + | Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts. | ||
| + | |||
| + | ===[https://sourceforge.net/tracker/?func=detail&aid=3234965&group_id=76834&atid=835555 foot]=== | ||
| + | |||
| + | Moss Ontology definition: The base of the sporophytes in mosses | ||
| + | |||
| + | '''Proposed name and def.: sporophyte foot:''' A plant organ (?) that is the base of a whole plant in the sporophytic phase, below the seta, that attaches it to the gametophore. (ref: Schofeld) | ||
| + | |||
| + | Comment: Found in bryophytes. The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum) | ||
| + | |||
| + | participates_in sporophytic phase, has_part transfer cell, only_in_taxon bryophytes (I know this isn't a clade, will have to create a pseudo-clade). | ||
| + | |||
| + | - Should we add a term for sporophyte foot haustorium when we deal with portions of plant tissue or is the whole foot the haustorium? | ||
=Upcoming meetings 2011:= | =Upcoming meetings 2011:= | ||
Revision as of 19:04, 28 March 2011
POC meeting, Webex Conference Call; Date: Tuesday Apr 5th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_3-29-11?
Issues arising from last week's meeting:
Sporangium and its parts
This is continued from our discussion at the POC_Conf._Call_3-8-11
Plant organs:
cauloid
- This is the term used for the gametophore stem or axis.
Suggest using gametophore axis as primary name, cauloid as synonym.
Proposed def'n: A shoot axis that is part of a gametophore.
Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
intersection_of: is_a plant axis, intersection_of: part_of gametophore
-Also suggest adding terms for gametophore stem and gametophore branch.
gametophore stem: A stem that is part of a gametophore.
is_a stem, part_of gametophore
gametophore branch: A branch that is part of a gametophore.
is_a branch, part_of gametophore
-If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or branch).
perigonial bract
- The specialized phyllids surrounding the antheridia.
Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.
Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase
Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.
foot
Moss Ontology definition: The base of the sporophytes in mosses
Proposed name and def.: sporophyte foot: A plant organ (?) that is the base of a whole plant in the sporophytic phase, below the seta, that attaches it to the gametophore. (ref: Schofeld)
Comment: Found in bryophytes. The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum)
participates_in sporophytic phase, has_part transfer cell, only_in_taxon bryophytes (I know this isn't a clade, will have to create a pseudo-clade).
- Should we add a term for sporophyte foot haustorium when we deal with portions of plant tissue or is the whole foot the haustorium?
Upcoming meetings 2011:
* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York
LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted)
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?
-BS suggested we might want to submit a short paper which could be published in longer form later- see above
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Early-bird registration ends May 13.
Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.
Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.
For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
Early bird registration deadline - Extended 1 March 2011 Deadline for registration by presenters 1 March 2011
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
