POC Conf. Call 2-22-11
POC meeting, Webex Conference Call; Date: Tuesday Feb 22th, 2011 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_2-15-11?
Physcomitrella terms
Completing items worked on last week
Will fill in after 2-15 meeting.
New items
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 definition: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase
Synonyms: cauloid, gametophyte axis
Also suggest adding terms for gametophore stem and gametophore branch (similar to stem and branch).
perigonial bract - The specialized phyllids surrounding the antheridia. 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 definition: 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.
perichaetal bract - MO did not request this term, but it is commonly used in mosses, so suggest adding it at the same time.
Proposed definition: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.
Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.
Suggest adding the term gametophytic perianth as well.
Proposed definition of gametophytic perianth: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts that are fused laterally and surround the calyptra (or should it be surrounds the capsule, in case no calyptra is present). has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)
Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
seta- The stalk of a moss sporophyte. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
Suggested definition: A plant axis that is a stalk that hold up a spore capsule. participates_in sporophytic phase
Cardinal organ parts
Terms requested by MO:
calyptra
base
peristome
theca
lid
foot
neck canal
Other terms, not from MO
epiphram
spore capsule mouth
pseudopodium
venter
Plant Tissues
paraphyllium - Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."
Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
MO has this listed as a plant organ
Proposed definition: A phyllome/portion of plant tissue that is a small filamentous, scale-like, or leaf-like outgrowth from the epidermis between the leaves of a gametophore axis.
Comment: Paraphyllia are much smaller than leaves. Found in pleurocarpous mosses and a few leafy liverworts.
The paraphyllia are the small, dark structures between the leaves.
midrib
rhizoid
archesporium
amphithecium
endothecium
jacket layer
paraphysis
axilliary hair
tmema
Gametangium, antheridium, archegonium
Plant Cells
archesporial cell
apical cell
shoot apical cell
phyllid apical cell
alar cell
brachycyte
chloronema cell
caulonema cell
tmema cell
jacket layer cell
axillary hair terminal cell
axillary hair base cell
neck canal cell
side branch initial
Other terms, not requested by MO:
hyrdoid
leptoid
rhizoid initial
Upcoming meetings 2011:
- Phenotype Ontology RCN Summit
February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,
Laurel and Pankaj will be attending.
From RW: -What is official PO strategy for dealing with phenotypes?
-Should it differ between description of mutant phenotypes and descriptions needed for systematic studies?
-Should PO develop a list of terms to be submitted to PATO (rather than our current piecemeal suggestions)?
-Possible case study: description of inflorescence types.
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: The deadline for workshop and tutorial proposals for the ICBO conference has been extended to February 15th, 2011
- We decided we are too shorthanded to put together a PO workshop, but Melissa, Alan and Chris are organizing an anatomy ontology workshop.
- 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
* 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.
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
