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| | '''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)''' | | '''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)''' |
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| − | In attendance: | + | In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU) |
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| − | POC members:
| + | Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY) |
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| − | Absent:
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| − | Collaborators: | + | Collaborators: none |
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| | + | Acceptance of the minutes from the [[POC_Conf._Call_3-8-11]]? |
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| | + | ''There were no changes, additions, or deletions.'' |
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| − | Acceptance of the minutes from the [[POC_Conf._Call_3-8-11]]?
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| | =Issues arising from last week's meeting:= | | =Issues arising from last week's meeting:= |
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| | Special technical meeting? | | Special technical meeting? |
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| − | =Physcomitrella terms=
| + | ''The conference call will take place on 3-17-11, at 4PM PDT.'' |
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| − | ==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium and related terms]==
| + | ''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it. Will post possible alternative solutions on the [[POC Technical Issues Page]].'' |
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| − | May want to use the name '''plant gametangium''', to make it clear that we are not including algae.
| + | =Physcomitrella terms= |
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| − | Current definitions:
| + | ''Discussion of new terms was postponed until next week, due to low attendance.'' |
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| − | '''plant gametangium''' (PO:0025124): A cardinal organ part (or an organ?) that is part of a whole plant in the gametophytic phase and produces gametes.
| + | ==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium and related terms]== |
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| − | '''antheridium''' (PO:0025125): A gametangium that produces antheridium sperm cells.
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| − | '''archegonium''' (PO:0025126): A gametangium that produces archegonium egg cells.
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| − | Need definitions that distinguishes gametangia from megagametophyte (embryo sac) and microgametophyte (pollen). The current definitions are circular (see definitions below of archgonium egg cell and antheridium sperm cell)
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| − | Current definitions of--
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| − | '''megagametophyte''' (PO:0020092): A gametophyte that produces female gametes.
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| − | '''microgametophyte''' (PO:0020091): A gametophyte that produces pollen sperm cells.
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| − | -This would be a good place to introduce the "only in taxon" and/or "never in taxon" relations
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| − | We also have the terms:
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| − | '''archegonium egg cell''' (PO:0025122): An egg cell that is produced by an archegonium.
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| − | '''embryo sac egg cell''' (PO:0025123): An egg cell that is produced by a megagametophyte.
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| − | '''antheridium sperm cell''' (PO:0025120): A sperm cell that is produced by an antheridium.
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| − | '''pollen sperm cell''' (PO:0025121): A sperm cell that is produced by a microgametophyte.
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| − | Having both sets of egg and sperms cells is redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations.
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| | ==apical cell== | | ==apical cell== |
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| − | Moss Ontology has requested the term '''apical cell'''.
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| − | We already have the term '''apical cell (PO:0004000)''', which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." Suggest renaming PO:0004000 '''embryonic apical cell''' for clarity. The embryonic apical cell can also be found in non-angiosperms.
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| − | Growth in mosses (and other bryophytes) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. The moss apical meristem may differ from that of vascular plants, but it is still possible to call it an apical meristem.
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| − | Apical cell is consistent with the definition of meristematic cell (synthesizing protoplasm and producing new cells by division and with only a primary cell wall). Meristematic cell is part_of meristem, and a meristem is a portion of tissue and therefore two or more cells. We do not need to add apical cell part of apical meristem, but logically it will be part of a meristem.
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| − | Non-seed vascular plants can also have an apical cell, similar to bryophytes. Suggest we add separate terms for sporophytic apical cell and gametophytic apical cell.
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| − | '''Proposed def. of gametophytic apical cell:''' A meristematic cell at the apex of a gametophore or non-vascular leaf.
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| − | Comment: Occurs in mosses and other bryophytes. Something about how it divides.
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| − | '''Proposed def. of sporophytic apical cell:''' A meristematic cell at the apex of a shoot apical meristem that ...something about being distinct from other cells at the apex and/or about being a single cell rather than an indistinguishable group of cells.
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| − | Comment: Occurs in lycopods and ferns (what about Psilotum?).
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| − | Moss ontology also requested '''shoot apical cell''' and '''phyllid apical cell'''.
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| − | Proposed definitions:
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| − | '''gametophore apical cell:''' A gametophytic apical cell at the apex of a gametophore.
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| − | Comment: Divides to produces leaf initial cells and other stem tissues.
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| − | '''phyllid apical cell:''' A gametophytic apical cell at the apex of a phyllid
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| − | Comment: Divides to produce phyllid tissues. (C. Jill Harrison et al. (2009): Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens.)
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| | ==Collective plant structures:== | | ==Collective plant structures:== |
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore]===
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| − | Def'n supplied by Moss Ontology: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.
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| − | Suggest is_a shoot system.
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| − | Proposed def'n.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase
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| − | Comment: A gametophore is the leafy part of a moss gametophyte, without the protonema. Antheridia and archegonia arise on the gametophore.
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud]===
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| − | The term "bud" has been requested:
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| − | Def'n supplied by Moss Ontology: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove
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| − | Suggest a new term '''gametophore bud'''. This could be a child of bud (PO:0000055: An undeveloped shoot system).
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| − | Proposed def'n: A bud on a protonema that develops into a gametophore. participates_in gametophytic phase
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| − | Comment: Occurs in mosses.
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| | ==Plant organs:== | | ==Plant organs:== |
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]===
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| − | - This is the term used for the gametophore stem or axis.
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| − | Suggest using '''gametophore axis''' as primary name, cauloid as synonym.
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| − | Proposed def'n: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase
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| − | Synonyms: cauloid, gametophyte axis
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| − | Also suggest adding terms for '''gametophore stem''' and '''gametophore branch''' (similar to stem and branch).
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract]===
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| − | - The specialized phyllids surrounding the antheridia.
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| − | Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
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| − | 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.
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| − | Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase
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| − | 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.
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| | ==Additional moss terms:== | | ==Additional moss terms:== |
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| − | These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we may as well add them now.
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perichaetal bract]===
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| − | Proposed def'n: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.
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| − | 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.
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth]===
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| − | Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on an axis that are fused laterally and surround the calyptra.
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| − | Should it be surrounds the capsule, in case no calyptra is present?
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| − | -has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)
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| − | Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185175&group_id=76834&atid=835555 seta]===
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| − | -The stalk of a moss sporophyte.
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| − | Suggested def'n: A plant axis that that holds up a spore capsule. participates_in sporophytic phase
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| − | Comment: Found in mosses
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| | ==Cardinal organ parts== | | ==Cardinal organ parts== |
| − | Terms requested by MO:
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| − | * '''calyptra'''
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| − | Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.
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| − | We also have a request (from PJ) for calyptra, which is part of the fruit in Eucalyptus. That term should be named '''fruit calyptra''' (see below under operculum), and this term should be named '''spore capsule calyptra''', to distinguish them.
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| − | Proposed name and def.: '''spore capsule calyptra:''' A cardinal organ part that develops from an archegonium wall and surrounds the sporangium.
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| − | Comment: Found in mosses. The calyptra ia a membranous or hairy cap composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and be carried upward as the seta elongates.
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| − | (Definition suggests that we should add a term for archegonium wall, is_a gametangium wall)
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| − | *'''base'''
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| − | Moss Ontology definition: The sterile bottom of the sporangium. Also called neck or if swollen apophysis or hypophysis. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
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| − | Need to look up if we should add separate terms for apophysis and hypophysis, or add as synonyms.
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| − | Proposed name and def.: '''sporangium base'''
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| − | Synonyms: sporangium neck
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| − | *'''peristome'''
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| − | Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
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| − | *'''peristome tooth'''
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| − | Not requested by Moss Ontology, but should add it.
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| − | Proposed def: A cardinal organ part that is a lobe or tooth of the peristome.
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| − | *'''theca'''
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| − | Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
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| − | We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that anther theca.
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| − | Proposed name and def.: '''sporangium theca:''' The main body of the sporangium.
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| − | Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
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| − | *'''lid/operculum'''
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| − | Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.
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| − | We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.
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| − | Proposed name and def.: '''spore capsule operculum:''' A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
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| − | Comment: Found in mosses. May remain partly attached to the rest of the capsule.
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| − | '''Also add:'''
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| − | '''fruit operculum:''' A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. part_of fruit
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| − | Comment: Found in Eucalyptus.
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| − | Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
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| − | '''fruit calyptra:''' A cardinal organ part that is the basal part of a capsular fruit that separates from the fruit operculum during dehiscence. part_of fruit
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| − | Comment: Found in Eucalyptus. The capsule may remain attached to the plant after the fruit operculum dehisces.
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| − | *'''foot'''
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| − | Moss Ontology definition: The base of the sporophytes in mosses
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| − | Proposed name and def.: '''sporophyte foot:''' The base of the sporophyte (seta?) that attaches it to the gametophore. (From Schofeld)
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| − | Comment: The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum)
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| − | - Can add term for sporophyte foot haustorium when we deal with portions of plant tissue. Contains transfer cells.
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| − | ===Other related terms for mosses, not from Moss Ontology===
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| − | *'''spore capsule mouth'''
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| − | Proposed definition: A plant anatomical space that is the opening on the distal end of a spore capsule.
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| − | Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be partially covered by a peristome.
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| − | *'''epiphram'''
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| − | Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
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| − | From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
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| − | '''Proposed definition:''' A portion of plant tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.
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| − | Comment: Present in some moss species of the family Polytrichaceae.
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| − | What kind of tissue is it?
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| − | *'''pseudopodium'''
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| − | From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
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| − | From Schofeld: "An elongated mass of leafless gaemtophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
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| − | '''Proposed definition:''' An extension of a gametophore axis on which a spore capsule is borne.
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| − | Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
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| − | * '''venter'''
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| − | *'''neck canal'''
| + | ''See [[POC_Conf._Call_3-22-11]] for details.'' |
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| | =Upcoming meetings 2011:= | | =Upcoming meetings 2011:= |
POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU)
Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
Collaborators: none
Acceptance of the minutes from the POC_Conf._Call_3-8-11?
There were no changes, additions, or deletions.
Issues arising from last week's meeting:
Special technical meeting?
The conference call will take place on 3-17-11, at 4PM PDT.
RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it. Will post possible alternative solutions on the POC Technical Issues Page.
Physcomitrella terms
Discussion of new terms was postponed until next week, due to low attendance.
apical cell
Collective plant structures:
Plant organs:
Additional moss terms:
Cardinal organ parts
See POC_Conf._Call_3-22-11 for details.
Upcoming meetings 2011:
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
ICBO
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)
LC is working with the other organizers to develop the workshop plans and a call for papers.
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, will submit a short paper/poster for the workshop (deadline April 1st).
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Plant Biology 2011
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.
TAIR 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 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
Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PDT
