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| | This meeting was postponed, as most of the curators will not be available. | | This meeting was postponed, as most of the curators will not be available. |
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| − | The agenda below is for reference only, and will be taken up at future meetings.
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| − | =Old agenda items=
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| − | ==Remaining terms without is_a parents==
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| − | (still need to fill in proposed parents and definitions)
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| − | stomatal complex: PO:0002000
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| − | current def: An opening pore on the epidermis of leaves and stems bordered by two guard cells and serving in gas exchange.
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| − | Suggested definition: a portion of epidermis that has as parts two guard cells and a stomatal pore. May also contain subsidiary cells.
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| − | is_a portion of epidermal tissue (had a conversation with Barry at an earlier meeting, in which he said it was okay for a portion of tissue to an anatomical space as a part).
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| − | Right now stomatal complex has part_of relations to leaf adaxial epidermis, leaf abaxial epidermis, leaf lamina adaxial epidermis, leaf lamina abaxial epidermis, and petiole epidermis. This is problematic, because not every stomatal complex can be a part of all those structures.
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| − | Suggest that stomatal complex be a general term, with part_of relations, and we create new child terms for each of the different portions of leaf epidermis: leaf abaxial stomatal complex, leaf lamina abaxial stomatal complex, petiole stomatal complex, etc.
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| − | Leaf trichome has a similar problem (it is part of leaf adaxial epidermis, leaf abaxial epidermis, leaf lamina adaxial epidermis, and leaf lamina abaxial epidermis). Suggest similar solution.
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| − | floral stomatal complex: PO:0008044
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| − | current def: An opening pore on the epidermis of floral organs bordered by two guard cells and serving in gas exchange.
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| − | Right now, we have a term floral epidermis, and floral stomatal complex is part of it.
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| − | I suggest that we obsolete floral epidermis, since it doesn't really make sense to refer to the epidermis of a flower, and we already have the floral parts organized as organs or cardinal organ parts. Instead, we should use the term phyllome epidermis (which we already have) and make petal epidermis, sepal epidermis, etc., children of phyllome epidermis. There is only one direct annotation to floral epidermis, and it could probably be moved to the more specific parts of the flower. I also suggest that we obsolete floral stomatal complex, and replace it with terms like petal stomatal complex.
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| − | shoot apex: PO:0000037
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| − | current def: "The topmost part of the shoot, situated at the distal extremity of the shoot axis, consists of apical meristem and the youngest leaf primordia." [TAIR:ki]
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| − | subset: reference
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| − | Proposed definition: A shoot axis that is the most distal part of a shoot and has as parts a shoot apical meristem and the youngest leaf primordia."
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| − | is_a shoot axis
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| − | root nodule: PO:0003023
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| − | current def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]
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| − | Proposed definition: A cardinal organ part that is an outgrowth of a root and is inhabited by nitrogen-fixing bacteria.
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| − | Comment: root nodules are a symbiosis between a plant (often, but not exclusively, of the Fabaceae) and bacteria of the genera Rhizobium, Bradyrhizobium, or Azorhizobium.
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| − | is_a cardinal organ part, part_of root
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| − | We may want to add the term root nodule meristem, dbxref: PMID:1809347
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| − | leaf axil: PO:0009023
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| − | current def: "The angle between the petiole of a leaf and the stem to which it is attached." [GR:cwt] relationship: part_of PO:0020040 ! leaf base xref: SF: 3007368
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| − | Suggest: is_a axil, part_of shoot system
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| − | Should the PO have a generic term [https://sourceforge.net/tracker/?func=detail&aid=3007368&group_id=76834&atid=835555 axil] and, if so, how it should be defined? See also older tracker item [https://sourceforge.net/tracker/index.php?func=detail&aid=1681621&group_id=76834&atid=835555 leaf base vs. axil?]
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| − | Suggested def. for axil: A plant anatomical space that is the space between a shoot axis and a leaf, brach or branch that branches from it.
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| − | Either we should keep the term leaf axil and make a parent term axil is_a plant anatomical space, or delete the term leaf axil and move it's annoation to axillary bud meristem.
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| − | tetrad of microspores: PO:0000032
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| − | current def: "A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte." [TAIR:ki] subset: reference
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| − | Proposed definition: A portion of plant tissue consisting of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte.
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| − | is_a portion of plant tissue, develops_from microsporophyte
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| − | valve: PO:0000033
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| − | current def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]
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| − | subset: Arabidopsis
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| − | In Arabidopsis, the fruit is composed of two fused carpels, so when it dehisces, each valve is developed from a carpel, which makes it an organ, unless only part of the carpel develops into the valve, in which case it would be a cardinal organ part.
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| − | In other dehiscent fruits such as legumes, each part that splits apart is from the same carpel, so it would be a cardinal organ part. However, I only found one paper on WOS that referred to the dehisced pod segments as valves.
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| − | The term valve has also been used to refer to dehiscent sections of an anther, which I think is synonymous with locule (maybe the locules become valves after they dehisce?)
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| − | Perhaps it would be better to restrict our definition of valves to parts of a fruit; call it fruit valve for clarity. May need to have separate terms: organ valve (is_a plant organ, develops_from carpel) and organ part valve (is_a cardinal organ part).
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| − | fruit columella: PO:0004540
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| − | current def: "Central axis of the fruit." [POC:curators] subset: Tomato
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| − | Suggested def: A portion of plant (parenchyma?) tissue that forms the central axis of a fruit.
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| − | portion of plant tissue or portion of parenchyma tissue?
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| − | hull (sensu Poaceae): PO:0006000
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| − | current def: "A leaf like structure often found enclosing the grass fruit, caryopsis. It is derived from the dried lemma (PO:0009037) and palea (PO:0009038) floral bracts found in the grass floret (PO:0006318)." [GR:pj] subset: Maize, subset: Poaceae, subset: Rice
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| − | pollen tube (see old agenda item): PO:0006345
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| − | current def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208] subset: reference
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| − | basal endosperm transfer layer: PO:0009019
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| − | current def: "A cell layer found in basal endosperm transfer cell." [GR:cwt] part_of basal endosperm transfer cell
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| − | This definition and relationship is wrong. The basal endosperm transfer layer is a layer of cells (composed of basal endosperm transfer cells) which is part of the endosperm.
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| − | Proposed definition for basal endosperm transfer layer: A portion of plant tissue that is part of the endosperm and is composed of basal endosperm transfer cells.
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| − | Proposed definition for basal endosperms transfer cell: A plant cell that is part of a basal endosperm transfer layer and is characterized by ingrowths of the cell wall (need to work on details of definition).
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| − | lodicule: PO:0009036
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| − | current def: "In a grass floret, one of two or three tiny scales or flaps of tissue outside the stamens, possibly representing reduced perianth segments." [APWeb:Glossary]
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| − | subset: reference
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| − | Proposed definitions: A phyllome in a grass floret that is one of two or three tiny scales or flaps of tissue outside the stamens
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| − | Comment: possibly represents a reduced perianth segment
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| − | is_a phyllome
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| − | microsporangium: PO:0009070
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| − | current def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary], subset: reference, synonym: "anther lobe" RELATED [], synonym: "pollen sac" RELATED []
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| − | aril: PO:0009090
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| − | current def: "A structure associated with and often partly or wholly covering a seed and developed from the funicle or raphe." [APWeb:Glossary] comment: Also used more generally to refer to a similar structure derived from any part of the ovule - there has been much and sometimes acrimonious debate over the correct definition of the term, so when used the origin of the aril should generally be given for clarity. subset: reference
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| − | arilloid: PO:0019022
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| − | current def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]
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| − | placentoid: PO:0020005
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| − | current def: "An inpushing of the anther wall." [APWeb:Glossary] subset: reference
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| − | root stele (see request from Traitnet below): PO:0020124, alt_id: PO:0003012
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| − | current def: "The central column of primary vascular tissue in the root and any tissue that it surrounds." [APWeb:Glossary] comment: Includes the pericycle as the outermost layer of the stele. subset: reference, synonym: "root vascular cylinder" RELATED []
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| − | ===parts of embryo===
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| − | embryo proper: PO:0000001
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| − | current def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]
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| − | [egg apparatus: PO:0020096
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| − | current def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr] subset: reference
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| − | suspensor: PO:0020108
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| − | current def: "A nearly always single file of cells at the base of the embryo derived from the basal cell." [GR:pj] comment: It anchors the embryo in the embryo sac and pushes it into the endosperm.
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| − | scutellum: PO:0020110
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| − | current def: "A more or less shield-shaped and absorptive portion of an embryo of grasses, probably a modified cotyledon." [APWeb:Glossary] synonym: "haustorial cotyledon" RELATED []
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| − | hypocotyl-root junction: PO:0004724
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| − | current def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki] subset: reference
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| − | ==User requests still open on Source Forge==
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| − | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3030644&group_id=76834&atid=835555 Musa terms]===
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| − | Requested by Rosemary Shrestha (July 2010). Many of these are synonyms of existing terms. Also see spread sheet attached to SF tracker item.
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| − | ====Completed Musa requests:====
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| − | We dealt following terms at the POC meeting on 11-5-2010 (see minutes from [[Friday,_November_5th]] for more details):
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| − | '''Petiole wing''': synonym of petiole lamina. Added new term petiole lamina.
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| − | '''Petiole margin''': Added comment: generally in flattened petioles, but may also occur as extensions of petioles that are rounded or c-shaped in cross section.
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| − | '''Cigar leaf''': Although it is a phenotype, we added the term for Musa subset. May apply to other species as well, especially in monocots. is_a vascular leaf.
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| − | '''Petiole margin edge''': Should just use petiole margin
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| − | '''Cigar leaf dorsal surface''': Added new term, cigar leaf abaxial epidermis, is a leaf abaxial epidermis, part_of cigar leaf.
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| − | '''Free tepal''': Added a new term to PO that is a cross-product of PO tepal and PATO free (need to request).
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| − | ''Need to ask Chris M if these new phenotype terms should have PO id's or should have a new id, like POXP''
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| − | '''Free tepal apex''': Added new terms tepal base and tepal apex (plus phyllome base and phyllome apex). Musa folks (and others) can describe fused tepal apex post-compositionally using tepal apex and fused tepal.''
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| − | Also added new term leaf tip, which is part of leaf apex.
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| − | '''Compound tepal lobe''': Musa folks (and others) can describe compound tepal lobe by post-compositionally using tepal apex and compound tepal.
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| − | '''Peduncle surface:''' New term peduncle epidermis added
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| − | '''Peduncle hairs''': New term peduncle trichome added
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| − | '''Bract apex''': New term added
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| − | '''Bract base''': New term added
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| − | '''Bract external face''': New term added: bract abaxial epidermis, sibling to leaf abaxial epidermis, child of new term phyllome abaxial epidermis.
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| − | '''Bract internal face''': New term added: bract adaxial epidermis, sibling to leaf adaxial epidermis, child of new term phyllome adaxial epidermis.
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| − | '''Hermaphrodite flower''': Added as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP
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| − | '''Female flower''': Added as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP
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| − | '''Issues arising from new terms:'''
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| − | '''Petiole canal:''' The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole
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| − | Added term 'adaxial petiole': A cardinal organ part that is the adaxial portion of petiole. Comment: Adaxial petiole may be concave or form a canal. Narrow synonym: petiole canal.
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| − | Also added abaxial petiole, with parallel definition.
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| − | Now that we have anatomical space, maybe we should add this as a space?
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| − | '''Compound tepal''': Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642).
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| − | RW (after meeting): this will cover the individual tepals, but also need to add a term '''compound collective tepal structure''', which is what they are actually describing.
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| − | suggested definition: A collective tepal structure in which the tepals are fused.
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| − | ====Musa requests still needing to be resolved:====
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| − | Below is a list of the requested terms, with definitions and is a or part of relations from Rosemary, followed by suggestions and/or proposed definitions for PO format.
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| − | 2. Musa flower terms
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| − | o '''Crown''': The raised ridge of tissue to which the pedicels are attached.
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| − | Is this part of an inflorescence, part of an inflorescence axis?
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| − | ''This refers to the inflorescence axes between individual flowers that do not elongate. It is a shoot system that is part of the inflorescence (which is also a shoot system).''
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| − | Added the following term:
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| − | Musa crown (PO:0025134): A shoot system that forms the basal part of an inflorescence in Musa species to which the pedicels are attached and in which the internodes do not elongate, giving the appearance of a ridge of raised tissue.
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| − | is_a shoot system, part_of inflorescence
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| − | o '''Basal flower''': First flowers emerging on the inflorescence with the potential to give rise to fruits. part_of CO_125.0000136 ! basal bud
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| − | Do we want to describe different flowers on the infloresence? If so, we could add general term basal flower: a flower at the proximal end of on an inflorescence. Comment: in Musa, the basal flowers are the first to emerge and have the potential to give rise to fruits.
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| − | o '''Male bud''': The usually persistent bud when it is only composed of bracts with male flowers. is_a: CO_125.0000146 ! bud; is_a: CO_125.0000146 ! bud
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| − | Proposed definition: An inflorescence bud that develops into a male inflorescence.
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| − | If we go this route, we will need to add male, female and hermaphrodite reproductive bud, male, female and hermaphrodite inflorescence bud, male, female and hermaphrodite floral bud, and male, female and hermaphrodite inflorescence, plus the floral terms described above.
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| − | 3. '''Musa fruit terms'''
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| − | o '''Bunch''': The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD
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| − | This could be a narrow synonym of infructescence (PO:0006342). Not sure what they mean by rachis in this definition
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| − | o '''Hand of fruits''': All the fruits that develop in the axil of a single bract. part_of CO_125.0000014 ! bunch
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| − | Musa flower is a compound spike. A branch of the spike develops from the axil of a single bract, and when mature produces a 'hand' of fruits. All of the branches of the compound spike together, when mature, are a bunch of bananas. A hand is an inflorescence branch that matures into a branch of an infructescence.
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| − | Current definition of infructescence (PO:0006342): The grouping or arrangement in which fruits are borne on a plant, is_a shoot system, develops_from inflorescence.
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| − | First we need to properly redefine inflorescence. Current definition of inflorescence: That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers, is_a reproductive shoot system.
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| − | '''Proposed definition of inflorescence:''' a reproductive shoot system that has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and that has as parts two or more flowers.
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| − | '''Proposed definition of infructescence:''' a reproductive shoot system that has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and has as parts two or more fruits. Develops_from inflorescence.
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| − | We already have the term inflorescence branch (PO:0009081: Any branch forming from the primary or the higher order inflorescence axis). Suggest modifying this slightly to: A secondary or higher order branch of an inflorescence. is_a reproductive shoot system, part_of inflorescence.
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| − | Based on this, we can add new term infructescence branch, which has the synonym hand.
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| − | '''Proposed definition of infructescence branch:''': A secondary or higher order branch of an infructescence. is_a reproductive shoot system, develops_from inflorescence branch, part_of infructescence. Synonym: hand [narrow]
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| − | o '''Flower relicts''': Remains of a female flower when it persists on the fruit. part_of CO_125.0000033 ! fruit
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| − | Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.)
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| − | 4. '''Musa shoot terms'''
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| − | o Sucker: Lateral shoot that develops from the corm and usually emerges close to the parent plant. is_a: CO_125.0000001 ! plant part
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| − | This would probably be a synonym of axillary shoot, but will depend on how we end up organizing shoot system (see above).
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| − | Will probably need to be a broad synonym, because (I think) people also use the term sucker to refer to root-borne shoots.
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| − | o Pseudostem: 'False stem' of cylinders formed by the concentric leaf sheaths through which the peduncle later grows. is_a: CO_125.0000001 ! plant part
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| − | Tricky. Could this be a collective phyllome structure?
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| − | o Pseudostem underlayers: Abaxial side of the inner sheath which is not visible until the outermost sheath has been removed. part_of CO_125.0000046 ! pseudostem
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| − | This is the abaxial portion of a leaf sheath (PO:0020104). We could make a new term leaf sheath abaxial epidermis (sibling of petiole abaxial epidermis, is_a leaf epidermis)
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| − | ===[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]===
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| − | This item has been open on SF since 6/2009
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| − | I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
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| − | Suggested stages:
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| − | -sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
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| − | -tuber initiation
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| − | -tuber growth
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| − | -tuber maturation
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| − | How we work these in will depend on restructuring of PGDSO
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]===
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| − | submitted by Austin Mast
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| − | Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
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| − | Fascicle,
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| − | Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure),
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| − | Phyllode,
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| − | Banner (as in a legume flower),
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| − | Wing (as in a legume flower), Keel (as in a legume flower),
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| − | Locule
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| − | ===Adding/modifying the [https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]===
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| − | submitted by Rich Zobel (Nov 2009)
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| − | ===TraitNet requests===
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]
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| − | proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground (is it always underground?)
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| − | child of stem (PO:0009047).
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]
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| − | Their comment: is synonym to Tubercle
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| − | podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
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| − | tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
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| − | proposed def:
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
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| − | definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
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| − | proposed def:
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080915&group_id=76834&atid=835555 stele]
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| − | We already have the term root stele (PO:0020124) which does not have a parent. Suggest we add a general parent term stele, plus a sibling shoot axis stele.
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| − | Existing definition of root stele: The central column of primary vascular tissue in the root and any tissue that it surrounds. [source: APWeb:Glossary] Comment: Includes the pericycle as the outermost layer of the stele.
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| − | definition of stele (from Beentje 2010): a part of a plant axis made up of the primary vascular system and its associated ground tissue.
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| − | suggested parent: cardinal organ part
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| − | suggested definitions:
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| − | stele: A cardinal organ part that is the central column of a plant axis that consists of the primary vascular tissue and the ground tissue it surrounds.
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| − | root stele: a stele that is part of a root.
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| − | shoot axis stele: a stele that is part of a shoot axis
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| − | (could have children stem stele and branch stele)
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]
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| − | definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
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| − | We could add this term as a kind of upper level bin term (similar to trichome)
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]
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| − | Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]
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| − | rom Crum (2001): a cluster of fern sporangia
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| − | from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
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| − | Proposed definition: a collective plant structure composed of two or more adjacent sporagia on the surface of a leaf (this will need refining)
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
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| − | Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
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| − | This is problematic, ontologically, because it can derived from multiple types of structures. May want to make separate terms: branch tendril (child of branch), leaf tendril (child of leaf), etc. Leaf tendrils could arise from the whole leaf or from a part of the leaf (leaflet). Alternative is to make these terms synonyms (as phenotypes), e.g., leaflet tendril is synonym of leaflet.
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| − |
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| − | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed development stages]===
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| − | This is a fairly new request for terms for cotton
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| − | ==Open tracker items==
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| − |
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| − | includes some terms that had no is_a parent, user requests, and simple changes
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| − |
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| − | [[Old_SF_tracker_items,_fall_2010]]
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| − | At the [[POC_Conf._Call_10-13-10]] we agreed to try to deal with these items on Source Forge, to save time at meetings.
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| − | RW, DWS and MAG have commented on most these items, plus other have commented on some of them. Can we close (at least some) of them?
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| − |
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| − | ==Other items (lower priority)==
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| − | -(MP) Elena Kramer suggested that we add the term [https://sourceforge.net/tracker/?func=detail&aid=3080941&group_id=76834&atid=835555 spur] to the PSO and consider dealing with [https://sourceforge.net/tracker/?func=detail&aid=3080945&group_id=76834&atid=835555 common primordia] in the PGDSO.
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| − | -(MP) Paula Rudall commented that the current definition of [https://sourceforge.net/tracker/?func=detail&aid=3080937&group_id=76834&atid=835555 central cell] has a different meaning in gymnosperms.
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| − | -(LP) [http://sourceforge.net/tracker/?func=detail&aid=1690786&group_id=76834&atid=835555 post harvest stages]: this is an old request, but no one ever commented on it.
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