Difference between revisions of "POC Conf. Call 12-8-10"
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===[https://sourceforge.net/tracker/index.php?func=detail&aid=3030644&group_id=76834&atid=835555 Musa terms]=== | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3030644&group_id=76834&atid=835555 Musa terms]=== | ||
| − | Requested by Rosemary Shrestha (July 2010). | + | 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:==== | |
| − | + | 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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| − | We dealt | ||
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'''Petiole wing''': synonym of petiole lamina. Added new term petiole lamina. | '''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. | '''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. | '''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 canal:''' The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole | '''Petiole canal:''' The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole | ||
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Now that we have anatomical space, maybe we should add this as a space? | Now that we have anatomical space, maybe we should add this as a space? | ||
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'''Petiole margin edge''': Should just use petiole margin | '''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. | '''Cigar leaf dorsal surface''': Added new term, cigar leaf abaxial epidermis, is a leaf abaxial epidermis, part_of cigar leaf. | ||
| − | + | ''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'' | ''Need to ask Chris M if these new phenotype terms should have PO id's or should have a new id, like POXP'' | ||
| + | '''Compound tepal''': Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642). | ||
| − | + | 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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''Add as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP'' | ''Add 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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| + | ====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. | ||
Revision as of 14:45, 29 November 2010
POC meeting, Webex Conference Call; Date: Wednesday Dec 8st, 2010 10am (PST)
In attendance:
POC members:
Absent:
Collaborators: none
Acceptance of the minutes from the POC Conf. Call 12-1-10?
Old agenda items
User requests still open on Source Forge
Musa terms
Requested by Rosemary Shrestha (July 2010). Many of these are synonyms of existing terms. Also see spread sheet attached to SF tracker item.
completed Musa requests:
We dealt following terms at the POC meeting on 11-5-2010 (see minutes from Friday,_November_5th for more details):
Petiole wing: synonym of petiole lamina. Added new term petiole lamina.
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.
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.
Petiole canal: The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole
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.
Also added abaxial petiole, with parallel definition.
Now that we have anatomical space, maybe we should add this as a space?
Petiole margin edge: Should just use petiole margin
Cigar leaf dorsal surface: Added new term, cigar leaf abaxial epidermis, is a leaf abaxial epidermis, part_of cigar leaf.
Free tepal': Added a new term to PO that is a cross-product of PO tepal and PATO free (need to request).
Need to ask Chris M if these new phenotype terms should have PO id's or should have a new id, like POXP
Compound tepal: Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642).
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.
suggested definition: A collective tepal structure in which the tepals are fused.
o Free tepal apex: Distal end of the free tepal that is often wrinkled. part_of CO_125.0000020 ! free tepal
We have the terms leaf base (PO:0020040) and leaf apex (PO:0020137). Suggest adding general terms phyllome base and phyllome apex, with new terms tepal base and tepal apex as children of these.
Will add 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.
Also need to add new term leaf tip, which is part of leaf apex.
o Compound tepal lobe: One of the 5 free apical portions of the compound tepal. part_of CO_125.0000021 ! compound tepal
This is a tepal apex that is part of a fused tepal.
Musa folks (and others) can describe compound tepal lobe by post-compositionally using tepal apex and compound tepal.
o Peduncle surface: Outer covering of the peduncle. part_of CO_125.0000039 ! peduncle
New term peduncle epidermis, is_a shoot epidermis (PO:0005679): A portion of shoot epidermis that is part of a peduncle.
Okay to add new term.
o Peduncle hairs: Hairs growing on the peduncle surface. part_of CO_125.0000036 ! peduncle surface
New term: peduncle trichome: A trichome that is part of a peduncle epidermis.
Okay to add new term.
o Bract apex: Distal end of the bract. part_of CO_125.0000052 ! male bract
Could be a child of the new term phyllome apex proposed above.
Okay to add
o Bract base: Proximal end of the bract. part_of CO_125.0000052 ! male bract
Could be a child of the new term phyllome base proposed above.
Okay to add
o Bract external face: External (abaxial) face of the bract. part_of CO_125.0000052 ! male bract
New term: bract abaxial epidermis, sibling to leaf abaxial epidermis, child of new term phyllome abaxial epidermis.
Okay to add
o Bract internal face: Internal (adaxial) face of the bract. part_of CO_125.0000052 ! male bract
New term: bract adaxial epidermis, sibling to leaf adaxial epidermis, child of new term phyllome adaxial epidermis.
Okay to add
o Hermaphrodite flower: Flower that contains both functional male and female parts. is_a: CO_125.0000019 ! basal flower
Do we want to add term hermaphrodite flower? Proposed definition: A flower that at maturity has as parts a a gynoecium and androecium.
Add as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP
o Female flower: Flower containing functional female parts and non-functional male parts. is_a: CO_125.0000019 ! basal flower
Do we want to add term female flower? Proposed definition: A flower that at maturity has as part a a gynoecium but no androecium. Comment: Androecium may be completely absent or may be present in early developmental stages then abort.
Can have corresponding definition fro male flower.
Add as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP
Musa requests still needing to be resolved:
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.
2. Musa flower terms
o Basal flower: First flowers emerging on the inflorescence with the potential to give rise to fruits. part_of CO_125.0000136 ! basal bud
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.
No resolution on this issue.
o Crown: The raised ridge of tissue to which the pedicels are attached.
Is this part of an inflorescence, part of an inflorescence axis?
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).
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
Proposed definition: An inflorescence bud that develops into a male inflorescence.
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.
No resolution on this item.
3. Musa fruit terms
Discussion of these terms was postponed for a future meeting.
o Bunch: The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD
This could be a narrow synonym of infructescence (PO:0006342). Not sure what they mean by rachis in this definition
o Hand of fruits: All the fruits that develop in the axil of a single bract. part_of CO_125.0000014 ! bunch
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.
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.
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.
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.
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.
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.
Based on this, we can add new term infructescence branch, which has the synonym hand.
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]
o Flower relicts: Remains of a female flower when it persists on the fruit. part_of CO_125.0000033 ! fruit
Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.)
4. Musa shoot terms
Discussion of these terms was postponed for a future meeting.
o Sucker: Lateral shoot that develops from the corm and usually emerges close to the parent plant. is_a: CO_125.0000001 ! plant part
This would probably be a synonym of axillary shoot, but will depend on how we end up organizing shoot system (see above).
Will probably need to be a broad synonym, because (I think) people also use the term sucker to refer to root-borne shoots.
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
Tricky. Could this be a collective phyllome structure?
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
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)
-(MP) Adding/modifying the root terms submitted by Rich Zobel (Nov 2009).
-(MP) Legume terms submitted by Austin Mast: Taproot, Stem Hair, Prickles, Fascicle, Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure), Phyllode, Banner (as in a legume flower), Wing (as in a legume flower), Keel (as in a legume flower), Anther pore and anther slit, Locule
-(MP) Elena Kramer suggested that we add the term spur to the PSO and consider dealing with common primordia in the PGDSO.
-(MP) Paula Rudall commented that the current definition of central cell has a different meaning in gymnosperms.
-(MP) TraitNet requested several new terms for the PSO: corm, spine, podarium, pneumatophore, stele, diaspore, cone, sorus, and tendril.
-(HP) tuber growth and development stages: open on SF since 6/2009
-(LP) post harvest stages: this is an old request, but no one ever commented on it.
-(MP) terms for seed development stages:this is a fairly new request for terms for cotton
