|
|
| (31 intermediate revisions by the same user not shown) |
| Line 3: |
Line 3: |
| | In attendance: | | In attendance: |
| | | | |
| − | POC members:
| + | This meeting was postponed, as most of the curators will not be available. |
| − | | |
| − | 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==
| |
| − | | |
| − | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3030644&group_id=76834&atid=835555 Musa terms]===
| |
| − | | |
| − | Requested by Rosemary Shrestha (July 2010). Most of these are synonyms of existing terms. Also see spread sheet attached to SF tracker item.
| |
| − | | |
| − | banana anatomy/morphology web site: http://www.ikisan.com/links/ap_bananaMorphology.shtml
| |
| − | | |
| − | ''We went through many, but not all of the terms. See notes below each term.''
| |
| − | | |
| − | | |
| − | 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.
| |
| − | | |
| − | '''1. Musa leaf terms'''
| |
| − | | |
| − | o '''Petiole wing''': Thin extension to the petiole margin. part_of CO_125.0000057 ! Petiole
| |
| − | | |
| − | Proposed def: A petiole margin that extends from a petiole that is otherwise rounded in cross-section. is_a petiole margin
| |
| − | | |
| − | An alternative would be to use petiole margin (PO:0025010) that is enlarged (PATO:0000586) lateral to (PATO:0001193) the petiole (PO:0020038)
| |
| − | | |
| − | ''This should be a synonym of petiole lamina. Need to add new term petiole lamina.''
| |
| − | | |
| − | | |
| − | o '''Petiole margin''': In section, the narrowing margins of the petiole canal. part_of CO_125.0000057 ! petiole
| |
| − | | |
| − | We already have the term petiole margin (PO:0025010). Can add comment: generally in flattened petioles, but may also occur as extensions of petioles that are rounded or c-shaped in cross section.
| |
| − | | |
| − | ''Okay to add comment.''
| |
| − | | |
| − | | |
| − | o '''Cigar leaf''': Youngest visible leaf, still rolled as a cylinder. CO_125.0000002 ! leaf. syn: "candle leaf" EXACT
| |
| − | | |
| − | This is a phenotype. Should annotate to leaf PO:0025034 and request PATO term for rolled. Can add cigar leaf and candle leaf as narrow synonyms of leaf.
| |
| − | | |
| − | ''Although it is a phenotype, we will add the term for Musa subset. May apply to other species as well, especially in monocots. is_a vascular leaf.''
| |
| − | | |
| − | | |
| − | o '''Petiole canal:''' The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole
| |
| − | | |
| − | Add 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.
| |
| − | | |
| − | Should also then add abaxial petiole, with parallel definition.
| |
| − | | |
| − | ''Okay to add terms adaxial petiole and abaxial petiole?''
| |
| − | | |
| − | ''RW (after meeting): now that we have anatomical space, maybe we should add this as a space.''
| |
| − | | |
| − | | |
| − | o '''Petiole margin edge''': Line running along the edge of the petiole margins." [ISBN:92-9043-307-8 "IPGRI-INIBAP/CIRAD. 1996. Descriptors for Banana (Musa spp.)"]. is_a: CO_125.0000006 ! petiole margins
| |
| − | | |
| − | Organ margin (of which petiole margin is a child) is defined as 'The edge of an organ and the area immediately internally adjacent to it.' Do we want to add term organ edge? Seems a little over the top, because where do you define where the edge begins and ends relative to a margin?
| |
| − | | |
| − | ''Should just use petiole margin?''
| |
| − | | |
| − | | |
| − | o '''Cigar leaf dorsal surface''': External (abaxial) face of the leaf (partly visible). part_of CO_125.0000008 ! cigar leaf
| |
| − | | |
| − | We have the term leaf abaxial epidermis (PO:0000049). See comments above for cigar leaf.
| |
| − | | |
| − | ''Can add new term, cigar leaf abaxial epidermis, is a leaf abaxial epidermis, part_of cigar leaf.''
| |
| − | | |
| − | | |
| − | 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 '''Free tepal''': The inner tepal which is free. is_a: CO_125.0000129 ! tepals
| |
| − | | |
| − | This is just a phenoypic descriptor of tepal. We could add free tepal as a synonym of tepal. Need to request PATO term free. Free is the default state for tepal or other phyllomes.
| |
| − | | |
| − | ''Can add 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''
| |
| − | | |
| − | | |
| − | o '''Compound tepal''': The outer perianth sheath of 5 fused tepals which has 3 major lobes and 2 minor ones. is_a: CO_125.0000129 ! tepals
| |
| − | | |
| − | This is really a phenotypic descriptor of a type of perianth. Use either collective tepal structure (PO:0025021) and fused (PATO:0000642) or tepal (PO:0009033) and fused (PATO:0000642).
| |
| − | | |
| − | ''Can add 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.''
| |
| − | | |
| − | | |
| − | 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''
| |
| − | | |
| − | | |
| − | 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)
| |
