POC Conf. Call 12-8-10
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
Remaining terms without is_a parents
axil
(also an open tracker item)
Should the PO have a generic term 'axil' and, if so, how it should be defined? See also older tracker item leaf base vs. axil?
Original data:
id: PO:0009023
name: leaf axil
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
Suggest: is_a axil, part_of shoot system
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 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
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.
Also added new term leaf tip, which is part of leaf apex.
Compound tepal lobe: Musa folks (and others) can describe compound tepal lobe by post-compositionally using tepal apex and compound tepal.
Peduncle surface: New term peduncle epidermis added
Peduncle hairs: New term peduncle trichome added
Bract apex: New term added
Bract base: New term added
Bract external face: New term added: bract abaxial epidermis, sibling to leaf abaxial epidermis, child of new term phyllome abaxial epidermis.
Bract internal face: New term added: bract adaxial epidermis, sibling to leaf adaxial epidermis, child of new term phyllome adaxial epidermis.
Hermaphrodite flower: Added as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP
Female flower: Added as synonym of flower. Need to request staminate and pistillate in PATO, so users can describe this terms as a XP
Issues arising from new terms:
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?
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.
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 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).
Added the following term:
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.
is_a shoot system, part_of inflorescence
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.
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.
3. Musa fruit terms
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
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)
tuber growth and development stages
This item has been open on SF since 6/2009
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).
Suggested stages:
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
-tuber initiation
-tuber growth
-tuber maturation
How we work these in will depend on restructuring of PGDSO
Legume terms
submitted by Austin Mast
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
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),
Locule
Adding/modifying the root terms
submitted by Rich Zobel (Nov 2009)
TraitNet requests
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground (is it always underground?)
child of stem (PO:0009047).
Their comment: is synonym to Tubercle
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
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).
proposed def:
definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
proposed def:
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.
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.
definition of stele (from Beentje 2010): a part of a plant axis made up of the primary vascular system and its associated ground tissue.
suggested parent: cardinal organ part
suggested definitions:
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.
root stele: a stele that is part of a root.
shoot axis stele: a stele that is part of a shoot axis
(could have children stem stele and branch stele)
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.
We could add this term as a kind of upper level bin term (similar to trichome)
Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
rom Crum (2001): a cluster of fern sporangia from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
Proposed definition: a collective plant structure composed of two or more adjacent sporagia on the surface of a leaf (this will need refining)
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
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.
terms for seed development stages
This is a fairly new request for terms for cotton
Other items (lower priority)
-(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.
-(LP) post harvest stages: this is an old request, but no one ever commented on it.
