POC Conf. Call 12-8-10

POC meeting, Webex Conference Call; Date: Wednesday Dec 8st, 2010 10am (PST)

In attendance:

This meeting was postponed, as most of the curators will not be available.

The agenda below is for reference only, and will be taken up at future meetings.

Old agenda items

Remaining terms without is_a parents

(still need to fill in proposed parents and definitions)

shoot apex: PO:0000037

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]

subset: reference

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."

is_a shoot axis

root nodule: PO:0003023

current def: "Enlargement or swelling on the roots of plants, particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria." [ISBN:0471245208]

Proposed definition: A cardinal organ part that is an outgrowth of a root and is inhabited by nitrogen-fixing bacteria.

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.

is_a cardinal organ part, part_of root

We may want to add the term root nodule meristem, dbxref: PMID:1809347

leaf axil: PO:0009023

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

Suggest: is_a axil, part_of shoot system

axil

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?

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.

tetrad of microspores: PO:0000032

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

Proposed definition: A portion of plant tissue consisting of four haploid cells that remained joined together shortly after meiosis.

Comment: Each cell will give rise to the male gametophyte

is_a portion of plant tissue, part_of anther? What about in non-angiosperms?

valve: PO:0000033

current def: "Portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity." [APWeb:Glossary]

subset: Arabidopsis

fruit columella: PO:0004540

current def: "Central axis of the fruit." [POC:curators] subset: Tomato

hypocotyl-root junction: PO:0004724

current def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki] subset: reference

hull (sensu Poaceae): PO:0006000

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

pollen tube (see old agenda item): PO:0006345

current def: "A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule." [ISBN:0471245208] subset: reference

basal endosperm transfer layer: PO:0009019

current def: "A cell layer found in basal endosperm transfer cell." [GR:cwt] part_of basal endosperm transfer cell

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.

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.

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).

lodicule: PO:0009036

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]

subset: reference

Proposed definitions: A phyllome in a grass floret that is one of two or three tiny scales or flaps of tissue outside the stamens

Comment: possibly represents a reduced perianth segment

is_a phyllome

microsporangium: PO:0009070

current def: "A sporangium producing microspores, usually many in number." [APWeb:Glossary], subset: reference, synonym: "anther lobe" RELATED [], synonym: "pollen sac" RELATED []

aril: PO:0009090

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

arilloid: PO:0019022

current def: "An outgrowth from parts of the seed other than from the funiculus or raphe." [ISBN:0080280293]

placentoid: PO:0020005

current def: "An inpushing of the anther wall." [APWeb:Glossary] subset: reference

root stele (see request from Traitnet below): PO:0020124, alt_id: PO:0003012

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 []

parts of embryo

embryo proper: PO:0000001

current def: "The body of the developing embryo attached to the maternal tissue in the ovule by filamentous suspensor." [TAIR:ki]

[egg apparatus: PO:0020096

current def: "The egg cell and two synergids located at the micropylar end of the embryo sac." [TAIR:lr] subset: reference

suspensor: PO:0020108

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.

scutellum: PO:0020110

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 []

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

corm

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).

podarium

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:

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def:

stele

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)

diaspore

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)

cone

Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?

sorus

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)

tendril

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

Open tracker items

includes some terms that had no is_a parent, user requests, and simple changes

Old_SF_tracker_items,_fall_2010

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.

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?

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.