POC Conf. Call 12-22-10
POC meeting, Webex Conference Call; Date: Wednesday Dec 22nd, 2010 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC Conf. Call 12-15-10?
Issues arrising from last weeks agenda
- Pavement cell was part of leaf adaxial epidermis, leaf abaxial epidermis, leaf lamina adaxial epidermis, and leaf lamina abaxial epidermis. Made new terms leaf pavement cell, leaf abaxial pavement cell and leaf adaxial pavement cell. While working on this, I noticed a problem with the definition of pavement cell.
Suggested definition:
Made long cell, short cell, and papilla cell is_a pavement cell.
- floral stomatal complex: PO:0008044
Obsoleted terms floral stomatal complex, floral guard cell, floral stomatal pore.
Added new terms phyllome stomatal complex, bract stomatal complex, carpel stomatal complex, petal stomatal complex, stamen stomatal complex, sepal stomatal complex, tepal stomatal complex.
Did not yet create corresponding guard cell and stomatal pore terms or ab/adaxial stomatal complex terms. Users can create those post-compositionally, if they need them, or we can create them later. If we create new terms, we will have to address the annotations for guard cell (1821 of them). Most of them will probably have to move to leaf guard cell. Any preferences?
- New subset for angiosperms -- have not added it yet, because OboEdit has a bug right now that won't let me name a subset. Will add later.
Timeline and Plan for Upcoming Release- Revised PSO:
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 new term petiole lamina (PO:0025129).
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 free tepal apex post-compositionally using tepal apex (PO:0025143) and free tepal (PO:0025136).
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 fused 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 plant anatomical space, maybe we should add this as a space?
Fused 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 fused 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 The term fascicle can refer to different structures in different taxa. Suggest we use the term Fabaceae fascicle in this case.
Suggested def: A reproductive shoot system that ...
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in that two to several flowers are initiated in each bract axil rather than just one as in a raceme. The cluster of flowers at each node is called a fascicle. The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows the fascicle to be a short shoot topped by a second order inflorescence apical meristem. This meristem initiates flowers in a bilaterally symmetrical order: a single abaxial flower, then two lateral flowers, another median abaxial, then two more laterals. The number of flowers per fascicle depends on the duration of the axillary inflorescence apex of the short shoot, which ceases activity after initiating the few flowers in the fascicle. No flowers are initiated adaxially (toward the first order axis) on the short shoot (Tucker, 1987b; Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be distinguished from a cyme in that every flower is bract subtended in a pseudoraceme." Source: Tucker, 2003, Floral development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
We added the term stipule spine. Could also add the term stipule bristle: A stipule that is (?)
Alternative is to suggest bristled to PATO
Phyllode Suggested def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
Banner (as in a legume flower) - maybe name Fabaceae banner
Suggested def: A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
Wing (as in a legume flower) - maybe name Fabaceae wing
Suggested def: One of two petals that is adjacent to the banner in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner and keel.
Keel (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name Fabaceae keel
Suggest three new terms:
fused petal: A petal that is fused to another petal. Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
fused corolla: A corolla in which the petals are fused. Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
keel: A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae. Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
Locule The term locule can be used to refer to the cavity in an carpel (an embryo sac and the carpel tissue that surrounds it) or in an anther (a pollen sac and the stamen tissue that surrounds it. In the PGDSO, we have the term PO:0001026 locules established, which is an anther development stage. For clarity, we may want to add two terms: anther locule and carpel locule .
anther locule: A cardinal organ part that is part of an anther and has as parts a single pollen sac and the layers of anther tissue that surround it.
carpel locule: A cardinal organ part that is part of a carpel and has as parts an embryo sac and the layers of anther tissue that surround it and contains at least one ovule. Comment: The embryo sac may have one or more ovules in one locule or may be divided into mutliple locules, each containing an ovule. (needs work)
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.
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: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
We dealt with this under terms without is_a parents
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 cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
Part_of vascular leaf, has_part sporangium
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
tendrils can derived from multiple types of structures. Suggest we make separate terms:
branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
Can add other types of tendrils if they come up or users need them.
terms for seed development stages
This is a fairly new request for terms for cotton
POC Conference Call Schedule for next term
We need to go through the doodle poll process again to Schedule the POC Conference Calls for next term.
Please visit the link below and fill in when you are available:
Winter term 2011 POC Conf Calls
Upcoming meetings 2010-2011:
- Plant and Animal Genome XIX Conference
January 15-19, 2011 PAG 2011
Laurel, Ramona, DWS and Justin Preece are attending. PJ may attend for the weekend only as he is teaching. Alejandra cannot attend.
PO Activities at PAG:
Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)
- Plant Phenotypes workshop and panel discussion:
" The Plant Ontology: Linking phenotypes and genomics across plant taxa"
Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am
- PAG_2011_Collaborators_Workshop and meeting with collaborators
Sunday Late Morning:
Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)
PO Workshop Reg'n site and Survey
- Poster: link to abstract TBA
- Outreach Booth being organized by MaizeGBD- More info TBA
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.
Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.
No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.
Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted the organizers to figure out how to nominate additional speakers, and will pass on information to the speakers. We hope to use the 6th time slot for a discussion session.
RW heard from organizers re. additional speakers. Will forward their information. Still waiting to hear about discussion session.
