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 arising 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.

Current definition: Epidermal cell with characteristic sinuous anticlinal cell walls that overall give a jigsaw like appearance to the leaf epidermis.

This is problematic, because there are many species in which the pavement cells are not sinuous. From my understanding, a pavement cell is an epidermal cell that is not a guard cell, subsidiary cell, trichome or socket cell. Papilla cell is_a pavement cell. I think bulliform cell is also a pavement cell.

Suggested definition: An epidermal cell that is not associated with a stomatal complex or trichome.

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.

Should we just keep the terms guard cell and stomatal pore, or should be add specific children for each of the different kinds of stomatal complexes?

• 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.

• Children of embryonic plant structure

Should the new terms embryonic plant cell and embryonic plant tissue have dual parentage (to embryonic plant structure and plant cell or plant tissue) or just to embryonic structure? Also: embryo cortex, embryo epidermis, embryo vascular system, embryonic shoot apical meristem (haven't moved these yet).

What about structures that are present in embryos but may also present after germination (e.g., hypocotyl)?

Also, revised the definition of epiblast somewhat: A portion of embryonic plant tissue that is a flap-like projection of the coleorhiza, inserted opposite the scutellum. part_of coleorhiza (from Esau).

Timeline and Plan for Upcoming Release- Revised PSO:

- put on Beta browser,

- look for annotations that need to be moved

- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)

see also Jan2010_Release_Page

PGDSO Terms without is_a parents

Only four terms remain without is_a parents: 1 pattern formation, 2 endoreplication, 3 branch formation 4 growth directionality.

All are part of leaf trichome development stage. Probably should be is_a trichome development stage, to be consistent with existing structure (may change in alter revisions)

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 (PO:0025010): 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 (PO:0025130): 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 (PO:0025010)

• cigar leaf dorsal surface: Added new term, 'cigar leaf (lamina) abaxial epidermis', is_a leaf (lamina) abaxial epidermis, part_of cigar leaf.

(do you mean 'cigar leaf lamina abaxial epidermis'(PO:0025135)?)

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)

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:

• Computer Demonstration:

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.