POC Conf. Call 12-22-10

POC meeting, Webex Conference Call; Date: Wednesday Dec 22nd, 2010 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Justin Preece (OSU), Alejandra Gandolfo; (Cornell University), Barry Smith (University at Buffalo, NY)

Absent: Pankaj Jaiswal (OSU), Justin Elser (OSU), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Acceptance of the minutes from the POC Conf. Call 12-15-10?

There were no additions, deletions or changes to the minutes of the last meeting.

Issues arising from last week's 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'.

Current def'n: 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'.

We had a healthy discussion about this term and its definition. DWS stated his objections with the use of the term 'pavement cell' because of its use in gymnosperm embryology, but it is used in the literature, especially for Arabidopsis; (see:Qian et al).

A suggested solution is to rename the term 'epidermal pavement cell'. MAG pointed out that the pavement cell and the guard cell have the same developmental origins (from the protodermal cell; see:SF tracker item ), but this would not be evident to the person looking at them in a mature form.

LC and BS felt we should avoid defining terms by what they are not (see bract as well). BS commented that in the future, with closer merging of OWL and OBO, these disjoint relationships will be much easier to add, but for now, we should just put them as comments.

epidermal pavement cell: New proposed def'n: A shoot epidermal cell that is relatively unspecialized at maturity (not perfect but better than what we had)

develops_from protoderm

comment: May have sinuous anticlinal cell walls that overall give a jigsaw like appearance to the leaf epidermis, not associated with a stomatal complex or trichome.

Will add disjoint_from relations to trichome cell, guard cell, and subsidiary cell.

Note: the terms 'long cell', 'short cell' are children of 'leaf pavement 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 (PO:0025215), bract stomatal complex (PO:0025216), carpel stomatal complex (PO:0025217), petal stomatal complex (PO:0025218), stamen stomatal complex (PO:0025219), sepal stomatal complex (PO:0025220), tepal stomatal complex (PO:0025221).

- 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?

We decided we should have 'phyllome guard cell' as a bin term, can add the rest later as needed

• Created new subset for angiosperms. Added a few terms to the subset, but list is not complete.

• 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 be present after germination (e.g., hypocotyl)?

BS: Avoid dual parentage if possible, this is a problem that many ontologies are dealing with. We decided for now to just include the embryonic plant structures that are only present in the embryo. This excludes terms like hypocotyl. May need to change some relations that are part_of to has_part (e.g., embryonic axis has part hypocotyl, rather than hypocotyl part_of embryonic axis.

Also epiblast

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

All in favor, accepted

• stylar ridge/gynoecium ridge need to be approved see: POC_Conf._Call_10-26-10

All in favor, accepted

• There are a bunch of terms where the name has been changed from something (sensu Poaceae) to Poaceae something. This means we have a mix of sensu and non-sensu terms.

Should we go through and fix these for this release?

All present were in favor of this, BS: these have been removed by the GO, PO should do the same.

Accepted, pending approval by PJ, who was not on the call today

Timeline and Plan for Upcoming Release- Revised PSO:

- complete changes discussed this week, put on Beta browser after Justin E returns from vacation, do 'internal' review before releasing it early in the New Year.

- look for annotations that need to be moved:

- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)

see also Jan 2011_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)

All were in favor of making this change, RW will post the resulting def'ns and make a SF tracker and send them to BS

User requests still open on SourceForge

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 with the 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.

We had discussion to clarify a vascular leaf; MAG: Is this redundant? when is a leaf not vascular? Moss leaves lack vascular tissue and so are non-vascular leaves. Megaphylls and microphylls are both vascular leaves. We will revisit the whole ontological structure of leaf at a future date.

• petiole margin edge: Should just use petiole margin (PO:0025010)

• cigar leaf dorsal surface: Added new term, 'cigar leaf lamina abaxial epidermis' (PO:0025135), is_a leaf lamina 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).

Note: 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 petiole canal as a space? See tracker for canal

All present agreed that canal should be a plant anatomical space, BS: check FMA

new proposed def'n: A canal that is part of a petiole. Comment: May occur on the abaxial or adaxial surface or be internal.

Will make children abaxial petiole canal and adaxial petiole canal.

• 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 has as parts at least two fused tepals.

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.

We still have a lot of work to do on these, so we will split the SF tracker up into 3 ind ones and hopefully be able to complete it next week. Will make a separate tracker for inflorescence and infructescence.

Musa flower terms

• 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

• 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.

• 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.

At the 11-5-10 POC meeting, we decided not to add separate terms for male and female flowers. Probably want to be consistent with bud.

Musa fruit terms

• 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 - probably the main axis of the infructescence.

• 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 all of the flowers borne by those axes. Must have two or more flowers as parts.

Proposed definition of infructescence: a reproductive shoot system that develops_from an inflorescence and has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and all of the fruits borne by those axes.

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]

• flower relics: 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.)

Musa shoot terms

• sucker: Lateral shoot that develops from the corm and usually emerges close to the parent plant. is_a: CO_125.0000001 ! plant part

This could be a synonym of axillary shoot system (PO:0006343): A shoot-borne shoot system that develops from an axillary vegetative bud.

Will probably need to be a broad synonym, because (I think) people also use the term sucker to refer to root-borne shoots. Alternatively, we could make the phrase "Musa sucker" a narrow synonym of axillary shoot system, and make "sucker" a synonym of root-borne shoot.

• 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? If not, we could make it a collective plant structure. If this structure is unique to Musa, we should call it "Musa pseudostem," but maybe it occurs in other taxa?

• 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), and add pseudostem underlayer as a narrow synonym.

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

Tentatively, it looks like Tuesday at 10am (PST) (1pm EST) works so far

Upcoming meetings 2011:

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Laurel, Ramona, DWS and Justin Preece are attending. PJ will 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: PO Poster Monday 3:00 pm - 4:30 pm

• Outreach Booth being organized by MaizeGBD- More info TBA

• Phenotype Ontology RCN Summit

The Phenotype Ontology RCN

February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,

Laurel and Pankaj will be attending.

* 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 these speakers to get their information and abstract; waiting for responses from them.

We received permission to use the 6th time slot for a discussion session, but need to have a commitment that someone will lead the discussion. PJ will do it.