POC Conf. Call 7-21-10

POC meeting, Webex Conference Call; Date: July 21st, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 7-14-10 meeting? All in favor?

Preparations for next release of PO -- We will discuss the document Lol sent out yesterday

1. Target dates

• Beta release upload:

• Prepare reviewers' template, summary and cover letter:

• Send to users:

-includes TAIR, NASC, VirtualPlant, Gramene, SoyBase, Genevestigator, SGN, OryzaBase PlantTribes, TraitNet, Challenge Program, CIMMYT, Mexico

• Send to po_announce and po-dev lists:

• Send to expert reviewers:

-do we want to meet with reviewers in person at NYBG instead?

-Potential revieweres: Sarah Hake, Quentin Cronk, Paula Rudall* (Kew Bot Garden), Sarah Matthews (Harvard), Elena Kramer (Harvard) Neelima Sinha (U C Davis), Chelsea Specht* (UC Berkeley), Rob Martienssen (Cold Spring Harbor), Peter Raven (MoBot) Gar Rothwell* (Ohio University), Peter Linder* (Switzerland), Chris Hardy* (Millersville University)

(*)plant anatomy experts

• Update documentation on web page and wiki:

-what we did and why we did it

-highlight things we want people to review

2. dev and beta file preparation

We discussed merging the developers files (currently po_anatomy_test.obo and po_temporal_test.obo) into one editors file. Once we do this and start making edits to it, it will be inconvenient to have separate the files again.

Is it okay to go ahead and make the merge?

Should this be done before the beta release?

Review of changes discussed last week

1. gametophyte and sporophyte were made obsolete. Added 'consider whole plant' relation to both, and comments to add participates_in gametophytic or sporophytic stage.

New terms for gametophytic and sporophytic phases were created in the PGDSO.

2. We rejected the new top level term plant structure system (PO:0025024): An anatomical system in a plant.

- root system (PO:0025025) and shoot system (PO:0009006) were made children of collective plant structure.

Vascular system (PO:0000034) is now a child of portion of vascular tissue.

We discussed having the terms 'vegetative shoot system' and 'reproductive shoot system', but this could cause problems of multiple parentage. For example, a term like axillary reproductive bud is_a bud, and therefore is_a shoot system. It would logically also be is_a reproductive shoot system if we had that term.

3. New term plant axis (PO:0025004) was accepted.

-is_a plant organ.

-Children are:

-root (PO:0009005) and the new term shoot axis (PO:0025029).

Last week's minutes say that definition of stem is that it has parts nodes and internodes, but any shoot axis could have nodes and internodes, therefore, that should perhaps go there, instead of under stem. Also, should it be what a comment rather than part of definition, if we want to include moss or liverwort stems?

4. stem was made a child of shoot axis.

Because stem is only the primary axis, and does not include branches or secondary axes, we will need to change all of it's part_of children (like stem cortex, interfascicular region, stem epidermis, etc.) to be part_of shoot axis and rename them accordingly. See separate agenda item below.

5. New term branch (PO:0025073) was accepted.

6. We decided that tuber (PO:0004543) is a secondary axis by definition, which equals branch (PO:0025073).

Proposed definition:A swollen storage branch. Comment: May bear scale leaves and subtending axillary buds. Found in potatoes.

Also:

Stolon (PO:0003024): A branch that is slender, prostrate or trailing and above-ground and produces roots and sometimes erect shoots at its nodes. (AP web)

rhizome (PO:0004542): A shoot axis that grows horizontally at or below the substrate surface and produces shoots above and roots or rhizoids below. Comment: In ferns and many monocots, a rhizome is a primary axis (stem), while in other species, it is a branch. Usually produces scale-like leaves.

Agreed that both tubers and rhizomes could be both determinate or indeterminate, so that should not be part of the definition.

7. Add terms vascular leaf and non-vascular leaf, as children of leaf. Current term leaf=vascular leaf, so change its name to vascular leaf, and make new parent term leaf.

phyllome (PO:0006001): A lateral plant organ produced by a shoot apical meristem.

>leaf (PO:0025034): A phyllome that is not part of a flower.

>>non-vascluar leaf (PO:0025075): a leaf in a non-vascular plant. Comment: includes moss and liverwort leaves.

>>bract (PO:0009055): A leaf, usually different from foliage leaves, subtending a reproductive structure.

>>vascular leaf (PO:0009025): A leaf in a vascular plant. Comment: Commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud.

>>>cotyledon (PO:0020030): A leaf formed at the first node of a sporophyte.

8. fruit

'Proposed new def.: A collective plant structure that develops from a gynoecium containing one or more embryos. Comments: A fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.

The presence of an embryo implies fertilization (in normal case), so we don't need to say post-fertilization. This will also cover cases where an embryo develops without fertilization.

Dbx ref to parthenogenesis: Medical subject heading Ontology D010312

Should we include develops_from gynoecium relation?

Add dbxref to NCBI taxon Angiosperm

Comment: only in angiosperm

9. embryo

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Came up with a working def. of embyro: A whole plant in the post zygotic, sporophytic phase, consisting of not yet fully-differentiated tissues.

Comments from Source Forge:

PJ: '....consisting of undifferentiated tissues.' may not work. Sometimes, it has differentiated tissue portions, cell types and may have differentiated organs in early or juvenile phases. Majority have an apical meristem.

RW: Better to say that it consists of not yet fully differentiated tissues, rather than say undifferentiated.

DWS: Here are two things that might resolve this. Incorporate something "on prior to meiosis" which takes care of the bryophytes and charophytes and "prior to cotyledon expansion", which takes care of all of the vascular plants.

PJ: prior to meiosis in non vascular plants and prior to germination in vascular plants.

RW: I don't understand how prior to meiosis describes the embryo in bryophytes. Seems like this would include most of the sporophytic phase. I prefer prior to cotyledon expansion in vascular plants, because prior to germination only works for seed plants.

-Usually develops_from zygote (Adventitious embryos, somatic embryos, or other embryos that do not arise from zygotes -add a comment about these)

-See Cultured embryo PO:0000010 for definition of in vitro plant embryo -- includes microspore (haploid) embryos

Fixing part_of children of stem to match new ontology structure

There were several terms that had 'stem' in there name that could refer to either a stem or a branch. Those term names were changed to include 'shoot axis' instead of stem, so it is clear that they can be in either stems or branches.

• Changed interfascicular region (PO:0006202) to part of shoot axis, instead of part of stem.

• Changed stem cortex to shoot axis cortex (PO:0000223): A portion of ground tissue that is part of a cortex and part of a shoot axis. Comment: Can occur in a stem or branch.

• Changed stem endodermis to shoot axis endodermis (PO:0005058): A portion of endodermis that is part of a shoot axis cortex. Comment: Can occur in a stem or branch.

• Changed stem hypodermis to shoot axis hypodermis (PO:0005057): A portion of hypodermis that is part of a shoot axis cortex. Comment: Can occur in a stem or branch.

• Changed stem pith to shoot axis pith (PO:0005041): A portion of pith that is part of a shoot axis. Comment: Can occur in a stem or branch.

• Changed stem perimedullary zone to shoot axis perimedullary zone(PO:0025064): A perimedullary zone that is part of a shoot axis pith. Comment: Can occur in a stem or branch.

• Changed stem epidermis to shoot axis epidermis (PO:0000112): A portion of shoot epidermis that is part of a shoot axis. Comment: Can occur on a stem or branch.

• Changed stem trichome to shoot axis trichome (PO:0005003): A trichome on/from the epidermis of the shoot axis. Comment: Can occur on a stem or branch.

• Changed stem periderm to shoot axis periderm (PO:0005048): A portion of periderm that is part of a shoot axis. Comment: Can occur on a stem or branch.

• Changed stem vascular system to shoot axis vascular system (PO:0000039): A vascular system that is part of a shoot axis. Comment: Can occur in a stem or branch.

• Did not change stem node (PO:0020141), because we already have the term node, which encompasses nodes on any shoot axis. Change definition slightly to fit g-d form. Added term branch node (PO:0025024) for completeness. Same thing for stem internode (PO:0020142).

>>>Made stem and branch terms narrow synonyms of all terms (e.g., stem cortex and branch cortex are narrow synonyms of shoot axis cortex). If we want, we can add them as children instead, as the need arises.

Changes that need approval

1. stalk (PO:0025066)

(See SF Tracker: stalk)

This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.

current def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.

Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.

-made it a child of cardinal organ part (as per its definition) rather than an organ.

Proposed children of stalk: (Test: do all of these fit the definition?)

• filament: A stalk that is part of a stamen.(stamen:organ)

• petiole: A stalk that is the basal part of a leaf. Supports the lamina. (leaf:organ)

• petiolule: A stalk that is the basal part of a leaflet. Supports the leaflet lamina. (leaflet:cardinal organ part)

• funicle: A stalk that attaches the ovule to the
 placenta.(ovule: cardinal organ part)

• leaf rachis: (See SF Tracker: leaf rachis)

current def'n: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ). Proposed def.: A stalk that is the main axis of a pinnate compound leaf, that bears leaflets or divisions of the axis.

• gynophore: 

(see SF item for stalk).

current def'n: A stalk at the base of the ovary.

>>The gynophore is an elongation of the floral axis (a stem or branch) that bears the carpels. This makes it a shoot axis that is part of a flower, not a stalk.

proposed def.: A shoot axis that is an elongation of the floral axis that supports the carpels. Comment: In many flowers, the gynophore is not present, because there is no elongation of the axis between the androecium and gynoecium.

• peduncle: (peduncle)

current def'n: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves.

>>This should probably be is_a branch (secondary or higher order shoot axis)

proposed def'n: A branch of an inflorescence or an individual flower (R, E, E 4th edition).

• pedicel: (See SF Tracker: pedicel)

current def'n: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

>>This should probably be is_a branch (secondary or higher order shoot axis)

proposed def'n: A branch that supports an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).

2. New is_a children of cardinal organ part (See SF Tracker: new is_a children of cardinal organ part)

• receptacle: (See SF Tracker: receptacle)

Current def'n: The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].

proposed def'n: A cardinal organ part that is the region at the top of either a peduncle or a pedicel where the floral appendages (for example, sepals, petals, stamens, and pistils) are attached.(Brooklyn Botanic Garden http://www.bbg.org/gar2/topics/botany/parts_flowers.html). Part_of inflorescence.

• hypanthium(See SF Tracker: hypanthium)

Current def'n: A cup- or tube-like structure bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary of a flower.

proposed def'n: A cup- or tube-like cardinal organ part, bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary.

made part_of receptacle instead of part_of flower

• pulvinus: (See SF Tracker: pulvinus)

Current def'n: A more or less abrupt swelling, especially at the apex or base of a petiole or leaf sheath, often glandular and/or being the place where a plant responds to touch, gravity or light, in panicoid grasses a swollen region in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary]

-currently is_a (an) organ, should be cardinal organ part.

Proposed def: A cardinal organ part that consists of a swelling at the apex or base of a petiole, petiolule, leaf sheath, or branch.

Comments: Often glandular. Often in movement of a plant structure in response to touch, gravity or light. In panicoid grasses a swollen region in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary]

3. nodes and internodes

Shoot node had no is_a parent. Should be is_a cardinal organ part (since it is part of shoot axis).

Proposed def: A region of a shoot system that is part of a shoot axis where a spikelet, flower, floret, branch, bud and/or leaves are attached.

Part_of shoot axis instead of shoot system.

Children:

-inflorescence node (PO:0006325): A shoot node that is part of an inflorescence axis and where a spikelet, flower, floret or inflorescence branch is attached. (EXISTING TERM)

-stem node (PO:0020141): A shoot node that is part of a stem. (EXISTING TERM)

-branch node (PO:0025024): A shoot node that is part of a branch. (NEW TERM)

Shoot internode had no is_a parent. Should be is_a cardinal organ part (since it is part of shoot axis).

Proposed def: A region of a shoot system that is part of a shoot axis between two nodes.

Part_of shoot axis instead of shoot system.

Children:

-inflorescence node (PO:0006326): A shoot internode that is part of an inflorescence axis. (EXISTING TERM)

-stem node (PO:0020142): A shoot internode that is part of a stem. (EXISTING TERM)

-branch node (PO:0025024): A shoot internode that is part of a branch. (NEW TERM)

4. Progress on is_a completeness

Is_a parents have been added for ~78 existing PSO terms. See the attached document for a list of the terms, their definition and their new parents (File:Is a parents.pdf ).

Changes were only made to terms where the parent was clear. In some cases a general parent term (like portion of plant tissue) was added, but with additional thought, a more specific parent (like portion of ground tissue) may be possible. I figured having a general parent was better than none at this point.

There are now 53 terms that don't have is_a parents. These terms require additional research or discussion before a parent term can be assigned. Some are immaterial entities (like pores or grooves).

I have created a number of Source Forge pages for these terms, grouped by category:

tissues

meristems

cardinal organ parts

types of vascular tissues

plant cells

leaf veins

branches

nodes and internodes

miscellaneous

placenta

Upcoming Conferences and Meetings: Updates:

• International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia

Our proposal for the symposium 'Bio-Ontologies for Plant Sciences' has been accepted, under the theme Genetics, genomics and bioinformatic. The organizers have asked us to confirm three speakers and titles by July 16th. Ramona asked for an extension, because she has not yet heard back from Angelica Cibrian (Harvard, Genomics of Seed Plants project).

As of our last discussion, Ramona and Pankaj were planning to attend and give talks. Lol could attend to help organize outreach efforts. Must confirm that grant money can be used for international travel and confirm third speaker.

Pankaj received approval from OSU for international travel. Ramona and Dennis will work to secure approval for funding for Ramona.

Do we want to organize an annotation workshop for this meeting?

Important dates

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation, Outreach Booth and Annotation Workshop with Gramene.

Laurel is organizing a booth with other database groups: Gramene, SGN, maizeGDB, TAIR and BAR.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. 62 people are signed up! more details TBA

* Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island. Dennis, Alejandra attending, Ramona presenting, 15 minute oral presentation, Abstract submitted 3/26/10.

* POC meeting to be held at NYBG in fall 2010. Date TBD.

What are the goals for this meeting?

Doodle Poll with available dates.

Next meeting scheduled for: Weds, July 28th, 10am

No meeting on August 4th, since most everyone will be traveling. What is everyone's schedule for August?