POC Conf. Call 7-14-10

POC meeting, Webex Conference Call; Date: July 14th, 2010 10am (PDT)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG),

Absent: Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab).

Collaborators: Rex Nelson

Acceptance of the minutes from the 6-30-10 meeting? All in favor? There were no additions, deletions or changes to the minutes of the last meeting.

Report from the Bio-Ontologies 2010: Semantic Applications in Life Sciences. Conference

July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB).

-Laurel and Ramona attended and presented a poster. Ramona presented a 'flash update talk' BioOntologies program.

-Had discussions/meetings with people from OBI (Helen Parkinson), Cell Ontology (Terry Meehan), GCP Crop Ontology (Rosemary Shrestha), BioPortal (Trish Whetzal) and many others.

Poster, 1 page write-up, and talk are posted on POC_Outreach_Events wiki page.

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.

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.

Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if she is not available.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, will contact them again.

Do we want to organize an annotation workshop?

Important dates (http://www.ibc2011.com/Dates.htm)

Pankaj received approval from OSU for international travel. Ramona and Dennis will work to secure approval for funding for Ramona. Still waiting to hear from Angelica, will ask for extension on time.

Preparations for next release

This was discussed at the Corvallis Workshop.

We had talked about trying to get the beta release done for July 15th- we need to access if this is feasible.

What needs to be done?

• Review recent changes (see next agenda item)

- We have made a number of changes that need to be reviewed and approved

• Finish edits related to recent changes (parts of stem/shoot)

At least one day of editing, maybe two.

• Prepare documentation on wiki/for reviewers

• ?Work on is_a completeness; fix known errors in ontology; address open Source Forge items?

~10 open older Source Forge items ~135 terms without is_a parents. Ramona has assigned parents for about 30 of these, could do more -known errors include terms with dual parentage, terms whose definitions need work (Ramona has notes, includes terms like primordium, node)

• Compile and load final beta version

• Contact reviewers, post notice

General agreement that we would like to have the beta version out before travel to our respective meeting at the end of July. Goal is to have test file ready for upload to beta by 7/21/2010.

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Review of changes discussed at POC Meeting and Workshop June 29-30th, Corvallis

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

-Part_of and is_a children of these terms were moved to 'whole plant'.

-Also deleted the temporary terms gametophytic cell and sporophytic cell.

These changes were accepted. Need to request new terms gametophytic phase and sporophytic phase on Source Forge.

2. Made new term embryo sac (PO:0025074): a female gametophyte in angiosperms. Is_a female gametophyte.

-Antipodal cell, central cell and egg apparatus are part_of embryo sac (rather than part of female gametophyte).

-egg cell (PO:0020094) was part_of egg apparatus, but this does not allow for eggs that are not in angiosperms. Therefore, changed relation to egg_apparatus has_part egg cell.

These changes were accepted.

3. New top level term plant structure system (PO:0025024): An anatomical system in a plant.

-Has new child root system (PO:0025025): An axial plant structure system that produces root apical meristems and the plant structures that arise from them.

• Renamed shoot to shoot system (PO:0009006): An axial plant structure system that produces shoot apical meristems and the plant structures that arise from them.

Related synonym: shoot, narrow synonyms: crown (sensu Poaceae) and crown.

Do we want to keep this as a rename of shoot, or should be make a new term shoot system, and merge shoot with it?

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.

Maybe these terms would be better as children of 'collective plant structure'?

Vascular system (PO:0000034) could be a child of plant structure system, may be better as child of portion of vascular tissue.

Agree that shoot system and root system should be children of collective plant structure. Will destroy term plant structure system, and move vascular system to child of vascular tissue.

4. Made new term plant axis (PO:0025004): An axial plant organ. Comment: Includes roots and shoots.

-is_a plant organ.

-Children are:

-root (PO:0009005):A plant axis that is part of a root system

and the new term shoot axis (PO:0025029): A plant axis that is part of a shoot system. Comment: often bears leaves and branches. Related synonym: shoot. Children: stem, branch

Last week's minutes say that a stem has parts nodes and internodes, but any shoot axis could have nodes and internodes, therefore, that should perhaps go here, 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?

These changes were accepted.

5. stem was made a child of shoot axis. Proposed definition: A shoot axis that is the primary axis of a plant.

Comment (from old definition): Often bears leaves and buds. It is usually above ground, more or less negatively geotropic, and exogenous in origin. Often has indeterminate in growth.

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.

• Will do this after we agree on final definitions for stem and shoot terms.

Stem term was accepted. Need to make necessary edits to part_of children.

6. Made new term branch (PO:0025073): A shoot axis that develops from an axillary meristem or from equal divisions of the shoot apical meristem. Narrow synonyms: secondary axis, tertiary axis, higher-order axis.

Branch term was accepted. Need to make necessary edits to part_of children of stem.

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

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

See also comment under grandparent term (shoot axis) that it may bear leaves and branches.

Also made stolon (PO:0003024) and rhizome (PO:0004542) children of branch.

Proposed definitions:

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

Rhizome: A branch that grows horizontally and produces shoots above and roots or rhizoids below. Comment: Usually produces scale-like leaves. May produce rhizoids, especially in Pteridophytes.

Need to determine if tubers are always determinate and if rhizomes are always indeterminate.

Changes for tuber and stolon were accepted. Agreed that both tubers and rhizomes could be both determinate or indeterminate, so that should not be part of the definition.

Some discussion of rhizomes. In ferns and many monocots, rhizomes are the primary axis, so they should be child of stem, not branch. Suggest making rhizome direct child of shoot axis, so that it can encompass cases where the rhizome is either a primary or secondary axis. Need to make Source Forge item for rhizome.

8. 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)

>leaf (PO:0025034): new term; needs a definition

>>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 in form from the foliage leaves, subtending a flower or inflorescence (This fits vascular bracts, so maybe should be a child of vascular leaf), but sometimes the term bract is used in bryophytes).

>>vascular leaf (PO:0009025): 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.

The terms and organization for leaf were accepted.

New def. for bract: A leaf, usually different from foliage leaves, subtending a reproductive structure.

Rewrote definition for phyllome: A lateral plant organ produced by the shoot apical meristem.

Wrote new definition for leaf: A phyllome that is not part of a flower.

Should change definition of vascular leaf to: A leaf in a vascular plant. Move original definition to the comment.

Some discussion of whether or not a cotyledon is a vascular leaf, but decided to leave it there for now.

Older unresolved terms

1. fruit (fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.

Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312

On a previous call, Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.

Proposed new def. in response to comments above: A collective plant structure that contains a post-fertilization stage gynoecium. 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.

Should we include develops_from gynoecium relation?

Rex pointed out that 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.'

Came up with a new proposed definition: A collective plant structure that develops from a gynoecium containing one or more embryos. Keep original comments.

2. Embryo (See SF Tracker: embryo)

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

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants

Relationships:

(a) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity

(b) Usually develops_from zygote (Adventitious embryos and somatic embryos do not arise from zygotes -add a comment?)

(c) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)

-See Cultured embryo PO:0000010 for definition of in vitro plant embryo

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

Discussion of stalk was postponed until future meeting.

3. 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 which attaches the ovule to the
 placenta.(ovule: cardinal organ part)

• gynophore: A stalk at the base of the ovary. 

(ovary: 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)

• 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 supporta an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).

Upcoming Conferences and Meetings: Updates:

* 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 Outreach 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.

Will invite outside experts, scientists, students and postdocs.

Please fill out Doodle Poll re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg

We need to pick a date for this meeting ASAP so folks who are flying in can get tickets!

Next meeting scheduled for: Weds, July 21th, 10am