POC Conf. Call 7-21-10

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab).

Absent: Dennis Stevenson (NYBG),

Collaborators: None

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

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

Preparations for next release of PO

See the timeline and plan sent out 7-19-10 File:Plan PO Release (LC 7-19-10).pdf

1. July 21 POC Conference call - We will review and approve (or discuss) the most recent changes and all the Consortium members will be able to have a look at it before we send it out. At this point most the changes have been discussed on SourceForge and at the previous meetings already. Assuming there are no further major changes, we will proceed with getting it loaded onto the Beta browser (see below):

2. Notices will be posted on the PO mail lists: po-announce, po-dev, the PO web page and the Jaiswal lab web page that the beta version is available for review.

3. Documentation will be posted on the 2010 Release Notes Page with a link from the PO webpage with details of the changes made in the new release.

4. An announcement will be sent directly to the direct user groups listed on the 6-29-10 Conference Call page. We need to identify who the are contact people at these groups.

• TAIR
• NASC
• Gramene
• MaizeGDB Carolyn Lawrence
• VirtualPlant
• SoyBase Rex Nelson
• Genevestigator
• SGN Lukas Mueller+Naama Menda ?
• OryzaBase Yukiko Yamazaki?
• PlantTribes
• TraitNet Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
• Generation Challenge Program, CIMMYT, Mexico Rosemary Shrestha
• BRENDA
• UniProt

We will send the email to the 'contact' email address at each of these groups.

5. Over the next ~ 3 weeks we will take feedback from our direct user groups- one of the ways will be through meetings and discussions at the ASPB and BSA meetings and through a feedback box on the PO-beta.plantontology.org page and of course, through emails.

Note: We can use the same feedback page that is on the main PO site, we will ask Justin E to make a link to it from the header on beta.plantontology.org browser. The feedback box captures the context of the comment ( ie: which page you are looking at).

6. Aug 8-26- The beta version will be ready to send it out to our panel of experts and also to the user groups for final review. - The letter and review template will be sent out to the panel of experts (along with the user groups) that were identified on the 6-29-10 Conference Call .

-Reviewers will be asked to send their comments by Aug 26th. This will give them about 2 weeks to respond. PJ: We should ask them ahead of time if they are willing and able to do the reviewing, then give them the 2 weeks, with flexibility if they need it.

-We will follow the way the reviews were done in 2005, where the reviewers will be asked to look at specific sections or branches of the ontology. - Laurel will send out an email inquiry (copied to DWS and PJ and po-internal?) to the reviewers asking them if they would be willing to do it.

-Once we all get back from vacation, we will make the required changes and prepare the release.

(Ramona out Aug 20th- Sept 7th, Laurel out Aug 27th- Sept 8th, Pankaj gone Aug 11th- Sept 3rd)

To do: Identify reviewers for specific branches of the ontology:

Note: PO page has a link to the list of reviewers who did it last time: Acknowledgements

-Potential reviewers: 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), Rob Last (trichomes) (*)plant anatomy experts

Other Potential Reviewers: David Jackson, Cold Spring Harbor Laboratory, jacksond@cshl.edu

Peter Steven Angiosperm Phylogeny website (peter.stevens@mobot.org (Missouri Botanical Garden), or stevensp@umsl.edu (University of Missouri, St Louis))

Robert Stevens- will need it in OWL format for him

Barry Smith will perform the OBO Foundry checks

How about Aaron Liston?

7. Update documentation on web page and wiki:

-what we did and why we did it

-highlight things we want people to review

-wiki page has been created. We will load documentation of changes as we go along.

8. Week of Sept 9th-15th - Laurel and Ramona will compile the feedback and comments from expert reviewers and user groups, make final changes, complete any additional documentation needed. Sept 15th- Release live version

PJ is presenting at the NSF review meeting in early Sept and so he can report on our release at that time.

9. Mid Oct: Submit update paper to Plant Physiology as discussed at 6-29-10 Conference Call .

Merging files for dev and beta browsers

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 (but possible, since they will still have separate name spaces).

Is it okay to go ahead and make the merge?

Once files are merged, we will be able to make relation between temporal and structural anatomy.

Should this be done before the beta release?

Rename beta version file po_anatomy_beta or similar.

We will wait until after the beta release to merge the files. We will not rename the files _beta (to prevent accumulating too many files on SVN). Instead, we ill use a set version number of the files for the beta release.

Once the files are merged and relations between them have been made, it will be a bit more difficult to separate them, but it can be done by extracting three files (one for temporal, one for anatomy, and a bridge file with relations or XPs between the two).

New Items

- Alejandra is making good progress on putting the images up on Plant systematics.org. They will have a link to PO and will display the PO logo.

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.

OK

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.

Since the vascular system can also contain non-vascular tissues, it can't be a child of portion of plant tissue. Make it a child of plant structure.

proposed def'n: Vascular system: A plant structure that includes the totality of the portions of vascular tissue in their specific arrangement in a whole plant or in a constituent part thereof.

Comment: The vascular system may also contain portions of ground tissue.

This will allow terms like leaf vascular system to be a child of vascular system.

On a side note, we should add a comment to plant structure (PO:0009011) that it is a product of the coordinated expression of genes, with reference to FMA. RW: we already have a dbxref to CARO anatomical structure, which is defined as 'Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.'

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?

OK

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.

OK

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

OK

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.

OK

7. Added terms vascular leaf and non-vascular leaf, as children of leaf. Current term leaf=vascular leaf, so changed its name to vascular leaf, and made 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.

OK

8. fruit

Proposed def.: A collective plant structure that develops from a gynoecium containing one or more embryos.

Proposed new def.:A collective plant structure containing one or more embryos, which as a whole, develops from a 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.

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? Yes

Add dbxref to NCBI taxon Angiosperm?

Comment: only in angiosperm

9. embryo

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

Proposed def.: A whole plant in the post zygotic, sporophytic phase, consisting of not yet fully-differentiated tissues.

Proposed new def'n: A whole plant in the post-zygotic stage in which it does not yet consist of fully differentiated tissues.

RW: I changed phase to stage, because a few weeks ago we discussed using phase only with sporophytic and gametophytic, and stage with other portions of a plant's life (such that a stage is a part of a phase).

Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010) are in vitro plant structures.

Additional comment: Embryos occur prior to germination in vascular plants.

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.

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.

OK

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.

BS: Suggestion: shape- make comment to see PATO, url's are better, define sub cylindrical in comment.

CM: submit sub cylindrical to PATO

RW: PATO already has terms for cylindrical (PATO:0001873) and subcylindrical (PATO:0002226), so I just put dbxrefs to those terms. I also added a comment that stalks can be ridged or grooved.

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.

OK

• 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.

OK. Can add related term androphore as needed.

• 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).

OK

• 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).

OK

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.

OK

• 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

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

Check if PATO has cup or tube shaped - refer to PATO

RW: PATO has term cup-shaped (PATO:0002227) and tube-shaped is a synonym of cylindrical (PATO:0001873), so I put in dbxrefs to those terms.

• 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]

Proposed new def: A cardinal organ part at the apex or base of a petiole, petiolule, leaf sheath, or branch that is differentiated from the remaining organ parts by its swollen size.

RW: PATO defines swollen as: A structure quality inhering in a bearer by virtue of the bearer's exhibiting transient abnormal enlargement, not due to cell proliferation. This is not we want to convey, so instead, I used the phrase 'enlarged cross section' (PATO:0000586, enlarged = increased size).

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.

Proposed new def: A cardinal organ part of a shoot axis where one or more spikelet, flower, floret, branch, bud or leaf may arise.

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.

Proposed new def: A cardinal organ part of a shoot axis between two nodes of the axis.

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 ).

>>These changes will provide a framework for future work on the ontology.

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

We will accept these changes without review for now. Can be changed for future releases if need be.

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 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.

Goals for this meeting:

Plan next phase of PO development.

Include experts in bryophytes and gymnosperms.

Doodle Poll will be extended with dates until late November.

• 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

Meeting dates

No meeting on scheduled for next Weds, July 28th and August 4th, since most everyone will be traveling. What is everyone else's schedule for August?

August Meeting dates: Weds, Aug 11th, 18th, 25th (?)

No Meeting Weds, Sept 1st as we will all be on vacation.