POC Conf. Call 10-13-10

POC meeting, Webex Conference Call; Date: Oct 13th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 10-6-10 meeting?

Status and Update of Progress: PO Release

• Amigo browser: There are no icons for relations that we added (has_part, derives_from). Show up as question marks.

Priorities for next release

Overall priorities for next release: restructuring of the PGDSO and the addition of non-angiosperm terms to the PSO.

Any comments or changes?

Target date for next release: ontology structure ready by early/mid December so release can go out before PAG in mid January

Any comments or changes?

Housekeeping Items

(HP=higher priority, LP=lower priority, ?=need to decide priority)

• (HP) Merging the plant structure and plant developmental stages ontologies

Will do this ASAP. Need to know what to name the file. Justin E. will have to change dev browser so it points to the new file.

• (HP) is_a parents for remaining terms (will require work on upper level structure for non-material entities)

~50 terms. Link to list of terms without is_a parents

• (?) add links to more images through PlantSystematics.org

Tepal is only term linked right now (no longer working?). Plantsystematic terms hould be linked to the PO ids - have PO ids embedded in the Plantsystematics.org database. Need to discuss how to create annotations to areas within individual images, labels using HTML.

We will go over the technical aspects in more detail during the Oct. 20th conference call, when Ramona is at Cornell with Ale.

• (?) Lol and Ramona will focus more on adding annotations-

LC will set up a call with RW and PJ to discuss. 1-2 days per week. EST libraries, RNA seq datasets.

• (?) Complete compliance with OBO foundry principles-

Laurel will ask BS what stage we are in the acceptance process. is_a completeness is a priority for this.

• (LP) Convert to intersection_of relations

Can try it out, but maybe not the highest priority for next release.

• (LP) Convert existing definitions to genus-differentia form

Will continue converting definitions whenever terms are worked on.

Changes to PSO

• (HP) add terms for non-angiosperm structures- need to select areas of focus and create list

Ramona will work on list. Should focus on reproductive structures, terms used by model systems such as Phsyco, Selaginella, Loblolly pine, etc., plus whatever terms are needed for the EST library from the Genomics of Seed Plants project.

• (?) is_a completeness

Most of the terms that still lack a parent are the difficult ones, so this may take some time. We will need to address the issue of how to categorize non-material entities and trichomes. May need to go through many of the items one by one.

• (?) closing oldest SF items

many of the older items that are on SF are pretty straightforward to deal with, but we will need to either spend one or two meetings talking about them or get a commitment from all curators to look at them and approve them (or not) on SF (see Old SF tracker items, fall 2010)

• (?) new term requests from users and reviewers (see more details for each item are available on New SF tracker items, fall 2010)

The goal for today's meeting is to prioritize the following items, not to have detailed discussions of each item:

-Musa terms requested by Rosemary Shrestha (July 2010)

-Adding/modifying the root terms submitted by Rich Zobel (Nov 2009).

-Legume terms submitted by Austin Mast: Taproot, Stem Hair, Prickles, Fascicle, Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure), Phyllode, Banner (as in a legume flower), Wing (as in a legume flower), Keel (as in a legume flower), Anther pore and anther slit, Locule

-New terms requested by reviewers:

-Elena Kramer suggested that we add the term spur to the PSO and consider dealing with common primordia in the PGDSO.

-Paula Rudall commented that the current definition of central cell has a different meaning in gymnosperms.

-TraitNet requested several new terms for the PSO: corm, spine, podarium, pneumatophore, stele, diaspore, cone, sorus, and tendril.

• embryo

We have a proposed definition of embryo from 7/2010. We need to finalize this and close the tracker.

• Primordium

Need a class primordium, and need to make one definition for it. Also need to organize primordium terms

We may also want to link primordia to stages in the PGDSO, where appropriate.

For example, ovule primordium (PO:0000018) participates in ovule primordium visible (PO:0007620) or ovule primordium visible (PO:0007620) has_participant ovule primordium (PO:0000018).

• reorganization of shoot system

We started working on this during the last round of revisions (with bud, and terms like reproductive shoot system), but it still needs some tweaking. Need to discuss vegetative shoot system.

• primordium, meristem, bud, shoot system

Doesn't have a tracker item. Should consider aligning the children of these terms.

• axil: We need to discuss whether or not to have a generic term 'axil' and, if so, how it should be defined. See also older tracker item leaf base vs. axil?.

• cortex: We need a brief discussion of how to define cortex (see tracker item). Once we decide this, we can define other tissue types similarly.

Changes to PGDSO

• better organization of descendants of portion of plant tissue

-this category is the home for many terms w/o parents. Needs to be organized better, add some new categories for tissue types

Open SF tracker items Plant Structure Ontology

Newer tracker items and other issues with the PSO

The goal for today's meeting is to prioritize the following items, not to have detailed discussions of each item:

• Adding Musa terms requested by Rosemary Shrestha (July 2010)

• Root terms

-Adding/modifying the root terms submitted by Rich Zobel (Nov 2009).

We (sort of) dealt with the upper level root terms that Rich requested: basal root, primary root (taproot), shoot-borne root, but we still need to deal with the rest. Includes 3 new terms: internode root, non-pericyclic lateral root, non-pericyclic basal root.

He also suggested modifications to the definitions of the following additional 14 terms: List of root terms

-adventitious root- this was flagged for consideration during the revision of shoot-borne root (PO:0000042)

• Adding Legume terms submitted by Austin Mast*

Taproot, Stem Hair, Prickles, Fascicle, Bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure), Phyllode, Banner (as in a legume flower), Wing (as in a legume flower), Keel (as in a legume flower), Anther pore and anther slit, Locule

• embryo

We have a proposed definition of embryo from 7/2010. We need to finalize this and close the tracker.

• New terms requested by reviewers (from Ahrestani, Kramer and Rudall)

-Elena Kramer suggested that we add the term spur to the PSO and consider dealing with common primordia in the PGDSO.

-Paula Rudall commented that the current definition of central cell has a different meaning in gymnosperms.

-TraitNet requested several new terms for the PSO: corm, spine, podarium, pneumatophore, stele, diaspore, cone, sorus, and tendril.

• Primordium

Need a class primordium, and need to make one definition for it. Also need to organize primordium terms

We may also want to link primordia to stages in the PGDSO, where appropriate.

For example, ovule primordium (PO:0000018) participates in ovule primordium visible (PO:0007620) or ovule primordium visible (PO:0007620) has_participant ovule primordium (PO:0000018).

• reorganization of shoot system

We started working on this during the last round of revisions (with bud, and terms like reproductive shoot system), but it still needs some tweaking. Need to discuss vegetative shoot system.

• primordium, meristem, bud, shoot system

Doesn't have a tracker item. Should consider aligning the children of these terms.

• axil: We need to discuss whether or not to have a generic term 'axil' and, if so, how it should be defined. See also older tracker item leaf base vs. axil?.

• cortex: We need a brief discussion of how to define cortex (see tracker item). Once we decide this, we can define other tissue types similarly.

Open SF tracker items Plant Growth and Development Stage Ontology

gametophytic phase and sporophytic phase

These were moved to be children of whole plant growth stage (PO:0007033) and the term "plant life cycle phase (PO:0028001) was obsoleted for now till we have further discussion on it.

Also, the top class in the ontology is 'plant growth and developmental stage(s)' def'n = The succession of changes leading from the zygote to the mature plant- that is only the sporophytic phase.

We should rethink the entire upper level structure of the PGDSO, and how we can incorporate all plants

tuber growth and development stages

open on SF since 6/2009

Plans for a publication to detail the updates in the PO

-This is a priority for the fall to detail the changes in the PSO

-We have been keeping track of the changes on the 'Summary of Changes' page

-Target journal: Current Opinions in Plant Biology or Plant Physiology

POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th

Date: Thursday Nov 4th (LC and RW), all day on Friday, November 5th and Sat Morning, Nov 6th

• Wiki page for the meeting has been created. We will be adding items to this over the next few weeks

• Should we invite outside experts, scientists, students and postdocs? Time to do so is getting short.

-Farshid Ahrestani from TraitNet has been invited, can also invite Dan Bunker (both from NJIT in Newark, so could attend for only a few hours without too much travel)

-Bruce Kirchoff? He would have to travel from South Carolina. It might be better to just organize a conference call.

-Folks from the NYBG- review the PGDSO and comment on terms from non-angiosperms. Suggestions?

Other Items

• Fall exhibition at NYBG- DWS: ask PJ about the details of this?

From the grant:

(2) Dr. Stevenson, a co-PI from NY Botanical Garden (NYBG), will involve PO project in the ongoing outreach activities of the NYBG in developing Plant Biology tools for 6-12 teachers in NY City public schools as well as the general public and education programs at NYBG for K-12. NYBG being a Museum gives us an opportunity to reach out to parents and students alike and in ways that a university setting like Cornell may not provide. He will organize three annual exhibitions (one per year) at NYBG.

Deliverables: Years 2-4: Student workshop at NYBG.

*Update from Alejandra about images for the PO

Ramona will go to Ithaca on Oct. 20th to work with Alejandra on loading images onto Plantsystematics.org and linking them with the PO. We will work on technical aspects of this during the conference call that day.

*Question from Daniel Lang <daniel.lang@biologie.uni-freiburg.de> (to Pankaj Sept 2009)

"I am looking for estimates of the number of cell types and the number of different tissue types in the gametophytic and sporophytic generations of the following angiosperms:

Arabidopsis lyrata, Arabidopsis thaliana, Carica papaya, Glycine max, Medicago truncatula, Populus trichocarpa, Ricinus communis, Vitis vinifera, Oryza sativa, Sorghum bicolor and Zea mays (current estimate: total 100 cell types)

I've already tried to extract part of this data using the plant_structure associations from the database dump, but I am unsure whether the annotations are comprehensive enough to give a reliable answer?

PO term associations including transitive indirect annotations: Arabidopsis thaliana gametophyte 10 Arabidopsis thaliana sporophyte 229 Oryza sativa gametophyte 4 Oryza sativa sporophyte 145 Zea mays gametophyte 2 Zea mays sporophyte 42

I would be excited to hear your estimates/data on this! Do you know of any web resources, literature or databases that would help us answer these questions?

To conserve the data for future use, I will post the numbers to BioNumbers (http://bionumbers.hms.harvard.edu)."

Has anyone responded to him??

Dennis and Ramona should report back at this meeting.

• Setting up conference call with Bruce Kirchoff to discuss the Plant Ontology and the issues he raised at the Botany Meeting

His comments: "I hope you understand that my comments were not directed at you, or the work that you are doing with the plant ontology. I do understand the need for the ontology, at least from a database perspective, and I think that the improvements that you and the plant ontology group have made to the initial ontology are important, and substantial. However, I feel that there are still serious problems with any attempt to bring all aspects of plant morphology together under a unifying ontology. Perhaps the word "ontology" was coined for these controlled vocabularies with tongue-in-cheek, but the attempts to extend the ontology beyond their use in databases tends to remove the jest, at least in my opinion. I very much believe in open discussion as a way of advancing science. It was for this reason that I convinced the Botanical Society to institute the discussion sections that now are a standard part of the annual program. I would be interested in continuing the discussion of plant trait ontology at the next botanical society meetings, in a discussion session. Perhaps you and your colleagues would be interested in organizing one of these sessions with me."

This was scheduled to be done after Sept 20th, so we should probably decide when we want to do it.

Laurel can set up a Doodle poll?? Who wants to take part? Maybe invite to meeting at NYBG?

• Mailing lists

We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal. I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?

In mid-August the new list po-discuss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers.

We all agreed that these need to be reviewed and we need to deal with the spam problem as well. May be able to use images instead of textual links to email addresses.

We will need to update the links to this lists on the PO web site (http://plantontology.org/mailarchs/mail_list.html)

• New curator hired at NYBG: Angelica Cibrian has been hired and will be a split appointment between Genomics of Seed Plants project (3/4 time) and the PO (1/4). She will spend part of her time NYBG and rest at NYU. She has been working on using GO terms and annotations to analyze the Seed Plant data, and so can act as an interface between the Seed Plant project and the PO, perhaps provide annotations to the PO.

She started on Friday. Will she take place in POC conference calls? Should we add her to PO mailing lists (dev, internal, discuss)?