POC Conf. Call 10-6-10

POC meeting, Webex Conference Call; Date: Oct 6th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 9-29-10 meeting?

Priorities for the Next Round of Revisions

What is the target date for the next release?

-Merging the plant structure and plant developmental stages ontologies

-Adding Musa terms requested by Rosemary Shrestha

-root terms submitted by Rich Zobel,

-adventitious root

From 9-15-10 PJ: We also should discuss root terms with Phil Benfey (Duke) and Leon Kochian (Cornell). They are developing software for root type recognition. Should work to integrate PO with their software. Don't know if Rich is involved in discussions with them.

-Legume terms submitted by Austin Mast

-New terms requested by reviewers (from Ahrestani and Kramer)

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

-add terms for non-angiosperm structures

-better organization of descendants of portion of plant tissue

-convert to intersection_of relations?

-Convert existing definitions to genus-differentia form?

-work on PGDSO

-tuber growth and development stages, open on SF since 6/2009

-add links to more images through PlantSystematics.org

PJ: Lol and Ramona will focus more on adding annotations

-Complete compliance with OBO foundry principles

-Others??

Other Items

• POC meeting to be held at NYBG in fall 2010.

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

Unfortunately, the NYBG apartment is not available for these nights, but there is a hotel in Yonkers near where DWS lives Hamptons Inn

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

• We have been contacted by Stefan Rensing, University of Freiburg, Germany re: setting up an ontology for bryophytes with a focus on the model moss Physcomitrella patens.

Ramona and Dennis responded to him with an explanation of why we chose the current structure. He responded:

'We will aim to setup bryophyte terms with regard to the new structure and (if possible) suggest terms that are broad enough to cover all land plants in the process.'

'FYI, the current, but now obsolete, PO-MO term mapping is at Moss_Ontology'

This site has a list of moss tissue and cell types, as well as life cycle/developmental stages that we could use a a guide for adding new terms.

Issues arising from this:

This groups is setting up their own ontology for their immediate needs, but as the PO includes more moss terms, it will probably become redundant. Should we work with this group to meet their needs quickly, so they don't have to develop their own ontology? They may be able to develop a moss PO slim.

We will keep in contact with this group. DWS: we also have a moss expert at the NYBG who can consult on this (Bill Buck)

*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 will discuss this during the week and report back at the next 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?

Will schedule this after the release. Maybe invite to meeting at NYBG

PJ suggested preparing a slide (for presentations like IBC or BSA) that shows how PO can be used with data matrices, to appeal to systematists who are not necessarily using genomics. DSW suggested we work with people like David Spooner (USDA Wisconsin) or Sandy Knapp (British Museum) from the Solanacea network, or Paula Rudall (Harvard, already a reviewer) who are already moving between systematics and genomics.

• Status of BSA announcement for bulletin

Notice came out in this quarter's issue of the Plant Science Bulletin. Can be viewed online at: BSA Bulletin on p. 102 (great location - on the first page).

We can also post an online announcement with the BSA when the final release is ready.

• 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)

Tabled for next meeting

• 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 will start on Friday

• 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.

Tabled for next meeting

• Plans for a publication to detail the updates in the PO

-This was discussed a bit in May/June, but we have not made any detailed steps towards getting it done yet

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

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

-What are peoples feelings about doing this right now? Is it justified at this point?

Tabled for next meeting

*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. -