POC Conf. Call 10-6-10

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

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Alejandra Gandolfo, (Cornell University), Justin Elser (OSU), Justin Preece (OSU).

Absent: Barry Smith (University at Buffalo, NY), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators:None

Acceptance of the minutes from the 9-29-10 meeting? There were no additions, deletions or changes to the minutes of the last meeting.

Status and Update of Progress: PO Release

-I have put the full version up at dev.plantontology.org. Please check for any final adjustments to be made. I will work on the release notes script, and if I hear no changes needed in the next few hours, I will move it over to live. (Justin Elser)

-We have received the rest of the annotation files from SGN

We reviewed the new version on the po-dev browser. There are a number of new annotations. PJ noted that it would better if the SGN annotations were broken down on the release notes page by species and also should include the common names. Release should be named by month and year.

Need to list scientific and common names for all species on release notes page, check capitalization, fix typo

• Source: Gramene Seedling vigor QTLs (SDLGVIG) that were on PO:0009003: sporophyte should also be on sporophytic growth phase (PO:0028002) in the PGDSO.

Seedling vigor QTLs are already associated with PO:0007131 seedling growth and whole plant (PO:0000003) in the PSO as well.

101 annotations from'po_anatomy_qtl_oryza_gramene.assoc' copied to po_growth_qtl_oryza_gramene.assoc and assigned to sporophytic growth phase (PO:0028002)

-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 live version is available, as well as being sent out the the user groups.

Changes to PO web page

See the detailed discussion of this on [9-29-10 Conf Call]

-Acknowledgments page has been updated

-The documentation page will be posted on the POwiki page and the PO webpage with details of the changes made in the new release (see below:).

-need to work on changes to front page

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

Dennis tried to reserve the NYBG apartment for the nights of Nov. 4th and 5th..

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

From DWS: There is a Ramada on Tucahoe Rd, next to the Royal Regency Hotel. He said the Ramada is not as nice as the Hamptons Inn, but it is acceptable (other visitors have stayed there) and more convenient.

• 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 too just organize a conference call.

-Folks from the NYBG?- review the PGDSO

Priorities for the Next Round of Revisions

We need to define some goals for the next round of revisions.

PJ: Plant Growth and development Stage Ontology restructuring should be a focus -- to add terms from non-angiosperms

What is the target date for the next release?

Have ontology structure ready by early/mid December so release can go out before PAG in mid January

"Housekeeping Items"

• Merging the plant structure and plant developmental stages ontologies

It's okay to do this as soon as the release is out.

• 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

• 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

• Convert to intersection_of relations?

Advantages: easier editing, especially for terms with many relations; faster reasoning

Disadvantages: will need to maintain script to assert implied relations so they show up on the browser, or have editors assert links and save them each time changes are made. Can try it out, but maybe not the highest priority for next release. Also, we want to avoid having multiple versions of the obo file.

• Convert existing definitions to genus-differentia form?

Can continue converting definitions whenever terms are worked on.

• 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.

• add links to more images through PlantSystematics.org-

Ramona will visit with Ale in October 20th and will work on this. Tepal is only term linked right now (no longer working?). Should 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 can go over the technical aspects in more detail during the Oct. 20th conference call.

• 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-

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

-Others?? PO Web page- see above

We have a number of open items on the sourceforge trackers that need to be dealt with. We need to develop a priority ranking to focus our efforts.

Open SF tracker items Plant Structure Ontology

Adding Musa terms requested by Rosemary Shrestha (July 2010)

1. Musa leaf terms: Petiole wing, Petiole margin, Cigar leaf, Petiole canal, Petiole margin edge, Cigar leaf dorsal surface

2. Musa flower terms: Bunch, Basal flower, Free tepal, Compound tepal, Crown, Free tepal apex, Hermaphrodite flower, Compound tepal lobe, Peduncle surface, Male bud, Female flower, Peduncle hairs, Bract apex, Bract external face, Bract internal face, Bract base

3. Musa fruit terms: Hand of fruits, Flower relics

4. Musa shoot terms: Sucker, Pseudostem, Pseudostem underlayers

Laurel sent a message to Rosemary to see if there were any changes, and there were not any. The spreadsheet listing all the CO numbers and definitions of the terms has been posted on the original SF tracker, above.

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.

In his Root mini-ontology, he proposed the following three 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)

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.

Adding Legume terms submitted by Austin Mast

Taproot Stem Hair (Esau's Anatomy of Seed Plants gives "hair" as a sub-category of "trichome") 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 (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

Right now, we don't have a general term for primordium. Do we want one?

Also, different types of primordia are defined consistently. Currently, there are two different types of definitions:

1. anther primordium (PO:0006089): An organized group of cells that will differentiate into anther.

2. carpel primordium (PO:0004703): The very first appearance of a carpel. It initiates from the carpel anlagen region of the floral meristem.

There are multiple examples of each type.

As it is, each type of primordium is a child of what it is the primordium of. For example, carpel primortium is_a carpel, anther primordium is_a anther. These relationships make sense with definition type 2, but not with defintion type 1.

We may also want to link these 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.

Open SF tracker items: Plant Growth and Developmental 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.

This needs work

tuber growth and development stages

open on SF since 6/2009

Other Items

• 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 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?

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

• 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)

• 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)?

• 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.

Upcoming meetings 2010-2011:

• Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010. To qualify for reduced registration rates, must register by October 15th.

Lol and Ramona are planning on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Alejandra cannot attend. PJ is not attending as he is teaching.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology.