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

• The new release is on the live, public PO web page! Thanks to everyone for all their hard work, it has definitely been a team effort.

• The PO front page, release notes, acknowledgments pages have all been revised.

• The PO is on FaceBook!

Issues:

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

What about participates_in?

• The new species annotated by SGN are not reflected in the drop down box on the advanced search page.

Missing: Anisodus acutangulus, Atropa baetica, Coffea arabica (coffee), Nicotiana tabacum (tobacco), Physalis spp., Solanum insanum (eggplant)

We do not have Lycopersicum esculentum tomato, (but we do have Solanum lycopersicum)

Priorities for next release

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

Target date for next release:

Any comments or changes?

From PJ: Top priority for the short term should be addressing the term lack are lacking is_a parents. This will require work on upper level structure for non-material entities. The longer term (mid February goal for the next release will involve restructuring of the PGDSO.

The next revision with the completed is_a parents should be ready by early/mid December so release can go out before PAG in mid January. Then the longer term goal will be revision of the PGDSO upper levels to accommodate non-flowering plants

Prioritizing work that needs to be done:

We do not need to discuss the details of any of these items this week, but should rank them as high or low priority.

Housekeeping Items

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

BS- need documentation and use cases of plant ontology to justify our existence

PDO- BS has interested collaborators

PJ- strawberry genome GO annotations to 70% of gene models, used dataset to project metabolic pathways. being published Gramene renewal: annotate next gen datasets to PO, link to expression

DWS: Gymnosperm grant renewal, transcriptome phylogenetics, match PO to GO for gene discovery, wrt phenotype Annotate expression libraries GEO with PO terms

• (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. proposed file name: plant_ontology.obo? There is already an old merged one on the SVN.

Done- plant_ontology.obo

• ('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. See more comments below under PSO

• (?) 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.

BS- Add BFO terms to PSO and PGDSO, filling in the missing parents will help with this process. The top level parent term "all" is problematic and should have a definition that states :'this is an artefact created by the AmiGO browser. Inclusion is required"

Not sure how we do this since it does not show up in OE. It is present in GO, but does not have a definition there.

• (?) Laurel 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. Lists of candidate papers are being prepared.

Friday 1:30pm PDT on Skype. We will discuss the Ilic 2007 paper in Plant Physiology.

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

Tepal is only term linked right now (no longer working?). Plantsystematic terms 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 will go over the technical aspects in more detail during the Oct. 20th conference call, when Ramona is at Cornell with Ale.

JE said after the call that he found out what the problem was and did a manual fix, but the better solution would be to have it one the GO DbX refs. Ask Chris M about?

• (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. See list of terms without is_a parents

• (?) 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.

• (?) Other issue (see more details for each item are available on New SF tracker items, fall 2010)

-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

-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: 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.

-egg cell and sperm cell: we need to finalize the definitions for these terms, and make sure they work for all plants.

-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.

-better organization of descendants of plant cell: Needs to be organized better, maybe add some new categories for cell types.

-placenta: this new term was added during the last round of revisions, but we have never discussed it. Need to make sure definition is good.

-strobilus: this new term was added during the last round of revisions, but we have never discussed it. Need to make sure definition is good. Also, need to fix spelling in live version (stobilus).

Changes to PGDSO

• (HP) 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.

• (HP) reorganize the entire upper level structure of the PGDSO, so we can incorporate all plants

• (?) begin to add specific growth and development stages for non-flowering plants (in consultation with experts from those taxa)

• (?) tuber growth and development stages: open on SF since 6/2009

• (?) post harvest stages: this is an old request, but no one ever commented on it.

• (?) terms for seed development stages:this is a fairly new request for terms for cotton

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.

*Modification of the Conference Call Schedule: Barry has a conflict with scheduling of the calls as the NCBO has (after a lot of argument) decided to hold its calls at this time on the 2nd and 4th Wednesday of every month. Do you think we can avoid these days in future scheduling of PO calls?

Laurel is out of town on Oct 27th as well, can we move that week's meeting to Tuesday Oct 26th?.

The following week, Nov 3rd LC will be traveling to the NYBG meeting- Conf call Friday Nov 5 for those that cannot make it in person? Weds Nov 10th- Barry cannot attend

Weds Nov 17th-ok

Weds Nov 24th- No meeting, pre-Thanksgiving break

Weds Dec 1st-ok

Weds Dec 8th-Barry cannot attend

Weds Dec 15th-ok

Weds Dec 22nd- Barry cannot attend

*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)?

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.