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?

Status and Update of Progress: PO Release

-Release TBA soon

-Waiting for the last of the annotation files from SGN

-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.

-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:).

An announcement will be sent directly to the direct user groups.

• TAIR email: curator@arabidopsis.org
• NASC ??? email: bioinfo@arabidopsis.info (not really clear who to send it to here)
• Gramene email: gramene@gramene.org
• MaizeGDB Carolyn Lawrence
• VirtualPlant
• SoyBase Rex Nelson
• Genevestigator
• SGN Lukas Mueller+Naama Menda ?
• OryzaBase Yukiko Yamazaki?
• PlantTribes
• TraitNet
• Generation Challenge Program, CIMMYT, Mexico Rosemary Shrestha
• BRENDA
• UniProt

We will send the email to the 'contact' email address at each of these groups, or the contact people at these groups, if we do not have a generic email.

Priorities for the Next Round of Revisions

What is the target date for the next release?

Open SF tracker items Plant Structure Ontology

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 terms:

shoot-borne root (PO:0000042)- dealt with above

crown root (PO:0000043)- proposed def: "A nodal root formed at the crown of the plant (as in corn where the crown is below the soil surface)." [TAIR:ki] comment: Definition changed to eliminate adventitious. This is still within the sense of the TAIR definition. is_a: PO:0003005 ! nodal root

prop root (PO:0000044)- proposed def: "A root formed at stem nodes above the ground and growing directly into the soil." [TAIR:ki] comment: This term is perhaps best defined functionally to prop the plant up. synonym: "brace root" EXACT is_a: PO:0003005 ! nodal root

embryonic root (PO:0000045)- proposed def: "Root that is initiated in the developing embryo." [TAIR:ki] synonym: "radicle" EXACT relationship: part_of PO:0009009

seminal root (PO:0000046)- proposed def: "A basal root formed within the hypocotyl of the embryo." [ISS:Weinhold1967 "Weinhold L. 1967. Histogenetic studies of rht boundary root problem [Histogenetische Studien zum Grenzwurzelproblem]. Beitr. Biol. Pflanzen 43:367-454.", TAIR:ki] comment: Definition changed to represent the relationship to basal root. synonym: "scutellar nodal root" RELATED synonym: "secondary root" BROAD is_a: ID:0000001 ! basal root

nodal root (PO:0003005)- alt_id: PO:0003008 alt_id: PO:0003009 def: "A shoot-borne root that forms at a shoot node rather than an internode." [1] comment: Cleaned up the definition to fit ISRR terminology. is_a: PO:0000042 ! shoot-borne root

scutellar node (PO:0004708) proposed def: "The region in the embryo between the primary root (enclosed in the coleorhiza) and the plumule (enclosed in the coleoptile) to which the scutellum is attached." [MaizeGDB:lv, TAS:Esau1965 "Esau, K. 1965. Plant Anatomy. New York. Wiley. pp. 767", TAS:Fahn1990 "Fahn A. 1990. Plant Anatomy 4th Ed. Elsevier."] comment: Scutellar node is specifically for corn. In general it refers to the mesocotyl which is for monocots in general, and the hypocotyl is a term appropriate for all plants. synonym: "hypocotyl" EXACT synonym: "mesocotyl" EXACT relationship: part_of PO:0009009

hypocotyl-root junction (PO:0004724) proposed def: "Junction point of the embryonic root and hypocotyl." [TAIR:ki, TAS:Esau1965 "Esau, K. 1965. Plant Anatomy. New York. Wiley. pp. 767", TAS:Fahn1990 "Fahn A. 1990. Plant Anatomy 4th Ed. Elsevier."] synonym: "Scutellar plate" EXACT [] relationship: part_of PO:0019018

root (PO:0009005) alt_id: PO:0003006 proposed def: "A plant organ which is usually underground and more or less positively geotropic, only rarely bears shoots. Primary functions are support and absorption of water and minerals. There are four primary types of root taproot, basal root shoot-borne root and lateral root." [TAS:Fahn1990 "Fahn A. 1990. Plant Anatomy 4th Ed. Elsevier.", TAS:Zobel2009 "Zobel RW. 2009 Report of the Root Nomenclature Workgroup ISRR V (1996) a Reprise. Proceedings of the Seventh Symposium of the International Society for Root Research, September 4, 2009, Vienna. \"http://rootrap.boku.ac.at/index.php?id=28\"; then click on \"Report of the Root Nomenclature Workgroup ISRR V (1996) a Reprise\""] comment: Commonly thought of as one of the three basic parts of the seed plant body. is_a: PO:0009008 relationship: part_of PO:0009003

radicle (PO:0020031) proposed def: "The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive." [APWeb:Glossary] is_a: PO:0000045 ! embryonic root relationship: part_of PO:0019018

mesocotyl (PO:0020037) proposed def: "In monocots, the region between the base of the cotyledon, and the radicle or taproot." [TAS:Fahn1990 "Fahn A. 1990. Plant Anatomy 4th Ed. Elsevier."] synonym: "hypocotyl" EXACT [] relationship: part_of PO:0009009

hypocotyl (PO:0020100) proposed def: "The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte." [APWeb:Glossary] is_a: PO:0009008 relationship: part_of PO:0019018

lateral root (PO:0020121) proposed def: "A root developing from a parent root." [TAS:Esau1965 "Esau, K. 1965. Plant Anatomy. New York. Wiley. pp. 767", TAS:Zobel2009 "Zobel RW. 2009 Report of the Root Nomenclature Workgroup ISRR V (1996) a Reprise. Proceedings of the Seventh Symposium of the International Society for Root Research, September 4, 2009, Vienna. \"http://rootrap.boku.ac.at/index.php?id=28\"; then click on \"Report of the Root Nomenclature Workgroup ISRR V (1996) a Reprise\""] comment: Those roots that branch off axile roots are first order laterals. The branches off of first order laterals are second order. etc. is_a: PO:0009005 ! root

primary root (PO:0020127) alt_id: PO:0020089 def: "The root which develops directly from the embryonic radicle." [ISBN:0122151704] comment: A discontinued term.(RWZ) synonym: "taproot" EXACT [] is_a: ID:0000000 ! taproot

-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.

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.

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 tweeking. Need to discuss vegetative shoot system.

Open SF tracker items: Plant Growth and Developmental Stage Ontology

gametophytic phase and sporophytic phase

This upper level term has no definition.

proposed def'n: The life cycle of all plants is characterized by the alternation of generations (or phases). A multicellular 2n (sporophytic) phase alternates with a multicellular 1n (gametophytic) phase.

alternative proposed definition: A phase in the life cycle of a plant that begins with either meiosis or fertilization. Comment: the sporophytic phase has twice the chromosome complement of the gametophytic phase.

Also, its parent 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 will either have to rework this definition or follow Ramona's suggestion to move these to children of whole plant growth stages, and the current children of whole plant growth stage could be children of sporophytic phase.(or both).

tuber growth and development stages

open on SF since 6/2009

"Housekeeping Items"

• Merging the plant structure and plant developmental stages ontologies

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

• better organization of descendants of portion of plant tissue

• Convert to intersection_of relations?

• Convert existing definitions to genus-differentia form?

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

• add links to more images through PlantSystematics.org

• 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 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.

• 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?

*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.