POC Conf. Call 5-25-10

POC meeting, Webex Conference Call; Date: May 25th, 2010 10am (PDT)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY)

Collaborators: Rex Nelson-SOYBase, USDA-ARS, Ames, Iowa, Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico

Absent: Chris Mungall (Lawrence Berkeley National Lab)

Acceptance of the minutes from the 5-11-10 meeting? All in favor? There were no additions, deletions or changes to last weeks minutes.

Minutes are in italics below each agenda item

Agenda:

1. NEW ITEMS: Term Requests from Naama Menda, Solanaceae Genomics Network

a. tuber flesh

Proposed def'n: The flesh layer of the tuber (SGN:NM).

b. tuber eye

Proposed def'n: The structure on the tuber surface that can sprout. It also has a significance in determining the processing quality.(SGN:NM).

c. tuber epidermis

Proposed def'n: Epidermal layer of a tuber.(SGN:NM)

BS: Terms like 'flesh' are 'mass' nouns and should be avoided, better to use 'count' nouns. Also commented on the need to make the ontology correct, rather than making fit the canonical uses of terms.

DWS: the proper botanical term is storage parenchymal tissue, starch filled, could use 'flesh' as a synonym

PJ, RN: the ontology must be understandable to the users like plant breeders

We looked at a diagram of the potato tuber anatomy online and saw that the 'flesh' is actually several different layers. There was discussion about how the users would be able to know where the annotations would go. There is a similar issue for the epidermis, which in mature potatoes is actually periderm.

Tuber flesh: We decided that we should make a term for storage parenchyma tissue, with children tuber storage parenchyma, and grandchildren aerial tuber storage parenchyma tissue and subterranean tuber storage parenchyma tissue. (Using the prefix portion of in each case). Tuber flesh can be a synonym of tuber storage parenchyma tissue. There will also be specific terms for each part of the tuber flesh (medulla, perimedulla, cortex), which will have part_of relationships to subterranean tuber storage parenchyma tissue.

Tuber eye: This is really a vegetative axillary meristem. Can make term tuber vegetative axillary meristem, with children for aerial and subterranean tubers.

Tuber epidermis: In potatoes, the skin is actually two layers, an epidermis underlain by a periderm (bark) (need to check references on this). We can make terms tuber periderm and tuber epidermis, with children for aerial and subterranean tubers. Epidermis should be used for species (like monocots) that have no secondary growth, and also for young tubers, before the periderm has developed. These terms should probably be children of shoot periderm and shoot epidermis.

We will need to make a new subset for terms that are used by people who study potatoes.

2. Report from the Cell Type Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME.

Laurel and Ramona attended and Laurel gave a short presentation "Introduction to the Plant Ontology™".

Cell Type Ontology Workshop Wiki page

Action Items from CL Workshop

Major decisions and action items from Cell Ontology meeting:

CL Goals and Action Items:

• Restructure top level terms of CL to eliminate multiple inheritance:

Cell

>eukaryotic cell

>>plant cell (sub-structure and terms to be curated by PO)

>>animal cell (sub-structure and terms curated by CL, lowest level terms may be curated by species ontologies such as Zfin, Flybase, and FMA)

>>fungal cell, etc

>prokaryotic cell (included for continuity, not really being used)

• Provide free text definitions, pubmed IDs, and if possible, logical definitions for CL terms

• Design a quick term template or interface for certain types of fairly trivial requests

• Better documentation for CL structure, development

• Improve response time on CL Sourceforge tracker items

• Consider funding sources for the short-term funding gap (6 months between the end of ARRA funding and the start of the next GO cycle) and longer term funding goals

• Move hemo_CL subontology into the main CL ontology

• Experimentally modified cell types will be moved into OBI (see below:)

Other Comments:

• CL will maintain an "uber-ontology" of upper level terms that apply across species as well as additional versions that include all or selected sets of species specific terms.

• Where a taxon--specific group exists, they will will be responsible for curating terms for that taxon. PO will provide IDs and definitions for all plant cell types.

• Different ontologies can use the same name for a term, which is specified as the user group name (or something like that) but should also supply a term name that is unique in the OBO foundry. For example, we could use the term 'epidermal cell' within the PO, but it would also have an OBO name 'plant epidermal cell'. The use of ID numbers make this practice somewhat redundant, but it may eliminate some confusion when working with multiple ontologies.

Action items for PO:

• We need to work on our plant cell structure and definitions so that when we meet with them again, we have a well thought out plan. Currently on the dev-browser, the cell terms are divided into sporophytic, gametophytic and whole plants. Do we want to keep this structure? Other options?

Laurel, Ramona and Pankaj will schedule a conference call for next week and work on a proposal to bring to the whole group at a future meeting. BS: Are there any cell types that are common between plants and animals?

• Coordinate with CL on getting the plant cell terms into the ontology

• Consider moving in vitro terms to OBI, or at least use cross-products with OBI terms

Take part in conference call with OBI curators: Helen Parkinson (European Bioinformatics Institute) and Bjorn Peters (La Jolla Institute of Allergy & Immunology) (OBI on BioPortal)- in progress...

• Provide logical definitions for upper-level PO terms based on cross-products with CARO or other ontologies.

• Provide logical definitions for lower-level PO terms based on cross-products with GO, etc. (we are planning to do this anyway)

PJ: We will need to coordinate with groups doing the fungal and microorganism ontologies

3. Meeting with TraitNet (Plant Trait Ontology) people.

Ramona has scheduled a tentative meeting with Dan Bunker (New Jersey Institute of Technology) and Farshid Ahrestani (Columbia University) to discuss possible collaborations with PO. Want to find out why they are working outside OBO to develope their own ontology rather than using PO. FYI, Dan is an old office mate of Ramona's.

Here is a blurb on Traitnet:

In November, TraitNet along with CNRS, France, organized a meeting to discuss developing a trait ontology. Nineteen scientists met in Montpellier, France, November 5-7, to discuss, design and develop a ?Functional Trait Ontology? for ecologists. As the majority of ecologists present studied plants, it was decided that the ontology would initially focus on plant traits. The ontology would be developed by merging plant trait concepts listed in two categories, plant entities and plant characteristics. Plant entities are the physical parts of the plant, and plant characteristics are either direct, or derived, measurements made by ecologists/biologists of plant entities.

A semantic web-based application tool developed by the group would be used to coordinate the clarification of the definitions, and define a hierarchal structure and relatedness between the plant trait concepts. It was decided to build the ontology using the OWL language rather than the OBO standard. Besides the ontology, it was decided that a semantic based registry of databases relevant to ecologists would be developed to showcase the usefulness of working with data in a semantic framework.

Ramona will meet with Dan and Farshid on Friday. Will put them in contact with Pankaj if they have further questions.

4. Possible collaboration with Rich Zoebel from the International Society of Root Research (ISRR).

Should we work more closely with their group to insure consistency with PO and get input from root experts?

Everyone agreed we should do so.

Rich requested new PO terms in 2009 (SF tracker 5 new and 14 modified terms).

• • We also have 11 other open term requests on SF that we should address.

Items carried over from last week's agenda: Tabled for future discussion.

1. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.

Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312

Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.

2. Embryo (See SF Tracker: embryo)

Discussion of embryo was postponed until next meeting.

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants

(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes -add a comment?

Relationships:

(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity (2) develops_from zygote (see comment above) Usually (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)

4. Upcoming Conferences and Meetings: Updates

* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.

Alejandra cannot travel that day -- can attend via conference call.

Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th. Ramona has sent a request to schedule her talk on the 27th or 28th. Barry will be in France this week and can't attend. DWS may be in England after all.

Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).

Laurel will be working on plans for the meeting in the next few weeks, will contact Chris and see if he can come up.

* Bio-Ontologies 2010: Semantic Applications in Life Sciences. July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona are registered.

Our one page write up has been selected for a 'flash update talk' along with the poster. Final revisions were submitted Friday May 14th.

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation and Annotation Workshop with Gramene.

Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. more details TBA

• Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island. Ramona presenting, Dennis attending, 15 minute oral presentation, Abstract submitted 3/26/10.

* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):

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

Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities.

Pankaj will be co-organizer with Ramona. Laurel and Ramona are interested in going and speaking if funds are available.

Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.

• Latin American Congress of Botany (http://www.botanica-alb.org/X_Congreso/index.php). La Serena, Chile, October 4-10; MAG: "I am not sure about due dates for this one due to the earthquake".

from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

• Workshop to be held at NYBG in fall 2010. Will invite outside experts, scientists, students and postdocs.

Ramona will set up a doodle poll so we can start looking at dates

8. Next meeting scheduled for Tuesday June 1st at 10am PDT.