POC Conf. Call 6-1-10

POC meeting, Webex Conference Call; Date: June 1st, 2010 10am (PDT)

Minutes in italics below agenda items

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG),

Absent: Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: None in attendence

Acceptance of the minutes from the last meeting? All in favor?

Both of us (Laurel and Ramona)accepted the minutes as posted.

Agenda:

1. POC workshop to be held in Corvallis on June 29th/30th.

I have set up a page on the POWiki [Corvallis Workshop June 29th and 30th, 2010]

We need to think about what the goals of the meeting will be and who will be invited, etc.

Laurel will assist with local arrangements.

2. Term Requests from Naama Menda, Solanaceae Genomics Network

a. tuber flesh

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

Comments from last week's meeting:

BS: Terms like 'flesh' are 'mass' nouns and should be avoided, better to use 'count' nouns.

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. There was discussion about how the users would be able to know where the annotations would go.

We looked at a diagram of the potato tuber anatomy online and saw that the 'flesh' is actually several different layers.

Created new terms to deal with tuber flesh (see dev browser):

• Portion of storage parenchyma tissue (child of portion of parenchyma tissue): A portion of parenchyma tissue specialized for carbohydrate storage. (Still need to work on definition with possible XPs to GO or ChEBI terms). Comment: This tissue could be found in any organ, but often occurs in fruits or tubers.

• Portion of fruit storage parenchyma tissue: A portion of storage parenchyma tissue that is part of a fruit. Syn: fruit flesh

• Portion of tuber storage parenchyma tissue: A portion of storage parenchyma tissue that is part of a tuber. Syn: flesh, flesh tissue (maybe these should be synonyms of storage parenchyma rather than tuber storage parenchyma)

• Portion of aerial tuber storage parenchyma tissue: A portion of tuber storage parenchyma tissue that is part of an aerial tuber.

• Portion of subterranean tuber storage parenchyma tissue: A portion of tuber storage parenchyma tissue that is part of a subterranean tuber. Syn: potato tuber flesh

Comments: This is the term that would be used to refer to potato tuber flesh. See more specific terms for different portions of subterranean tuber flesh (Still need to add these terms).

• Problem is that storage parenchyma can actually be several types of parenchyma tissue, like cortex or pith, which creates problems of multiple inheritance if we have a catch-all term like storage parenchyma .

Also updated term names and definitions of relevant parent terms:

• ground tissue became portion of ground tissue. Had no definition.

Proposed def: Any portion of plant tissue other than the dermal or vascular tissue. Develops from the ground meristem (meristem L2 and meristem L3).

This is a case of 'defining by what it's not,' but it is the most common definition out there. We can work on a better definition later.

• parenchyma became portion of parenchyma tissue

Proposed def:A portion of ground tissue composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate living protoplasts. Comment: Parenchyma contains relatively unspecialized cells. Synonyms (exact): parenchyma, parenchyma tissue, ground tissue

This is a relatively minor change from the original definition, adjusted to fit the genus/differentia form. Original def: Relatively unspecialized tissue composed of polyhedral cells typically with thin, non-lignified cellulose cell walls and nucleate living protoplasts.

Questions:

• Do we need to call parenchyma 'portion of parenchyma tissue,' or can the term parenchyma be used as a count noun? It would simplify the term names. If we change this, we will have to change all the other tissue types like collenchyma, sclerenchyma, epidermis, etc.

• What is the rule/policy on having the same synonym for multiple terms? If someone is searching for flesh, they may mean either tuber flesh, fruit flesh, or flesh in some other tissue, so it might make sense to have flesh be a synonym of portion of storage parenchyma tissue, portion of fruit storage parenchyma tissue, portion of tuber storage parenchyma tissue, portion of aerial tuber storage parenchyma tissue, and portion of subterranean tuber storage parenchyma tissue.

We decided that the word 'tissue' on the end of each term was unnecessary, but the group still has to decide if we should use 'portion of.'

Decided to classify parts of the tuber flesh (like medulla and perimedulla) under there respective part (pith or cortex) and make them a part_of subterranean tuber storage parenchyma.

Discussed tuber eye and tuber epidermis, but decided to wait until more of the group was present before making any decisions on them.

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).

Comments from last week's meeting:

DWS: the eye of a tuber is an axillary bud or meristem

Created new terms to deal with tuber eye (see dev browser):

• tuber axillary vegetative bud: An axillary vegetative bud that is part of
a tuber. 


• aerial tuber axillary vegetative bud: A tuber axillary vegetative bud that
is part of an aerial tuber.

• subterranean tuber axillary vegetative bud: A tuber axillary vegetative bud that is
part of a subterranean tuber. Syn: eye, potato eye, tuber eye. 
Comments: In potatoes, axillary vegetative buds (eyes) can determine
 processing quality.

Problems with parent terms:

• Axillary vegetative bud is both an axillary bud and a vegetative bud. Also, bud has no is_a parent (is part_of shoot).

• Axil Axillary bud is currently defined as: Bud formed in the axil of a leaf or shoot. [source: POC:curators]. There are no scholarly references to shoot axil. PO has the term leaf axil. Should change def. of axillary but to remove reference to shoot.

c. tuber epidermis

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

From last weeks meeting: the skin of a potato is actually a periderm, but there are tubers (including young dicot tubers and monocots) that have an epidermis, so we will need both tuber epidermis and tuber periderm.

Created new terms to deal with tuber epidermis (see dev browser):

• Tuber periderm: A periderm that is part of a tuber.

• Aerial tuber periderm: A tuber periderm that is part of an aerial tuber.

• Subterranean tuber periderm: A tuber periderm that is part of a subterranean tuber. Syn.: potato skin

• Tuber epidermis: A shoot epidermis that is part of a tuber.

• Aerial tuber epidermis: A tuber epidermis that is part of an aerial tuber.

• Subterranean tuber epidermis: A tuber epidermis that is part of a subterranean tuber.

Also updated term names and definitions of relevant parent terms:

• change dermal tissue (PO:0009014) to portion of dermal tissue

Original definition: Tissue derived from the protoderm that covers the surface of the plant body. [source: GR:pj, ISBN:0122151704]

Proposed def: A portion of plant tissue that covers the surface of the plant.

• epidermis

Original def: An outermost cell layer of primary tissues of the plant, sometimes comprised of more than one layer. [source: GR:pj, ISBN:0080374913]

Proposed def: A portion of dermal tissue composed of epidermal cells that develops from the protoderm and covers the plant in the primary state.

Comment: The epidermis can be composed of one or more layers of cells.

• periderm

Original def: Secondary protective tissue that replaces the epidermis in stems and root, rarely in other organs. [source: GR:pj, ISBN:047124529]

Proposed def: A portion of dermal tissue that is secondarily derived and composed of phellogen, phellem, and phelloderm.

Comment: Replaces the epidermis in stems and roots, rarely in other organs.

d. New term for root tuber.

This is an old request. We already have the terms aerial tuber (PO:0004548) and subterranean tuber (PO:0004547), which may have been added in response to this request. Suggest that we close this item while we are working on tubers.

e. Added new subset for potatoes

3. Report on meeting with TraitNet

Ramona met with Dan Bunker (New Jersey Institute of Technology) and Farshid Ahrestani (Columbia University and NJIT) to discuss possible collaborations with PO.

TraitNet is an NSF research coordination network.

Minutes of the POC-Traitnet meeting 05-28-2010, NYBG are on the PO wiki.

Any who wants to learn more about this meeting can look at the minutes or contact Ramona directly.

4. Complete one branch of ontology for demonstration purposes?

This would provide material for presentations at meetings this summer.

Would allow outside users to evaluate the ontology before we completely rework it. They could provide us with feedback on the ontology structure.

Discussed what would be a good example. The tuber terms above could be good useful, but we really need an example that spans the divide from bryophytes to angiosperms.

Upcoming Conferences and Meetings: Updates:

* Infectious Disease Ontology Workshop

To be held in Dallas, Dec. 8th and 9th, 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.

It would be good to have someone there to represent the interests of the PO with regard to plant infectious diseases. This may be especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research. Either one of the POC coordinators could attend, or we could suggest a colleague who is an expert on plant infectious diseases.

Any suggestions?

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

* 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. Dennis, Alejandra attending, Ramona presenting, 15 minute oral presentation, Abstract submitted 3/26/10.

• Annotation workshops to be held at NYBG in fall 2010. Date TBD.

Will invite outside experts, scientists, students and postdocs.

Please fill out Doodle Poll re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg

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