POC Conf. Call 6-8-10

POC meeting, Webex Conference Call; Date: June 8th, 2010 10am (PDT)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Absent: Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG), Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY),

Collaborators: Rex Nelson-SOYBase, USDA-ARS, Ames, Iowa

Acceptance of the minutes from the 6-1-10 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. 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]

The main goals of the meeting will be ontology development and preparation for a release, along with focused training on annotating genes and mappings.

Laurel can assist with local arrangements.

2. Modification of the POC Conference Call schedule: Alejandra has been selected for a committee at her University that conflicts with our meeting schedule and has requested that we consider modifying the time. Otherwise, she will not be able to ever attend. Please visit the Doodle poll and mark when you are available- so far it looks like Weds or Thurs am are good options.

Doodle poll

Term Requests from Naama Menda, Solanaceae Genomics Network

Two Important Questions (also circulated on email before the meeting:

1. Do we need to prefix all these terms like parenchyma with the 'portion of' or can the terms like parenchyma be used as count nouns? Not doing so would simplify the term names considerably (see diagram below), but may not be ontologically correct.

If these terms are all children of 'portion of plant tissue" then aren't they all 'portions of' already?

If we decide to use the 'portion of ' prefix, we will also have to change all the other tissue types like collenchyma, sclerenchyma, pith, cortex, etc.

Comments from email exchange:

CM: I am in favour of removing the "portion of" prefix. I don't think that removing this is prefix is ontologically incorrect - it's just a naming convention. What would be ontologically incorrect would be mixing up the entire parenchyma with bits of the parenchyma in the ontology.

The argument in favor of the prefix is that it prevents such errors. However, I think there are better ways to enforce correctness in the ontology without forcing biologist-unfriendly terminology on all PO users.

In particular:

• clear textual definitions
• axioms in the ontology that allow automated reasoners to find mistakes.
• manual checking of the ontology

"portion of X" can always be retained as an exact synonym.

BS: unfortunately they need to be prefixed by 'portion of' unless it is always the case what is meant is the whole (portion of) parenchyma, and then another solution may be available.

MAG: I agree with Chris, if parenchyma (or any other tissue) is already a "portion of plant tissue" , however we have to be careful when working "sclerenchyma" and "collenchyma", since transitional forms can be found between "parenchyma and collenchyma" and "collenchyma and sclerenchyma" Originally these two "tissues" are designated as the "stereome" and they are supporting and mechanical tissues. There are several differences among the three tissues. We will find the same problems when addressing the xylem cell types, because there are a lot of "transitional forms" among them.

Chris also pointed out that the definition must be precise and can be as 'wordy' as necessary, as it is the part that is inherited. Everyone felt that propagating the "portion of" was redundant and not-user friendly. It was decided based upon this reasoning to maintain the "portion of only for the upper level "portion of plant tissue"

2. 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 the following terms:

• portion of storage parenchyma
• portion of fruit storage parenchyma
• portion of tuber storage parenchyma
• portion of aerial tuber storage parenchyma
• portion of subterranean tuber storage parenchyma

Comments from email exchange:

CM: you can make "flesh" be a broad synonym for all of these - just not an exact.

MAG: I agree with this as well.

BS:you need to distinguish between exact synonyms and narrower than synonyms (Chris can help with this, I think)

During the call there was discussion about the necessity/utility of propagating the synonyms down through the child terms. We want to be sure users can find the specific terms they are looking for.

CM: I still don't think you need so many synonym assignments. If you have flesh as a broad synonym for "tuber storage parenchyma" why would you want to add the same string as a synonym for subclasses like "aerial tuber storage parenchyma"?

We also discussed the various synonym classes- broad, narrow, related, exact.

It was decided that the synonyms at the higher levels should be broad and become more specific or exact at the lower levels of the ontology.

a. tuber flesh

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

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

a1. Updated term names and definitions of relevant parent terms:

These upper level terms should be resolved before we make new children for them.

• ground tissue (PO:0000500) 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.

We discussed this definition and compared it to that in Raven et al, 4th edition, Chris commented that it is good practice to define the three siblings (ground, dermal and vascular tissue) in similar way; for example developmentally or compositionally.

This is a term that was added at the Ithaca meeting in Dec 2009- number does not fit our numbering convention

This was accepted without the "portion of" by everyone present

• parenchyma (PO:0005421) became portion of parenchyma

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 (to be removed)

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.)

This was accepted with out the "portion of" by everyone present

a2. New terms to deal with tuber flesh as a general term:

• Portion of storage parenchyma (PO:0025035; is_a portion of parenchyma tissue): A portion of parenchyma tissue specialized for carbohydrate storage.

(Can add XP to carbohydrate: CHEBI:23008 or starch: CHEBI:28017; GO does not have a term for carbohydrate storage, may want to request).

Comment: This tissue could be found in any organ, but often occurs in fruits or tubers.

• Portion of fruit storage parenchyma (PO:0025037): A portion of storage parenchyma tissue that is part of a fruit. Syn: fruit flesh

• Portion of tuber storage parenchyma (PO:0025036): 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 (PO:0025039): A portion of tuber storage parenchyma tissue that is part of an aerial tuber.

• Portion of subterranean tuber storage parenchyma (PO:0025038): A portion of tuber storage parenchyma tissue that is part of a subterranean tuber. Syn: potato tuber flesh

Comment: This term is used to refer to potato tuber flesh. See part_of children for individual components of subterranean tuber flesh.

These were accepted with out the "portion of" by everyone present

a3. Parts of the tuber flesh

These terms can be used to annotate specific parts of the tuber storage parenchyma:

tuber pith:

• tuber pith (PO:0025052): A pith that is part of a portion of tuber storage parenchyma.

• aerial tuber pith (PO:0025054): A tuber storage pith that is part of a portion of aerial tuber storage parenchyma.

• subterranean tuber pith (PO:0025053): A tuber storage pith that is part of a portion of subterranean tuber storage parenchyma. Comment: In potatoes, this is part of the flesh. Syn: medulla, water core

tuber cortex:

• Tuber cortex (PO:0025055): A stem cortex that is part of a portion of tuber storage parenchyma.

• Aerial tuber cortex (PO:0025056): A tuber cortex that is part of a portion of aerial tuber storage parenchyma.

• Subterranean tuber cortex (PO:0025057): A tuber cortex that is part of a portion of subterranean tuber storage parenchyma. Syn: outer storage tissue, Reeve et al. 1969

tuber interfascicular region:

• tuber interfascicular region (PO:0025050): An interfascicular region that is part of a portion of tuber storage parenchyma.

• aerial tuber interfascicular region (PO:0025051): A tuber storage interfascicular region that is part of a portion of aerial tuber storage parenchyma.

• subterranean tuber interfascicular region (PO:0025049): A tuber storage interfascicular region that is part of a portion of subterranean tuber storage parenchyma. Comment: In potatoes, the interfascicular region extends to the subterranean tuber axillary vegetative buds (eyes). Syn: medullary ray, pith ray.

perimedullary zone:

• perimedullary zone (PO:0025058): The outer layer of a pith. Comment: The term perimedullary zone is only used when the outer layer of the pith is distinct from the inner layer.

• root perimedullary zone (PO:0025065): A perimedullary zone that is part of a root pith.

• stem perimedullary zone (PO:0025064): A perimedullary zone that is part of a stem pith.

• tuber perimedullary zone (PO:0025061): A perimedullary zone that is part of a tuber pith.

• aerial tuber perimedullary zone (PO:0025062): A tuber perimedullary zone that is part of an aerial tuber pith.

• subterranean tuber perimedullary zone (PO:0025063): A tuber perimedullary zone that is part of a subterranean tuber pith.

Also updated definitions and structure for pith, cortex, and interfascidular region

We had some discussion about using both 'region' and 'zone'- but since these are in the literature, we may just have to live with them both.

Image of all new or updated terms for tuber flesh:

We ran out of time to talk about the last two terms, so we will finish them next week:

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

New terms to deal with tuber eye dev browser:

• tuber axillary vegetative bud (PO:0025040): An axillary vegetative bud that is part of 
a tuber. 


• aerial tuber axillary vegetative bud (PO:0025041): A tuber axillary vegetative bud that
is part of an aerial tuber.

• subterranean tuber axillary vegetative bud (PO:0025042): 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.

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.

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

• Tuber periderm (PO:0025043): A periderm that is part of a tuber.

• Aerial tuber periderm (PO:0025044): A tuber periderm that is part of an aerial tuber.

• Subterranean tuber periderm (PO:0025045): A tuber periderm that is part of a subterranean tuber. Syn.: potato skin

• Tuber epidermis (PO:0025046): A shoot epidermis that is part of a tuber.

• Aerial tuber epidermis (PO:0025047): A tuber epidermis that is part of an aerial tuber.

• Subterranean tuber epidermis (PO:0025048): 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 (PO:0005679)

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 (PO:0005046)

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

Upcoming Conferences and Meetings: Updates:

* 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[[1]] has been selected for a 'flash update talk' along with the poster. We decided Ramona would take the lead on this presentation, since Lol did the previous one..

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

Laurel is organizing a booth with other database groups: Gramene, SGN, maizeGDB, TAIR and BAR.

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. 62 people are signed up! 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

* Infectious Disease Ontology Workshop

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.

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

8. Next meeting scheduled for Next week- exact time and day TBA