POC Conf. Call 6-14-10

POC meeting, Webex Conference Call; Date: Monday June 14th, 2010 10am (PDT)

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

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: None in attendance

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

Minutes are in italics below each agenda item

Term Requests from Naama Menda, Solanaceae Genomics Network (cont'd from 6-8-10)

a. Summary of tuber flesh Terms- Accepted at 6-8-10 mtg

New general term:

• storage parenchyma (PO:0025035): A parenchyma specialized for carbohydrate storage.

Child terms:

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

• tuber storage parenchyma (PO:0025036): A storage parenchyma that is part of a tuber. Syn: tuber flesh

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

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

Comment: This term is used to refer to potato tuber flesh.

See part_of children (tuber pith, tuber cortex, tuber interfascicular region, and perimedullary zone) for individual components of subterranean tuber flesh

Link to summary image of tuber flesh terms: Media:Tuber_flesh_terms2.jpg

Barry suggested that we include the phrase "portion of" in the definitions, even if not in the terms names, so for example, fruit storage parenchyma would be: a portion of storage parenchyma that is part of of a fruit. This makes it clear that we are using count nouns and not mass nouns.

Alejandra requested that we add seed storage parenchyma. We will add this term, with endosperm parenchyma (PO:0005415) as a child of it.

These terms and their definitions were accepted as amended and this tracker item can be closed.

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.

Do we need to add tuber children of axillary bud meristem (PO:0000232) as well?

The new terms for tuber axillary vegetative bud were accepted by the group. Naama's proposed definition for tuber eye will be added as a comment to subterranean tuber axillary vegetative bud. We will also add tuber axillary bud meristem and its children.

Barry commented that we should not strive for completeness (because it is an impossible goal), but when and opportunity for more completeness comes along (like adding axillary bud meristem children), we should take it.

We had some discussion as to whether it was better to use common names like tuber eye as the primary name, because it may not be intuitive for users to search for a name like 'subterranean tuber axillary vegetative bud'. Long names are less user friendly, but more scientifically correct, and do not limit use to specific taxa. Ulitmately, the goal should be to have both primary names and synonyms appear in user interfaces.

Barry mentioned that software is being developed to allow users to create specialist view ontologies, that could replace names with synonyms used by particular groups. Jim Brinkley in Seattle Structural Informaticsis a person to contact re. these developments.

We also have a new subset of for potatoes and other existing subsets to help people working in specific taxa.

Hyperlinks to SF tracker items should be added to the obo file for all new terms. Perhaps we can make a shortcut link to these through the AmiGO database registry.

Need to add tuber bud as a synonym of tuber axillary vegetative bud.

These terms and their definitions were accepted as amended and this tracker item can be closed.

c. tuber epidermis

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

From previous 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 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.

We agreed with Dennis' SF tracker comment that dermal tissue should keep it's original differentia -- that it develops from protoderm. In this case, epidermis and dermal tissue are redundant terms, until someone can come up with an example of dermal tissue that is not epidermis.

We will obsolete the term dermal tissue (with note to move annotations to epidermis).

• 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.

New definition of epidermis: A portion of plant tissue composed of epidermal cells that develops from the protoderm and covers the surface of a plant structure. Comments: The epidermis can be composed of one or more layers of cells. In some species, the epidermis is replaced by periderm.

• 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

Periderm should not be a child of dermal tissue, but of ground tissue (since it develops from the ground meristem).

New definition of periderm: The peripheral portion of ground tissue in a plant structure that is composed of phellogen, phellem, and phelloderm. Comment: May replace the epidermis in stems and roots, rarely in other organs. In some cases, the epidermis is retained after periderm development.

We accepted the new terms for tuber epidermis and tuber periderm. Need to add comments that mature potato skin is periderm, young potato skin is epidermis, and that epidermis is replaced by periderm in most dicot tubers.

Barry suggested that we may want to use the relation periderm proceeded_by epidermis, but we decided that was too specific, since there are times when the epidermis remains after periderm development. We should try to think of other possible uses for proceeded_by in the PO.

Also discussed protoderm (should be is_a meristem, part_of apical meristem) and hypodermis (should be is_a ground tissue, part_of cortex).

These terms and their definitions were accepted as amended and this tracker item can be closed.

Barry suggested that any term that has the word tissue in the name should have prefix 'portion of.' We agreed to try this, as there are a limited number of such terms. He also was concerned about terms like secretory tissue and transfusion tissue, that are based on function rather than structure or position. We will have to address those later.

Thus, the term 'ground tissue' goes back to being called 'portion of ground tissue'.

Upcoming Conferences and Meetings: Updates:

• 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.

• 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 Laurel did the previous one.

Ramona and Laurel will circulate the proposed presentation for the group to review.

• 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.

• POC Meeting and Workshop Fall 2010 at NYBG, Date TBD

Will invite outside experts, scientists, students and postdocs.

There is now a wiki page for this meeting (POC Meeting and Workshop Fall 2010 at NYBG).

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- Weds June 23rd time: 10 am