POC Conf. Call 6-14-10

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

In attendance: POC members:

Collaborators:

Absent:

Acceptance of the minutes from the 6-8-10 meeting? All in favor?

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

a. Summary of tuber flesh Terms

New general term:

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

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

Child terms:

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

• 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)

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

• 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.

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.

New (older) items for 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)

x. Linking images to PO

• We can put in hyperlinks to individual images posted on plantsystematics.org

• More difficult to insert hyperlinks to collections of images, such as search results for keyword "pedicel," but it is possible

• If each image has a unique ID, Amigo can automatically generate hyperlinks to the database, so we would only have to input the ID. For example, we would enter PS:00123 under exteral dbxrefs, where PS would stand for PlantSystematics.org, and 00123 would be the unique ID number for an image, and in the Amigo browser, there would be a link to the image in Plantsystematic.org.

• Can we request that arrows be added to some of the existing images to highlight the feature we want to illustrate?

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..

* 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