POC Conf. Call 6-23-10

POC meeting, Webex Conference Call; Date: June 23rd, 2010 9am (PDT)

In attendance: POC members:

Collaborators:

Absent:

Acceptance of the minutes from the 6-14-10 meeting? All in favor?

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.

Term Requests from Naama Menda, Solanaceae Genomics Network (cont'd from 6-14-10)

b. tuber eye

New terms were added:

• tuber axillary vegetative bud (PO:0025040): An axillary vegetative bud that is part of 
a tuber. 
Exact syn: Tuber bud, tuber eye

• 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. Comments: A structure on the tuber surface that can sprout. In potatoes, axillary vegetative buds (eyes) can determine processing quality. Broad syn: eye, tuber eye, Exact syn: potato eye

• tuber axillary bud meristem (PO:0025068): An axillary bud meristem that is part of a tuber.

• aerial tuber axillary bud meristem (PO:0025069): A tuber axillary bud meristem that is part of an aerial tuber.

• subterranean tuber axillary bud meristem (PO:0025070): A tuber axillary bud meristem that is part of a subterranean tuber.

>>Question: Should a tuber axillary bud meristem be part_of tuber or part_of tuber axillary bud? The meristem starts out on the surface of the tuber (in the axil), but lives on as the apical meristem as the bud continues to grow.

I would say it probably is part_of tuber, since an axillary bud meristem is "a shoot meristem formed in the axil of the leaf." As the bud grows, the meristem switches from being an axillary meristem to being a shoot apical meristem.

• A new subset of for potatoes was added

• Ramona is in the process of adding hyperlinks to SF tracker items to the obo file for all new terms. Would like to be able to make a shortcut link to these through the GO database registry, or perhaps we can write a script to create the shortcuts.

These terms and their definitions were accepted last week and this tracker item can be closed.

b.1. bud

All of the grand-children of bud have dual parentage. See SF tracker item for explanation and suggestions.

c. tuber epidermis

New terms to deal with tuber epidermis):

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

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

• Subterranean tuber periderm (PO:0025045): A portion of tuber periderm that is part of a subterranean tuber. Comment: The skin of young potatoes is epidermis while the skin of mature potatoes is periderm. Narrow syn.: potato skin

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

Probably, this should read 'A portion of stem epidermis...', but right now, a tuber is_a shoot, and not a stem. Need to decide which it is.

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

• Subterranean tuber epidermis (PO:0025048): A tuber epidermis that is part of a subterranean tuber. Comment: The skin of young potatoes is epidermis while the skin of mature potatoes is periderm. Related syn.: potato skin

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'.

terms from SourceForge

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)

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:

* 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

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