POC Conf. Call 6-23-10

POC meeting, Webex Conference Call; Date: June 23rd, 2010 10am (PDT)

In attendance:

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

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

Collaborators: none present

Acceptance of the minutes from the 6-14-10 meeting? All in favor? There were no additions, deletions or changes to last week's minutes.

Minutes are in italics below each agenda item.

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.

We will have conference calls with the group on Tuesday June 29th 10am-12pm PDT POC Conf. Call 6-29-10 and Weds, June 30th 9am to 11am, PDTPOC Conf. Call 6-30-10.

I know some of you may not be able to attend the entire conference call, but please join in when you can. The agenda for the conference call on each day will be posted on the wiki page.

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

These terms were discussed last week. Below is a review.

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 children of axillary bud meristem

• 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.

RW: 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. This could be put in as a comment.

We decided to keep tuber axillary bud meristem as part_of tuber, since it is the meristem that develops into the tuber bud. These terms are accepted and Source Forge items will be closed.

Note: we need to address the definition of meristem (PO:0009013).

• A new subset of for potatoes was added

• Ramona added external dbx refs to SF tracker items to the obo file for all items since 11-15-09. 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. Right now, just have SF:#####. We can discuss this at the POC Corvallis meetings (see 'other items').

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. This issue came up while working on the terms for tuber eye.

bud (PO:0000055)

>axillary bud

>>axillary floral bud
>>axillary inflorescence bud
>>axillary vegetative bud

>floral bud

>>axillary floral bud
>>terminal floral bud

>inflorescence bud

>>axillary inflorescence bud
>>terminal inflorescence bud

>terminal bud

>>terminal floral bud
>>terminal inflorescence bud
>>terminal vegetative bud

>vegetative bud

>>axillary vegetative bud
>>terminal inflorescence bud

This means that a term like 'terminal floral bud' is_a 'terminal bud' and is_a 'floral bud', or 'axillary vegetative bud' is_a 'axillary bud' and is_a 'vegetative bud', etc.

This is useful if one wants to classify terms by different categories, but is not consistent with the goal of eliminating multiple inheritance.

At POC conference call, we preferred option #1 bud. In this case, only axillary and terminal buds direct children of bud. It may be more developmentally correct, because you will always know if a bud is terminal or axillary, but you may not know yet if it is floral, vegetative or inflorescence.

We agreed to add new terms: terminal reproductive bud (PO:0025071) and axillary reproductive bud (PO:0025072).

This will allow annotations of reproductive buds from non-flowering plants and 'terminal floral bud' and 'axillary floral bud' will be children of these terms.

The terms 'floral bud', 'vegetative bud' and 'inflorescence bud' are no longer useful and should be obsoleted.

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.

proposed def'n: A portion of stem 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: see below.

It was agreed by all present that tuber is_a stem,not a shoot.

Need to work on the def'n. of Tuber

Tuber PO:0004543 (tuber is a what?)

Current def'n: Swollen storage shoot with determinate growth.

From SF after the call: proposed def'n: A swollen or enlarged storage stem with determinate growth.

This would encompass both subterranean and aerial tubers.

• 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

LC: I am leaving this one open till we complete the tuber is_a stem discussion.

C.1. Also updated term names and definitions of relevant parent terms and related terms:

• dermal tissue (PO:0009014)

This term is redundant with epidermis. We will obsolete it, with note to move annotations to epidermis.

• epidermis (PO:0005679)

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

• periderm (PO:0005046)

Proposed def: A 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 agreed to obsolete dermal tissue and accept the new definitions of epidermis and periderm. A comment will be added to periderm that periderm may contain secondary phloem

We will also add a comment to periderm that it is derived from lateral meristerm. This can also be formalized in a relation but does not be in the definition.

Also discussed:

protoderm

should be is_a 'meristem', part_of 'apical meristem'.

Current def: The undifferentiated surface cell layer of the primary plant body, which gives rise to epidermis.

RW suggests that 'protoderm' should not be part_of 'apical meristem', rather that it develops from the outer layer of the AM.

Proposed def: A meristem that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.

We agreed that protoderm should be part_of apical meristem. We will add a separate tracker item for primary and secondary plant body and discuss how to include them later.

hypodermis and endodermis

should be is_a ground tissue, part_of cortex.

RW suggests that both of these terms should be is_a 'cortex', rather than part_of 'cortex' (see SF tracker item for explanation).

During the POC conference call on 6-23-10, it was decided that endodermis and hypodermis should be part_of cortex, but we will need to change the definition of cortex to allow this.

cortex (PO:0005708): The proposed new def'n will be: A maximal portion of ground tissue between the vascular system and the epidermis in a plant.

For hypodermis, endodermis, and similar terms (like perimedullary zone), Barry suggested that we define the parent terms as the maximal portion of a tissue, then the child terms can be part of.

hypodermis (PO:0005051): Current def'n: The outermost layer of a portion of cortex. A layer or layers of cells beneath the epidermis that is distinct in appearance from adjacent tissues.

Proposed def'n: A portion of ground tissue that is the outermost layer of a portion of cortex. comment:A layer or layers of cells beneath the epidermis that is distinct in appearance from adjacent tissues.

endodermis: (PO:0000252) Current def'n: The innermost layer of a portion of cortex. The layer of tissue forming a sheath around the vascular region and often having a casparian strip in its anticlinal walls; it may have secondary walls later.

Proposed def'n: A portion of ground tissue that is the inner most layer of a cortex and has a casparian strip in its anticlinal cell walls. Comment: Forms a sheath around the vascular system. It may have secondary walls later, part_of cortex

Other types of cortex, like stem cortex, then must also be defined as is_a ground tissue that is part_of cortex.

I will leave these open for now, until these changes are reviewed next week.

new term for root tuber

This is an old tracker item. Can we close it?

This item will be closed.

terms from SourceForge

Discussion of fruit and embryo was postponed until a future meeting.

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)

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)

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.

Draft of poster has been circulated. Comments?

* 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: POC Meeting in Corvallis- Conference Calls on Tuesday June 29th 10am-12pm and Weds, June 30th 9am to 11am