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)

put in summary of tuber epidermis and tuber eye

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.

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