POC Conf. Call 7-14-10

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

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 6-30-10 meeting? All in favor?

Preparations for next release

1. What needs to be done

Review of changes discussed at previous meetings

1. gametophyte and sporophyte were made obsolote. Add 'consider whole plant' relation to both, and comments to add participates_in gametophytic or sporophytic stage.

Part of and is_a children of these terms were moved to whole plant.

2. Made new term embryo sac ((PO:0025074): a female gametophyte in angiosperms. Is_a female gametophyte. Antipodal cell, central cell and egg apparatus are part_of embryo sac (rather than part of female gametophyte).

egg cell (PO:0020094) was part_of egg apparatus, but this does not allow for eggs that are not in angiosperms. Therefore, changed relation to egg_apparatus has_part egg cell.

3. New top level term plant structure system (PO:0025024): An anatomical system in a plant.

Has new child root system (PO:0025025): An axial plant structure system that produces root apical meristems and the plant structures that arise from them.

Renamed shoot to shoot system (PO:0009006): An axial plant structure system that produces shoot apical meristems and the plant structures that arise from them.

Older unresolved terms

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)

3. New is_a children of cardinal organ part (See SF Tracker: new is_a children of cardinal organ part)

*receptacle: (See SF Tracker: receptacle)

Current def'n: The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators].

proposed def'n: The region at the top of either the peduncle or pedicel where the floral appendages (for example, sepals, petals, stamens, and pistils) are attached.(Brooklyn Botanic Garden http://www.bbg.org/gar2/topics/botany/parts_flowers.html)

Comments: If both pedicel and peduncle is_a stalk, and stalk is_a 'cardinal organ part', then both pedicel and peduncle must be part of some organ for this to work.

• hypanthium(See SF Tracker: hypanthium)

Current def'n: A cup- or tube-like structure bearing perianth and stamens on its rim, so these arise above the base, and often above the top, of the ovary of a flower.

proposed def'n:

made part_of receptacle instead of part_of flower

• pulvinus: (See SF Tracker: pulvinus)

Current def'n: A more or less abrupt swelling, especially at the apex or base of a petiole or leaf sheath, often glandular and/or being the place where a plant responds to touch, gravity or light, in panicoid grasses a swollen region in the stem above the intercalary meristem - such a definition would also include stems of Chloranthaceae, Acanthaceae, Caryophyllaceae, Amaranthaceae, etc., cf. articulation. [source: APWeb:Glossary]

-currently is_a (an) organ

proposed def'n:

Upcoming Conferences and Meetings: Updates:

* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):

Our proposal for the symposium 'Bio-Ontologies for Plant Sciences' has been accepted, under the theme Genetics, genomics and bioinformatic. The organizers have asked us to confirm three speakers and titles by July 16th. As of our last discussion, Ramona and Pankaj were planning to attend and give talks. Must confirm that grant money can be used for international travel and confirm third speaker. Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if she is not available.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, will contact them again. Do we want to organize an annotation workshop?

Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.

* 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 and Ramona attended and presented our one page write up [[1]] as a 'flash update talk' and poster.

* 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 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

X. Next meeting scheduled for: Weds, July 21th, 10am