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-X-10 meeting? All in favor?

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)

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?

Terms from open SourceForge Trackers

1. stem and shoot (See SF Tracker stem and need to add SF item for shoot)

Problem: Stem has no is_a parent- should be a collective plant structure?

Stem def'n: The axial system of plants that bears leaves and buds. [source: APWeb:Glossary]

Synonyms: cane, culm, stalk, trunk

OR if we make it a child of plant organ, then penduncle, pedicel and gynophore can be stalks.

Shoot def: Part of the sporophyte composed of the stems and leaves, and includes shoot apical meristems. [source: POC:curators]

Tubers, rhizomes and stolons should be stems and not shoots.

Stolon PO:0003024 is defined as 'A slender, prostrate or trailing above-ground stem which produces roots and sometimes erect shoots at its nodes. [source: APWeb:Glossary]' but it is classified as a shoot.

Tuber is defined as 'Swollen storage shoot with determinate growth. [source: POC:curators]' while

subterranean tuber is 'A swollen rhizome or a part of the rhizome with determinate growth. [source: POC:curator]' and

rhizome is 'Underground shoot. [source: POC:curators]'

Subterranean tuber is_a tuber and part_of rhizome, so its definition should be 'A tuber that is part of a rhizome.' Tuber is already defined as determinate growth.

Tuber could be defined as 'A swollen stem with determinate growth that has part portion of storage parenchyma.'

We should request the term determinate from PATO.

2. stalk (See SF Tracker: stalk)

This was added as a new term at the Ithaca meeting on 12/2009, to cover a number of the terms lacking is_a parents.

def'n: An 
elongated, sub-cylindrical to cylindrical structure that supports another 
organ or regional part of an organ.

Proposed def'n: A cardinal organ part that is elongated and
 sub-cylindrical to cylindrical and supports an 
organ or another cardinal organ part.

-made a cardinal organ part (as per its definition) rather than an organ.

Proposed children of stalk: (Test: do all of these fit the definition?)

• filament: The stalk of a stamen.(stamen:organ)

• petiole: The stalk of a leaf. (leaf:organ)

• petiolule: The stalk of a leaflet (leaflet:cardinal organ part)

• funicle: The stalk which attaches the ovule to the
 placenta.(ovule: cardinal organ part)

• gynophore: The stalk at the base of the ovary.

(ovary: cardinal organ part)

• leaf rachis: That part of the main axis of a pinnate or more highly compound leaf, that bears leaflets or divisions of the axis.(leaf:organ) (See SF Tracker: leaf rachis)

• peduncle: The stalk of an inflorescence; that part of
 the inflorescence below the first flower or inflorescence branch and above 
the last foliage leaf/pair of foliage leaves. (See SF Tracker: peduncle)

propose revised def'n: The stalk of an inflorescence or an individual flower (R, E, E 4th edition).

• pedicel: Basal part of the ultimate branch of the inflorescence. [source: APWeb:Glossary]

(See SF Tracker: pedicel)

propose revised def'n: The stalk of an individual flower in an inflorescence that contains more than one flower (LC revised from R,E,E4th edition).

Note: We also have the term 'stem'. We need to decide if 'peduncle' and 'pedicel' fit better as stalk or stem.

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

Several weeks ago, we created new children of cardinal organ part, from terms that had no is_a parent. We can deal with definitions and relationships of each term later, but for now we simply need to approve moving them to cardinal organ part.

Some of them can be dealt with later, but the terms listed here are a higher priority and/or can be dealt with very quickly. Many of the definitions need to be worked on at a future meeting. See Source Forge items for additional comments.

*receptacle: The region at end of pedicel or axis to which parts of flower are attached. [source: APWeb:Glossary, POC:curators]. (See SF Tracker: receptacle)

propose revised 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- 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. (See SF Tracker: hypanthium)

made part_of receptacle instead of part_of flower

*pulvinus:-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] (See SF Tracker: pulvinus)

-currently is_a (an) organ

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