Minutes 3-16-10

Agenda and Minutes- POC Webex Conference Call, Tues Mar 16th, 11am PDT

In attendance: Laurel Cooper (minutes), Ramona Walls, Marie Alejandra Gandolfo, Chris Mungall, Dennis Stevenson. Absent: Pankaj Jaiswal, Barry Smith.

Minutes are added to agenda in italics under each item.

Agenda: The goal for today's conference call was to deal with the issues raised by gametophyte and sporophyte. At the same time we will need to discuss whole plant as they are interrelated. These items have been posted on SourceForge for people to comment on.

Items from last week's discussion:

 cardinal organ part and collective organ

Ramona and Laurel moved a group of terms so they are now children of these two structures. These include all the terms that don't have is_a parents and are appropriate, plus a few others (see below:) Note: The existing part_of relationships were retained except as noted below.

a. new children of cardinal organ part (currently without is_a parent):

anther (as part of stamen)

apical hook

auricle

awn

central zone of the leaf lamina

central zone of the petiole

connective

fruit distal end and proximal end (is a fruit an organ?) MAG: fruit fits our definition of a plant organ

hypanthium (made part_of receptacle instead of part_of flower)

hyperphyll

hypocotyl

leaf apex

leaf base

leaf lamina (and all other laminas)

leaf lamina base

leaf rachis (is_a stalk)

leaf sheath

leaflet

ligule

ovary

ovule

paleal apiculus

pedicel

petiole (is_a stalk)

proximal end and distal end of petiole

raphe (removed part_of link to ovary, because it is part of the funicle that is attached to the ovary, not part of the ovary)

antiraphe (definition is not clear. Is it part of the ovary or the funicle?)

receptacle (or is it an organ?)

root tip

sepal margin (and all margins)

stigma

stipel

style

transition zone

Also:

- pulvinus (currently is_a organ)

Note: stalk was moved from is_a organ to cardinal organ part.

b. new children of collective plant structure (currently without is_a parent):

andreocium

calyx

corolla

epicalyx

flower

gynoecium

inflorescence

infructescence

involucre

perianth

spikelet

Also:

-Made seedling is_a whole plant

-Made tepal is_a plant organ (since petal is)

-Floral bract and inflorescence bract were children of both plant organ and bract (which is_a organ). Deleted is_a relationships to plant organ and kept under bract.

-Made new term for organ margin (see notes from Ithaca meeting 12/2009). Then organ margin is_a cardinal organ part and types of margins are is_a children of organ margin.

-Deleted is_a relationships from lamina margin to leaf lamina.

Comments: - There may be others that should be reclassified but have not been found yet.

• Ramona and Laurel are wondering about the correct procedure for informing the POC group of changes like these (groups of terms) which we make to the ontology?

   * Do we need to open a SF tracker item for each and every one or can these be dealt with as a group under the corresponding parent term? 

The group agreed that it was best not to make separate SF Tracker items for each of these when dealing with groups of terms. PJ suggested the best way to deal with this is to create a new "children of" term for each of these and list the terms that are affected. He further commented that any terms where there was a change in the part_of (or is_a) relationship should have a new tracker item, with a link to the "new is_a children of COP/ CPS" terms

Action item: Ramona will create these on SF

New items for discussion:

1. gametophyte: current def'n: A haploid plant, or phase of a plant's life cycle, that bears gametes after mitotic events. proposed definition: A plant structure that arises through a meiotic event and is capable of producing gametes.

We had continued discussion about this term and came up with the following:

 New def'n: A plant structure that arises through meiosis and may produce gametes by mitosis.

2. sporophyte: current def'n: A plant or phase of a life cycle that bears spores formed by meiosis.

proposed definition: A plant structure that is a product of fertilization and is capable of forming spores through meiosis.

We had continued discussion about this term and came up with the following:

 New def'n: A plant structure that is a product of fertilization and produces spores through meiosis.

PJ suggested including the term 'and/or gametophytes' but the group felt that was not appropriate as the gametophyte arises from the product of meiosis (the spore)

Note: we will need to add the term spore to the PO. Action item: Laurel will post it on SF.

3. whole plant: current def'n: A plant structure which is a whole organism.

This item was tabled for discussion at the next meeting.

Action item: Ramona will post her comments to this term about making whole plant the parent to gametophyte and sporophyte, rather than a sibling to them, so people could comment there.

5. standard practices for writing definitions

Should we reword existing definitions (as time allows) to fit the machine readable format we have been using for new definitions? This is the best practice, if it is possible

Where should examples go, in the second part of the definition or in comments? Currently, there is a mix of both in the PO.

Comments from Barry Smith- via email:
 "The rule is that examples NEVER occur in definitions. They should always occur in comments. 
The best practice is as above (cases that were absolutely known to fit the definition), but we will need to address this issue again when we move to a formal version of the ontology.
 Incidentally, it is good to record also those examples which provide the reasons why we included specific clauses in definitions which might seem redundant to people who do not know the cases in question"
 BS

All agreed that this was the best practice

6. SourceForge issues

Should there be a separate SF tracker for growth and developmental stages?

CM suggested that this was perhaps not necessary, as all the same people are looking at them both. We could consider creating two 'groups' (1. Anatomy and 2. Growth and Development) then people could use the sort and display filters. Ramona created two groups: 1. Plant Structure and 2. Growth and Development Stages. New terms should be assigned to the appropriate group.

Do we need to get an email from SF every time someone makes a change?

LC- One option to reduce your inbox from getting clogged up is to have the PO_internal emails sent as a digest once per day.  
I think you can set this yourself, or let me know and I can set it for you.

You can also set up a filter on the email inbox to forward the messages into a specific subfolder- reduces clutter.

CM said there was a way to create a digest from SF, but it was complicated and involved a script running on a chron job.

Is there a way to see when an item has last been changed in SF, so someone could look at the list of items and see which ones have new comments?

No one knew of any way to do this. CM commented that he found the emails useful in this regard

7. Setting the date of next public release of the PO-anatomy database:

According to the NSF grant timeline, we should have a public release in the first quarter of 2010 (Feb-April).

How much more needs to be done before we are ready for a public release of the revised database?

PJ commented (before the meeting) that do not want to rush it and that we will need to thoroughly test the new structure with annotations from our collaborators.

8. New Item: Update from Marie Alejandra Gandolfo:

1- "Slide Type collection": I have identified more than 400 slides (from Algae to Flowering plants, NO fungi) for photographing. The majority of them can be used for more that one Plant Ontology Term (for example: sections of seed have also embryos, cross sections of leaves can be used for epidermis, and other tissues, etc.).

2- I am working with a representative of Data2 for purchasing the bar-coding labels, these will be used for the "slide type collection" for database and to easily retrieve images.

8. Next conference call- Tuesday March 23rd- 11am?. Remember that is Pacific Daylight Time.

Items for upcoming meetings:

• Complete discussion of gametophyte, sporophyte and whole plant.

• Complete discussion of new children of cardinal organ part and collective plant structure.

• Definitions of spore, simple organ and compound organ. Posted on SourceForge..