Minutes and agenda 3-9-10

Minutes for the POC Conference Call, Tues Mar 9rd, 11am PST

Minutes are added to agenda under each item in italics.

Agenda: We will continue with the discussions from the 3-3-10 conf. call. These items have been posted on SourceForge for people to comment on.

We decided to create two new parent terms directly under plant structure: "in vitro cultured plant structure" and "In vivo plant structure".

1. in vitro plant structure

New def'n: A plant structure that was derived from a part of a plant and involves microbe-free growth in a sterile environment such as a Petri dish or a test tube.

2. in vivo plant structure

Need to work on definition: A plant structure that is or was part of a plant that is growing ... (not in vitro).

I propose we either integrate the cultured terms, or leave the ontology the way it is on the live browser. What do you think?

I looked up some examples of how it is dealt with in other ontologies and cannot find any precedent for splitting the in vitro terms out.

For example, From Drosophilia Flybase Anatomical entity

<--material Anatomical entity
  <--anatomical structure
     <--cell
        <cultured cell- line

From the Xenopus anatomy ontology they have:

Anatomical entity
   <-- anatomical entity in vitro

The cell ontology has a listing for 'cell in vivo' as a child of 'cell', but they do not define 'in vivo'. They also have a listing for the in vitro cells under "experimentally modified cell" (is_a cell)

We decided to keep in vitro plant structure under plant structure as it is, but obsolete "in vivo plant" structure, because defining it was problematic. This goes back to the original format from before Ithaca meeting in December. Old name "in vitro cultured cell, tissue and organ" will be added as synonym. We decided to separate last part of definition.

New definition: "A plant structure that was derived from a part of a plant and involves microbe-free growth in a sterile environment. An example of a sterile culture environment is growth on or in a nutrient medium in a Petri dish or a test tube.

There will need to be a note that a sterile environment can include microbes that are intentionally added by the grower, such as co-culture with Agrobacterium.

3. plant structure

New def'n: An anatomical structure that is or was part of a plant, or was derived from a part of a plant.

4.gamete

New def'n: A plant cell that has half the chromosome complement of the sporophyte and is capable of fertilization to create a zygote.

It was decided to place 'gamete' as a child of 'plant cell' and to make it the parent term of 'egg cell' and 'sperm cell'

Comments?

New parent terms proposed by Ramona:

5. collective plant structure

New def: A plant structure that is a proper part of a plant and is composed of two or more (connected, contiguous?) organs.

Examples: flower, perianth, inflorescence. collective structure versus compound organ?

6. cardinal organ part Note: cardinal organ part was in SF originally as "organ segment or organ part."

def: A plant structure that is a proper part of an organ and includes portions of tissues of at least two different types. Examples include lobe, operculum, neck, petiole, leaflet. Note: if petiole is an organ part, then stalk probably also should be an organ part (not an organ, as it currently is).

Next conference call- Tuesday March 16th- 11am