Minutes and agenda 3-9-10

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

Minutes are added to agenda in italics under each item.

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

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.

Everyone agreed that this definition was okay as is. Item will be closed on SourceForge.

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?

Everyone agreed that this definition was okay as is. Item will be closed on SourceForge.

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?

We agreed that definition should include the words "two or more organs," but discussed the special cases where collective structures (particularly flowers) have been reduced to consist of a single organ (such as a single stamen). We decided to make a category called "reduced collective structure," which will be a child of plant structure for the time being, with a cross-reference to collective structure. May need to change it as we go forward. We discussed having the word connected or contiguous in the definition, and agreed that we could eliminate it by using the new wording given below. However, it is important that the multiple organs be adjacent to each other to be considered a collective structure. Barry asked whether there was anything else that could be contained in a collective structure, and we agreed that there could be portions of tissue as well, such as might occur between the whorls of a flower. We agreed that some structures are not collective plant structures, but compound organs, such as a compound leaf.

New definition: A plant structure that is a proper part of a plant and is composed of two or more organs and any associated portions of plant tissue.

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).

The proposed definition was accepted by the group. We discussed that there could be examples of organ parts that are themselves parts of larger organ parts (such as in doubly compound leaves). We discussed the format for comments, and Barry pointed out that our comments should be things that we know to be the case, and not a list of action items (which we should keep elsewhere). We agreed that stalk should be moved from organ to cardinal organ part, because we could not think of any examples of stalks that were not organ parts. Discussed meaning of cardinal. A cardinal organ part is one that has biological significance and is a plant structure, as opposed to one that is arbitrary.

Final definition: 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.

Next conference call- Tuesday March 16th- 11am