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Agenda for the POC Conference Call  2-23-10
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Minutes and agenda for the POC Conference Call  2-23-10
  
Items for discussion:
+
Present: Laurel Cooper, Pankaj Jaiswal, Ramona Walls, Dennis Stevenson, Chris Mungall
1.Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:  
 
  
* plant cell
+
''Minutes of the meeting have been added in italics to the end of each agenda item. -RW''
def: An anatomical structure that is or was part of a plant and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding cell wall.
 
  
New def:  
+
Agenda:
...is a cell, which is the basic functional unit of a plant, and that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.
 
Comments: applies to living or dead cells
 
  
Note: There is no "lumen" term in GO- so it should be added.
+
1. Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:
Raven, Evert and Eichhorn define the lumen as: "the space bounded by the cell wall".
 
Def: maximally connected lumen ??  is there a simpler way to word this?
 
  
* plant organ
+
'''* plant cell'''
def: "A maximal anatomical structure which is a proper part of a plant and which derives from a single ontogenetic event and includes as parts portions of tissues of at least two different types. Examples: stem, leaf,  root."
 
  
New def:  
+
New def: A cell, the basic functional unit of a plant, that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.
-is an anatomical structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path. 
 
(reworded slightly for readability)
 
Comments: May include individual cell types that are not part of tissues. example: stomatal cells which are part of the leaf, "proper" refers to not being the whole plant  
 
Examples: stem, leaf,  root
 
  
Note: in 2-11-10 talk, Barry Smith suggested having child terms of plant organ: simple, compound and complex plant organs- tabled for next discussion.         
+
Comments: Reference the definition of cell in GO(GO:0005623), see GO for definition of cell also: applies to living or dead cells
  
*portion of plant tissue
+
Note: There is no "lumen" term in GO- Ramona will request it.
def: "An anatomical structure in a plant that consists of cells and intracellular matrix." comment: See Esau on simple and compound tissue. **This still needs to be fixed.
+
Raven, Evert and Eichhorn define the lumen as: "the space bounded by the cell wall".
  
New def:  
+
Def: maximally connected lumen ?? is there a simpler way to word this?
-is an anatomical structure in a plant that consists of one or more cell types, organized into a structural and functional unit, and may include an intercellular matrix.
 
  
Comment:  intercellular matrix- def: middle lamella- "layer of intercellular (between the cells) chiefly, pectic substances, cementing together the primary walls of contiguous cells ( ref: Evert, 3rd ed 2006)
 
  
 +
Comments from DWS: "For me lumen has no meaning in this context. The lumen basically has no contents beyond space. It is the space inside the cell wall that is left after the protoplasm dies"
 +
 +
"Suggest using "basic structural unit" instead of "basic functional unit". In terms of function, isn't an organelle more basic?"
  
  
 +
Proposed new definition (by RW and DWS): '''A cell that is or was part of a plant, is the basic structural unit of a plant, and may be dead at maturity.'''
  
 +
Comments:  See GO term GO:0005623 for definition of cell, and GO term GO:0009505 for definition of plant-type cell wall. A plant cell that is dead at maturity will, such as a fiber cell, consists of only the plant cell wall and its lumen.
  
2. Whole plant was redefined as "A plant structure which is a whole organism." and gametophyte and sporophyte were moved under it.
+
''We decided that much of the existing proposed definitions was redundant with GO, and we should have simpler definitions.''
  
There was much discussion about this one and several good points were raised:
+
''Egg and sperm are not cells – nucleus with membrane – so definition of cell is still okay.''????
-Does this include single-celled plants?  Can something be a plant cell and a whole plant? 
+
''Other parts of definition should go in the comments.''
(Chris made a comment about disjoints in OBO-Edit- not too sure about this) 
 
- PJ- problem of having some terms that should be under both gametophyte and sporophyte- example is a leaf like structure- phyllome. Also, root-like structures eg. rhizoids
 
-also the problem of having term inflation if all the plant structures have to be qualified as either gametophytic or sporophytic
 
- gametophyte and sporophyte are really phases of development not plant structures, although botanists are used to referring to the "gametophyte and sporophyte"
 
-should gametophyte and sporophyte actually be siblings of 'whole plant', so that terms like microphyll can have multiple parentages. 
 
- there was discussion about actually dissolving the gametophyte and sporophyte terms, but we decided not to disrupt the ontology right now and do the following:
 
-move all terms that are currently under gametophyte and sporophyte under whole plant,
 
- then worry about populating gametophyte and sporophyte with specific terms
 
- figure out how to cross reference between the PO Structure and Development ontologies.
 
  
Note: Make sure that gametophytic stage and sporophytic stage are defined in the developmental stage ontology.  
+
'''Final definition: A cell that is part of a plant and that has as its part a plant cell wall.'''
  
 +
Comments: Be sure to add cross references to GO for definitions of cell and plant-type cell wall (their term).
  
  
3. in vitro cultured cell, tissue and organ was moved out the Plant Structure class and made a separate class.
+
'''* plant organ'''
def: "Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish."
 
-tabled for next discussion.
 
  
4. New parent terms proposed by Ramona:
 
*cardinal organ part
 
def: A plant structure that is a direct or immediate part of an organ that is often maximal(?) but is smaller than the organ itself. Examples include lobe, operculum, neck, petiole?, leaflet.
 
-tabled for next discussion.
 
  
* collective plant structure
+
New def: -A plant structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.
A plant structure that is composed of multiple organs but is not an organ. (Maybe something about a bona fide boundary, some way to distinguish it from whole plant).
 
Examples: flower, perianth, inflorescence. collective structure or compound organ?
 
-tabled for next discussion.
 
  
5. Term request from TAIR for "gamete"- proposed (RW): add gamete to the ontology (is_a parent, plant cell), with sperm cell and egg cell as siblings under a common parent 'gamete'.
+
(reworded slightly for readability)
-tabled for next discussion.
 
  
6 Assignment of Term numbers:  
+
Comments: May include individual cell types that are not part of tissues. example: guard cells which are part of the leaf, idioblasts
  
We need a set of numbers for the POC curators ( Lol and Ramona, mostly)- existing:
+
"proper" refers to not being the whole plant Examples: stem, leaf, root
  
Group
+
Note: in 2-11-10 talk, Barry Smith suggested having child terms of plant organ: simple, compound and complex plant organs- tabled for next discussion.
identifier range (from-to)
 
TAIR
 
0000001-0005000
 
Gramene
 
0005001-0010000
 
IRIS-IRRI
 
0010001-0015000
 
MaizeGDB
 
0015001-0020000
 
UMSL
 
0020001-0025000
 
  
Proposed:
+
''We agreed that the definition was okay as is.''
0025000-0030000 PO curators
 
0030001-0035000 NYBG
 
  
 +
''We must remember to include cross products to terms referenced in definitions, such as the reference here to portion of plant tissue.''
  
 +
Comment from BS: Make sure the definitions are consistent with the cross products to the PO term 'portion of plant tissue'
  
 +
Final Def'n: '''A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.'''
  
 +
 
 +
'''* portion of plant tissue'''
  
7.  Next conference call- Tues Mar 2nd at 11 am PST
+
New def: -A plant structure that consists of one or more cell types, organized into a structural and functional unit, and may include an intercellular matrix.
 +
 
 +
Comment: intercellular matrix- def: middle lamella- "layer of intercellular (between the cells) chiefly, pectic substances, cementing together the primary walls of contiguous cells ( ref: Evert, 3rd ed 2006)
 +
 
 +
''We decided on a new defintion.''
 +
 
 +
'''Final definition: Plant structure that has as its parts multiple cells and is a proper part of an organ.'''
 +
 
 +
Comment: These cells are organized into a structural unit, and may include an intercellular matrix.
 +
 
 +
 
 +
 
 +
 
 +
2. '''Whole plant''' was redefined at the Ithaca meeting as "A plant structure which is a whole organism." and gametophyte and sporophyte were moved under it.
 +
 
 +
But after much discussion (see Minutes 2-16), it was decided that it would be better to move all terms that are currently under gametophyte and sporophyte under whole plant, and make gametophyte and sporophyte siblings of 'whole plant'
 +
These changes were made and we can look at the results in the PO-dev browser.
 +
 
 +
''We had more discussion of the functionality of keeping gametophyte and sporophyte as siblings to whole plant, and agreed to keep them as they now are. We agreed that this structure would work, as long as we were careful of the "all-some" rule for all relationships. For example: if A is part_of B, then all instances of A must be part of B.''
 +
 
 +
''Pankaj still wanted to get rid of all child terms under gametophyte and sporophyte, but Ramona felt that there would be structures that are only part of one or the other and would need to be there. We agreed that our guiding principle should be to have general terms for all structures that would be part of whole plant, and that after that, we could make is_a chilren of those specific terms that are parts of gametophyte or sporophyte.''
 +
 
 +
''Our discussion raised the issue of needed a term such as root system, with children such as rhizoids, roots, and adventitious roots. Will also need some such term for shoots.''
 +
 
 +
 
 +
'''New Item: Presentations at national meetings this summer.''' Dennis and Ramona (with Ramona presenting) will prepare a oral presentation for the Botanical Society of America meeting this summer, for the Structural and Developmental Section. They will emphasize the use of the ontology as a vocabulary reference, and invite annotations.  Maybe prepare a poster too? Laural and Pankaj will give a workshop at the ASPB (?) meeting at the same time. Group will send around abstracts for presentations before submitting.
 +
 
 +
 
 +
 
 +
 
 +
'''''Items 3 through 5 were tabled for the following discussion.'''''
 +
 
 +
 
 +
3. ''' ''in vitro'' cultured cell, tissue and organ''' was moved out the Plant Structure class and made a separate class. def: "Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish."
 +
 
 +
4.New parent terms proposed by Ramona:
 +
 
 +
'''*cardinal organ part'''
 +
def: A plant structure that is a direct or immediate part of an organ that is often maximal(?) but is smaller than the organ itself. Examples include lobe, operculum, neck, petiole?, leaflet. -tabled for next discussion.
 +
 
 +
 
 +
'''* collective plant structure'''
 +
def: A plant structure that is composed of multiple organs but is not an organ. (Maybe something about a bona fide boundary, some way to distinguish it from whole plant). Examples: flower, perianth, inflorescence. collective structure or compound organ? -tabled for next discussion.
 +
 
 +
'''5.Term request from TAIR for "gamete"'''- proposed (RW): add gamete to the ontology (is_a parent, plant cell), with sperm cell and egg cell as siblings under a common parent 'gamete'. -tabled for next discussion.
 +
 
 +
'''6. Assignment of Term numbers:'''
 +
 
 +
New term numbers are to be used for the terms that are being added.
 +
 
 +
Existing:
 +
Group identifier range (from-to)
 +
 
 +
TAIR: 0000001-0005000
 +
 
 +
Gramene/OSU (Jaiswal lab): 0005001-0010000
 +
 
 +
IRIS-IRRI: 0010001-0015000
 +
 
 +
MaizeGDB: 0015001-0020000
 +
 
 +
UMSL: 0020001-0025000
 +
 
 +
New numbers to be added:
 +
 
 +
0025001-0030000 PO Consortium (for terms we decide upon as a group)
 +
 
 +
0030001-0035000 NYBG ( New terms from Dennis and Ramona)
 +
 
 +
0035001-0040000 Cornell/MAG
 +
 
 +
Action item:  Laurel will Update on POC webpage and PO wiki
 +
 
 +
 
 +
7.  Next conference call-  
 +
 
 +
''Dennis and Barry will not be available next Tuesday at the regular time, so Laurel will set up a Doodle poll to set up next week's meeting.''

Latest revision as of 07:52, 27 February 2010

Minutes and agenda for the POC Conference Call 2-23-10

Present: Laurel Cooper, Pankaj Jaiswal, Ramona Walls, Dennis Stevenson, Chris Mungall

Minutes of the meeting have been added in italics to the end of each agenda item. -RW

Agenda:

1. Discuss the Plant Structure parent terms that were defined at the meeting in Ithaca- these have been posted on Sourceforge for people to comment:

* plant cell

New def: A cell, the basic functional unit of a plant, that has as its parts a maximally connected lumen, the contents of this lumen and the surrounding plant cell wall.

Comments: Reference the definition of cell in GO(GO:0005623), see GO for definition of cell also: applies to living or dead cells

Note: There is no "lumen" term in GO- Ramona will request it. Raven, Evert and Eichhorn define the lumen as: "the space bounded by the cell wall".

Def: maximally connected lumen ?? is there a simpler way to word this?


Comments from DWS: "For me lumen has no meaning in this context. The lumen basically has no contents beyond space. It is the space inside the cell wall that is left after the protoplasm dies"

"Suggest using "basic structural unit" instead of "basic functional unit". In terms of function, isn't an organelle more basic?"


Proposed new definition (by RW and DWS): A cell that is or was part of a plant, is the basic structural unit of a plant, and may be dead at maturity.

Comments: See GO term GO:0005623 for definition of cell, and GO term GO:0009505 for definition of plant-type cell wall. A plant cell that is dead at maturity will, such as a fiber cell, consists of only the plant cell wall and its lumen.

We decided that much of the existing proposed definitions was redundant with GO, and we should have simpler definitions.

Egg and sperm are not cells – nucleus with membrane – so definition of cell is still okay.???? Other parts of definition should go in the comments.

Final definition: A cell that is part of a plant and that has as its part a plant cell wall.

Comments: Be sure to add cross references to GO for definitions of cell and plant-type cell wall (their term).


* plant organ


New def: -A plant structure that is a functional unit, is a proper part of a plant and includes portions of tissues of at least two different types which derive from a common developmental path.

(reworded slightly for readability)

Comments: May include individual cell types that are not part of tissues. example: guard cells which are part of the leaf, idioblasts

"proper" refers to not being the whole plant Examples: stem, leaf, root

Note: in 2-11-10 talk, Barry Smith suggested having child terms of plant organ: simple, compound and complex plant organs- tabled for next discussion.

We agreed that the definition was okay as is.

We must remember to include cross products to terms referenced in definitions, such as the reference here to portion of plant tissue.

Comment from BS: Make sure the definitions are consistent with the cross products to the PO term 'portion of plant tissue'

Final Def'n: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.


* portion of plant tissue

New def: -A plant structure that consists of one or more cell types, organized into a structural and functional unit, and may include an intercellular matrix.

Comment: intercellular matrix- def: middle lamella- "layer of intercellular (between the cells) chiefly, pectic substances, cementing together the primary walls of contiguous cells ( ref: Evert, 3rd ed 2006)

We decided on a new defintion.

Final definition: Plant structure that has as its parts multiple cells and is a proper part of an organ.

Comment: These cells are organized into a structural unit, and may include an intercellular matrix.



2. Whole plant was redefined at the Ithaca meeting as "A plant structure which is a whole organism." and gametophyte and sporophyte were moved under it.

But after much discussion (see Minutes 2-16), it was decided that it would be better to move all terms that are currently under gametophyte and sporophyte under whole plant, and make gametophyte and sporophyte siblings of 'whole plant' These changes were made and we can look at the results in the PO-dev browser.

We had more discussion of the functionality of keeping gametophyte and sporophyte as siblings to whole plant, and agreed to keep them as they now are. We agreed that this structure would work, as long as we were careful of the "all-some" rule for all relationships. For example: if A is part_of B, then all instances of A must be part of B.

Pankaj still wanted to get rid of all child terms under gametophyte and sporophyte, but Ramona felt that there would be structures that are only part of one or the other and would need to be there. We agreed that our guiding principle should be to have general terms for all structures that would be part of whole plant, and that after that, we could make is_a chilren of those specific terms that are parts of gametophyte or sporophyte.

Our discussion raised the issue of needed a term such as root system, with children such as rhizoids, roots, and adventitious roots. Will also need some such term for shoots.


New Item: Presentations at national meetings this summer. Dennis and Ramona (with Ramona presenting) will prepare a oral presentation for the Botanical Society of America meeting this summer, for the Structural and Developmental Section. They will emphasize the use of the ontology as a vocabulary reference, and invite annotations. Maybe prepare a poster too? Laural and Pankaj will give a workshop at the ASPB (?) meeting at the same time. Group will send around abstracts for presentations before submitting.



Items 3 through 5 were tabled for the following discussion.


3. in vitro cultured cell, tissue and organ was moved out the Plant Structure class and made a separate class. def: "Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish."

4.New parent terms proposed by Ramona:

*cardinal organ part def: A plant structure that is a direct or immediate part of an organ that is often maximal(?) but is smaller than the organ itself. Examples include lobe, operculum, neck, petiole?, leaflet. -tabled for next discussion.


* collective plant structure def: A plant structure that is composed of multiple organs but is not an organ. (Maybe something about a bona fide boundary, some way to distinguish it from whole plant). Examples: flower, perianth, inflorescence. collective structure or compound organ? -tabled for next discussion.

5.Term request from TAIR for "gamete"- proposed (RW): add gamete to the ontology (is_a parent, plant cell), with sperm cell and egg cell as siblings under a common parent 'gamete'. -tabled for next discussion.

6. Assignment of Term numbers:

New term numbers are to be used for the terms that are being added.

Existing: Group identifier range (from-to)

TAIR: 0000001-0005000

Gramene/OSU (Jaiswal lab): 0005001-0010000

IRIS-IRRI: 0010001-0015000

MaizeGDB: 0015001-0020000

UMSL: 0020001-0025000

New numbers to be added:

0025001-0030000 PO Consortium (for terms we decide upon as a group)

0030001-0035000 NYBG ( New terms from Dennis and Ramona)

0035001-0040000 Cornell/MAG

Action item: Laurel will Update on POC webpage and PO wiki


7. Next conference call-

Dennis and Barry will not be available next Tuesday at the regular time, so Laurel will set up a Doodle poll to set up next week's meeting.