Minutes and agenda 3-9-10 - Revision history

Cooperl at 23:55, 10 March 2010

2010-03-10T23:55:48Z

Cooperl at 19:45, 10 March 2010

2010-03-10T19:45:43Z

Cooperl at 19:42, 10 March 2010

2010-03-10T19:42:23Z

Cooperl at 19:41, 10 March 2010

2010-03-10T19:41:15Z

Cooperl at 19:40, 10 March 2010

2010-03-10T19:40:25Z

Cooperl at 19:33, 10 March 2010

2010-03-10T19:33:19Z

Cooperl at 19:29, 10 March 2010

2010-03-10T19:29:51Z

Cooperl at 19:26, 10 March 2010

2010-03-10T19:26:23Z

Cooperl at 19:24, 10 March 2010

2010-03-10T19:24:48Z

Cooperl at 19:20, 10 March 2010

2010-03-10T19:20:32Z

← Older revision		Revision as of 23:55, 10 March 2010
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−	''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.	+	''We decided to keep 'in vitro plant structure' under 'plant structure' as it is, but delete "in vivo plant" structure, because defining it was problematic. It does not need to be obseleted since was never used. This goes back to the original format from before Ithaca meeting in December.

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 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.'''
+'''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 should not be part of the def'n, but put into the comments.''
+ Examples include lobe, operculum, neck, petiole, leaflet, to be put into the comments.''

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 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.
-At the 3-3-10 meeting, we decided to create two new parent terms directly under plant structure: "''in vitro'' cultured plant structure" and "''In vivo'' plant structure".
+At the 3-3-10 meeting, 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'''

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 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.
-Laurel proposed we either integrate the cultured terms, or leave them under 'plant structure' (as shown on the live browser, before the changes made at the Ithaca mtg.
+Laurel proposed we either integrate the cultured terms, or leave them under 'plant structure' (as shown on the live browser, before the changes made at the Ithaca mtg).
 She showed some examples of how cultured cells etc are dealt with in other ontologies and could not find any precedent for splitting the in vitro terms out in a separate class or namespace.

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 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)
-'''New definition: A plant structure that was derived from a part of a plant and involves microbe-free growth in a sterile environment.'''
+'''Final 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.''
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 '''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.
+Final def'n: An anatomical structure that is or was part of a plant, or was derived from a part of a plant.
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 '''4.gamete'''
-def'n: A plant cell that has half the chromosome complement of the sporophyte and is capable of fertilization to create a zygote.
+Final 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'
 ''Everyone agreed that this definition was okay as is. Item will be closed on SourceForge.''
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 ''Once everyone has a chance to review these changes and agrees that this definition is okay, then these items will be closed on SourceForge.''
 '''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).
+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.
 ''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

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 Needed to work on definition: A plant structure that is or was part of a plant that is growing ... (not ''in vitro'').
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 ''Once everyone has a chance to review these changes and agrees that this definition is okay, then these items will be closed on SourceForge.''
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 '''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.
+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'
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-''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.''
+''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).
 '''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'''

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 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)
-''' 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.'''''
+'''New definition: A plant structure that was derived from a part of a plant and involves microbe-free growth in a sterile environment.'''
 ''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.''
+Old name "in vitro cultured cell, tissue and organ" will be added as synonym. We decided to separate last part of definition.''
 '''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'').
+Needed to work on definition: A plant structure that is or was part of a plant that is growing ... (not ''in vitro'').
@@ Line 48: / Line 51: @@
 ''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.''

@@ Line 13: / Line 13: @@
 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.
 Laurel proposed we either integrate the cultured terms, or leave them under 'plant structure' (as shown on the live browser, before the changes made at the Ithaca mtg.
@@ Line 36: / Line 31: @@
 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)
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 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.
+Laurel proposed we either integrate the cultured terms, or leave them under 'plant structure' (as shown on the live browser, before the changes made at the Ithaca mtg.
-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.
+She showed some examples of how cultured cells etc are dealt with in other ontologies and could not find any precedent for splitting the in vitro terms out in a separate class or namespace.
 For example, From Drosophilia Flybase
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   Anatomical entity
      <-- anatomical entity in vitro
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-''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.''
+''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.''
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