Difference between revisions of "POC Conf. Call 9-04-12"
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Back to [[POC Meetings Minutes]] | Back to [[POC Meetings Minutes]] | ||
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| + | =Top levels of '''plant structure development stage''' branch= | ||
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| + | ''under construction'' | ||
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| + | current structure: [[File:psds081312.jpg]] | ||
| + | |||
| + | At the [[POC Conf. Call 8-14-12]], we had a discussion about whether or not it is necessary to mirror all the upper level terms from the PAE or just add the relevant parent categories needed for the classes such as "flower development" or "corolla development. Decided that it needed additional study and that for the mean time, we will develop the hierarchy with out them and compare the two approaches. | ||
| + | |||
| + | |||
| + | proposed structure without mirror of PEA branch: | ||
| + | |||
| + | =Fruit development stages for fruits and whole plants= | ||
| + | |||
| + | ''under costruction'' | ||
| + | |||
| + | ==existing whole plant development stage terms== | ||
| + | Current hierarchy: [[File:fruitstages081312.jpg]] | ||
| + | |||
| + | All of these definitions should be reworded to make it clear that they refer to development stages of a whole plant. Technically, saying that they are fruit formation stages does that, but it is not obvious to readers. Names should also be changed accordingly. | ||
| + | |||
| + | ''Agreed after some discussion. We will proposed names and revised definitions at a meeting in the near future.'' | ||
| + | |||
| + | ''Discussed how these stages are not identified by a single fruit but by averaging across the fruits on a plant. We may want to add a comment about this.'' | ||
| + | |||
| + | ''These terms will probably not work for plant that have asyncronous fruiting, like indeterminate tomatoes.'' | ||
| + | |||
| + | For development stages of fruits (rather than whole plants with fruits), see [[Items_for_future_meetings#Fruit development stage (PO:0001002) and subclasses]] | ||
| + | |||
| + | *'''FF.04 fruit size 70% to final size stage (PO:0007027):''' A fruit formation stage that spans the interval when a fruit has reached 70% of its final size to its final size. | ||
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| + | related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79 | ||
| + | |||
| + | ''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch'' | ||
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| + | ''Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)'' | ||
| + | |||
| + | ''Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)'' | ||
| + | |||
| + | ''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)'' | ||
| + | |||
| + | |||
| + | *'''FR.00 beginning of fruit ripening stage (PO:0007036)''': The stage at which fruit maturation begins. | ||
| + | |||
| + | ''Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour | ||
| + | |||
| + | ''Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison '' | ||
| + | |||
| + | |||
| + | *'''FR.01 early stage of fruit ripening (PO:0007001):''' The early stage in fruit ripening | ||
| + | |||
| + | related synonym: BBCH principal growth stage 83 | ||
| + | |||
| + | ''Add related synonym: middle of veraison | ||
| + | |||
| + | |||
| + | *'''FR.04 fruit ripening complete stage (PO:0007038):''' The stage at which fruit ripening is complete. | ||
| + | |||
| + | related synonym: BBCH principal growth stage 89 | ||
| + | |||
| + | ''Add related synonym: grape E-L stage: 38; Berries ripe for harvest'' | ||
| + | |||
| + | |||
| + | References: | ||
| + | |||
| + | Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00086.x/abstract link] | ||
| + | |||
| + | Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 [http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.1995.tb00085.x/abstract link] | ||
| + | |||
| + | [http://en.wikipedia.org/wiki/BBCH-scale_%28grape%29 BBCH grapes] | ||
| + | |||
| + | ==Fruit development stage (PO:0001002) and subclasses== | ||
| + | This term is a subtype of collective plant structure development stage, but will move to multi-tissue plant structure development stage. There are currently no subclasses for this term. | ||
| + | |||
| + | current def.: | ||
| + | |||
| + | '''fruit development stage (PO:0001002):''' Stages of development of a fruit defined by characteristic morphological, structural, histological or other visible features. | ||
| + | |||
| + | '''proposed def.:''' A multi-tissue plant structure development stage (PO:new term) that has as primary participant a fruit (PO:0009001). | ||
| + | |||
| + | comment: (from original def.) ''Defined by characteristic morphological, structural, histological or other visible features.'' May have as part a seed development stage (PO:0001170). | ||
| + | |||
| + | New sub-classes based on whole plant stages from above? | ||
| + | |||
| + | ''We agreed that we should develop more specific subclasses for this term, but it may not be easy. PJ said that the reason there are not subclasses now is because there are not existing terminologies for comparing fruit development across all species.'' | ||
| + | |||
| + | ''After call: DWS suggested that we may be able to describe diverse types of fruit development by starting with the development of different parts of the fruit, like the mesocarp or endocarp, and then showing how development of different tissues leads to different types of fruits. Also, we could start with fertilization stage as a first stage in all fruit development (with parthenocarpy as an exception).'' | ||
| + | |||
=Upcoming meetings and Presentations 2012-2013:= | =Upcoming meetings and Presentations 2012-2013:= | ||
Revision as of 00:34, 1 September 2012
POC meeting, Webex Conference Call; Date: Tuesday Sept 4th, 2012 10am PDT/1pm EDT
In attendance:
POC members:
Absent:
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_8-14-12?
Back to POC Meetings Minutes
Top levels of plant structure development stage branch
under construction
current structure: 
At the POC Conf. Call 8-14-12, we had a discussion about whether or not it is necessary to mirror all the upper level terms from the PAE or just add the relevant parent categories needed for the classes such as "flower development" or "corolla development. Decided that it needed additional study and that for the mean time, we will develop the hierarchy with out them and compare the two approaches.
proposed structure without mirror of PEA branch:
Fruit development stages for fruits and whole plants
under costruction
existing whole plant development stage terms
Current hierarchy: 
All of these definitions should be reworded to make it clear that they refer to development stages of a whole plant. Technically, saying that they are fruit formation stages does that, but it is not obvious to readers. Names should also be changed accordingly.
Agreed after some discussion. We will proposed names and revised definitions at a meeting in the near future.
Discussed how these stages are not identified by a single fruit but by averaging across the fruits on a plant. We may want to add a comment about this.
These terms will probably not work for plant that have asyncronous fruiting, like indeterminate tomatoes.
For development stages of fruits (rather than whole plants with fruits), see Items_for_future_meetings#Fruit development stage (PO:0001002) and subclasses
- FF.04 fruit size 70% to final size stage (PO:0007027): A fruit formation stage that spans the interval when a fruit has reached 70% of its final size to its final size.
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79
Add related synonym: BBCH principle growth stage 77; Berries beginning to touch
Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)
Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)
Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)
- FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.
Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour
Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison
- FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening
related synonym: BBCH principal growth stage 83
Add related synonym: middle of veraison
- FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.
related synonym: BBCH principal growth stage 89
Add related synonym: grape E-L stage: 38; Berries ripe for harvest
References:
Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 link
Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 link
Fruit development stage (PO:0001002) and subclasses
This term is a subtype of collective plant structure development stage, but will move to multi-tissue plant structure development stage. There are currently no subclasses for this term.
current def.:
fruit development stage (PO:0001002): Stages of development of a fruit defined by characteristic morphological, structural, histological or other visible features.
proposed def.: A multi-tissue plant structure development stage (PO:new term) that has as primary participant a fruit (PO:0009001).
comment: (from original def.) Defined by characteristic morphological, structural, histological or other visible features. May have as part a seed development stage (PO:0001170).
New sub-classes based on whole plant stages from above?
We agreed that we should develop more specific subclasses for this term, but it may not be easy. PJ said that the reason there are not subclasses now is because there are not existing terminologies for comparing fruit development across all species.
After call: DWS suggested that we may be able to describe diverse types of fruit development by starting with the development of different parts of the fruit, like the mesocarp or endocarp, and then showing how development of different tissues leads to different types of fruits. Also, we could start with fertilization stage as a first stage in all fruit development (with parthenocarpy as an exception).
Upcoming meetings and Presentations 2012-2013:
NSF Plant Genome PIs Meeting
Arlington, VA, September 6-7, 2012
Need 2 pager and poster
Genome Informatics 2012
September 6th-9th Robinson College, Cambridge, UK
JP is attending and submitted a poster representing the PO
PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012
For more information see the wiki page: Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012
Dates: Sept. 13-15th
The focus of the workshop will be on mostly development stages and traits for the crop plants
Phenotype RCN meeting, Oct 26-29th 2012
Asilomar, CA
PAG 2013, San Diego, CA; January 12-16, 2013
- The PO will be running a workshop again- Need suggestions for speakers.
PJ: Suggestions- someone from GO in Berkeley, Nigam Shaw
- Want to focus on applications of the ontologies
- Can we offer something to entice the speakers, in addition to the $100 discount on registration offered by the conference?
PJ will check with DW about Gramene involvement
PRO-PO-GO meeting, ~May 2013
Location: Buffalo, NY
Goals:
1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination 2. To identify potentially fruitful applications which such enhanced coordination might bring 3. To enhance the Protein Ontology treatment of plant-related proteins 4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages 5. To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]
A first set of participants is as follows:
PO Consortium members: Pankaj Jaiswal, Dennis Stevenson, Barry Smith (Buffalo) who else?
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)
