Difference between revisions of "POC Conf. Call 9-04-12"
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In attendance: | In attendance: | ||
| − | POC members: | + | POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY) |
| − | Absent: | + | Absent:Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab), Justin Elser (OSU), Justin Preece (OSU) |
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| − | Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_8-14-12]]? | + | Any changes or corrections (additions/deletions, etc) needed in the minutes from the [[POC_Conf._Call_8-14-12]]? ''No additions, deletions, or changes.'' |
Back to [[POC Meetings Minutes]] | Back to [[POC Meetings Minutes]] | ||
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=Update from Cornell= | =Update from Cornell= | ||
| − | Added 25 more slides and 500 more images to the | + | Added 25 more slides and 500 more images to the CUPAC database |
=Fruit development stages for whole plants= | =Fruit development stages for whole plants= | ||
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We also have requests for new synonyms for these stages for grape. | We also have requests for new synonyms for these stages for grape. | ||
| − | Also, we will need to make similar changes to 6 ripening stage (PO:0007010), 4 flowering stage (PO:0007016), and 3 inflorescence detectable stage (PO:0007047), and their subclasses. (see | + | Also, we will need to make similar changes to 6 ripening stage (PO:0007010), 4 flowering stage (PO:0007016), and 3 inflorescence detectable stage (PO:0007047), and their subclasses. (see [[Items_for_future_meetings#Sporophyte_reproductive_stages]]) |
===Upper level term: 5 fruit formation stage (PO:0007042)=== | ===Upper level term: 5 fruit formation stage (PO:0007042)=== | ||
Revision as of 16:34, 5 September 2012
POC meeting, Webex Conference Call; Date: Tuesday Sept 4th, 2012 10am PDT/1pm EDT
In attendance:
POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY)
Absent:Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab), Justin Elser (OSU), Justin Preece (OSU)
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_8-14-12? No additions, deletions, or changes.
Back to POC Meetings Minutes
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=67965547&rKey=03f922d906861840
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=67965547&rKey=1cae0653c167aeb7
Update from Cornell
Added 25 more slides and 500 more images to the CUPAC database
Fruit development stages for whole plants
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.
For development stages of fruits (rather than whole plants with fruits), see below (POC_Conf._Call_9-04-12#Fruit development stage (PO:0001002) and subclasses)
We also have requests for new synonyms for these stages for grape.
Also, we will need to make similar changes to 6 ripening stage (PO:0007010), 4 flowering stage (PO:0007016), and 3 inflorescence detectable stage (PO:0007047), and their subclasses. (see Items_for_future_meetings#Sporophyte_reproductive_stages)
Upper level term: 5 fruit formation stage (PO:0007042)
current def.: Formation of the seed-bearing structure after flowering.
proposed new name and definition:
fruit formation stage of whole plant (PO:0007042): A sporophyte reproductive stage (PO:0007130) that begins with the initiation of the first fruit (PO:0009001) of a growing season and ends with the initiation of a fruit ripening stage of whole plant (PO:0007010).
Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit formation stage in its life, while a perennial may have one fruit formation stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun.
has_part fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)
subset for angiosperms
Upper level term: 6 ripening stage (PO:0007010)
current def.: Maturation of the fruit.
"GO:ripening is defined as a type of senescence. Should the term ripening be used only for fleshy fruits? Fruit drying also probably involves cell death, so perhaps it is type of ripening as well.
proposed new name and definition:
fruit ripening stage of whole plant (PO:0007042): A sporophyte reproductive stage (PO:0007130) during which a fruit (PO:0009001) on a whole plant (PO:0000003) is undergoing ripening (GO:0009835).
comment: This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An annual plant will only have one fruit ripening stage in its life, which is generally followed by a sporophyte senescent stage (PO:0007017), while a perennial may have one fruit ripening stage for each growing season. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant has begun.
has_part fruit development stage (PO:0001002) (could be more specific about this, after we add specific types of fruit development stages)
subset for angiosperms
Subclasses of fruit formation stage of whole plant (PO:0007042)
FF.00 fruit size up to 10% stage (PO:0007032)
current def.: A fruit formation stage that begins with the formation of a zygote and ends when the fruit has reached 10% of its final size.
comment: This fruit development stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This term can only be used of the final size of the fruit is known.
proposed new name and definition:
fruit formation stage of whole plant when fruit size up to 10%: A fruit formation stage of whole plant (PO:0007042) that begins with the formation of the first plant zygote (PO:0000423) of a growing season and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.
comment: This stage may begin without fertilization or formation of a plant zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
FF.01 fruit size 10 to 30% stage (PO:0007009)
current def.: A fruit formation stage that spans the interval when a fruit has reached 10% to 30% of its final size.
comment: This term can only be used of (sic) the final size of the fruit is known.
proposed new name and definition:
fruit formation stage of whole plant when fruit size 10 to 30%: A fruit formation stage of whole plant (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
FF.02 fruit size 30 to 50% stage (PO:0007029)
current def.: A fruit formation stage that spans the interval when a fruit has reached 30% to 50% of its final size.
comment: This term can only be used of the final size of the fruit is known.
proposed new name and definition:
fruit formation stage of whole plant when fruit size 30 to 50%: A fruit formation stage of whole plant (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
FF.03 fruit size 50 to 70% stage (PO:0007007)
current def.: A fruit formation stage that spans the interval when a fruit has reached 50% to 70% of its final size.
comment: This term can only be used of the final size of the fruit is known.
proposed new name and definition:
fruit formation stage of whole plant when fruit size 50 to 70%: A fruit formation stage of whole plant (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
FF.04 fruit size 70% to final size stage (PO:0007027)
current def.: A fruit formation stage that spans the interval when a fruit has reached 70% of its final size to its final size.
comment: This term can only be used of the final size of the fruit is known.
proposed new name and definition:
fruit formation stage of whole plant when fruit size 70% to final size: A fruit formation stage of whole plant (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79
New synonyms for grapes
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)
Subclasses of fruit ripening stage of whole plant (PO:0007010)
The current definitions are very vague and circular! For now, proposed just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages.
FR.00 beginning of fruit ripening stage (PO:0007036)
current def.: The stage at which fruit maturation begins.
proposed new name and definition:
beginning of fruit ripening stage of whole plant: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
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)
current def.: The early stage in fruit ripening
related synonym: BBCH principal growth stage 83
proposed new name and definition:
early fruit ripening stage of whole plant: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
Add related synonym: middle of veraison
FR.02 mid stage of fruit ripening (PO:0007031)
current def.: The stage when fruit ripening is midway.
mid fruit ripening stage of whole plant: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
FR.03 late stage of fruit ripening (PO:0007050)
current def.: The late stage of fruit ripening.
late fruit ripening stage of whole plant: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
FR.04 fruit ripening complete stage (PO:0007038)
current def.: The stage at which fruit ripening is complete.
fruit ripening complete stage of whole plant: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
related synonym: BBCH principal growth stage 89
Add related synonym: grape E-L stage: 38; Berries ripe for harvest
References for grape terms:
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 was a subtype of collective plant structure development stage, but should move to 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 plant structure development stage (PO:0009012) that has as primary participant a fruit (PO:0009001).
comment: 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?
After last week's 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.
We could start with fertilization stage as a first stage in all fruit development (with parthenocarpy as an exception).
Should include a stage for fruit ripening, as this is common across all fruits.
Fertilization, expansion and differentiation, ripening and/or drying.
New synonyms for anatomy terms for grapes
- fruit (PO:0009001):
narrow synonym: berry
- pericarp (PO:0009084)
add narrow synonym: grape berry skin
fruit storage parenchyma (PO:0025037): A portion of storage parenchyma that is part of a fruit.
add narrow synonym: grape berry flesh, grape berry pulp
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
CROP
PO*
GO
PRO
TO*
EO*
ENVO
PATO
Taxonomy- NCBI has most of the plants, causal organisms not sufficient
GAZ
Plant IDO*
Plant Diseases*
CHEBI
- to be developed by CROP group
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)
