POC Conf. Call 9-04-12

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

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)

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.

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 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.

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%:

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%:

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%:

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:

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)

subclasses of fruit ripening stage of whole plant (PO:0007010)

• 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

BBCH grapes

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.

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:

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)