POC Conf. Call 9-04-12

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

New proposed name: whole plant fruit formation stage

Slightly modified definition: 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 beginning of a whole plant fruit ripening stage (PO:0007010).

Maybe refer to initiation of first fruit ripening, instead of fruit ripening stage?

Some discussion of this as a population measure: If you want to apply this to a population, you may choose the point when, e.g., 50% of the plants have initiated fruit. BS suggested that this should be defined for an individual plant, and have population terms defined separately.

Initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then refer to those in these definitions.

For gymnosperms, we could have terms like whole plant strobilus development stage. Seed development stage should apply to gymnos as well as angiosperms.

Do we want a parent for both of these terms: "whole plant fruit development stage"? This would match more closely to fruit development stage (PO:0001002).

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

Add comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.

Modified name: whole plant fruit ripening stage.

Note: the different fruits on a plant may be in different stages, but the whole plant can only be in one stage.

When does the ripening stage end? For annuals, ripening stage is followed by senescence of whole plant in annuals, but for perrenials, maybe different. We need to incorporate this into the definition.

PJ: Some pear varieties do not ripen on the plant. Have to be picked and treated. In that case, the plant never enters the whole plant fruit ripening stage, but the individual fruits to.

We be good to tie this to seed development. Make the connection as part of the fruit development stages, and then link fruit stages to whole plant stages. Seeds may regulate development of fruit. Interaction between progeny and maternal tissue.

Subclasses of fruit formation stage of whole plant (PO:0007042)

Modify names slightly for all of these (see below). Change definitions to use updated name of parent term.

What if fruits vary in size? You can still judge what 50 or 70% of final size is, if size variation is known.

What about plants with asynchronous fruit development? Do we need to develop whole plant growth stages for these types of plants. RW and MAG will talk to Naama about this.

We need to make it clear for all these stages that we are dealing with the FMA calls a cannonical plant, that is, a typical plant. Also, when we talk about final fruit size being known, that implies that the phenotype of a given genotype is well known. Need to make these points in the paper.

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.

new name: whole plant fruit formation stage up to 10%

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.

new name: whole plant fruit formation stage 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%: 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.

new name: whole plant fruit formation stage 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%: 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.

new name: whole plant fruit formation stage 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: 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 name: whole plant fruit formation stage 70% to final size

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)

Will post these on SF so we can work on them at a later meeting.

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

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.

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

BS suggested that PJ create a web/wiki page (a one page document) describing his plans for the CROP initiative. At a minimum, it should include a list of the ontologies that will be used (see below), the names of the responsible person for each ontology, and some rules governing their development/participation in CROP.

Most of the agenda on Thursday is taken up with participants presenting what they work on. LC should please send BS her material on the PO and TO. BS will speak on Friday morning. LC will set up a Webex so that other members of the PO group can listen in remotely.

For Friday morning: BS would like to lay down some suggested rules, and then have discussion of those rules with the group. PJ: If we want to get funding from the plant genome panel, the motivation (biological questions) has to be closely connected to crop improvement, genomics, and genetics, not just ontology.

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

BS wanted to know if there will be any work on nutrient genomics. PJ said their would be things like "vitamin A content in grain", which will be a trait, with vitamin A coming from ChEBI.

List of plant diseases is being worked on. Participants are familiar with the disease so it is easy to develop a list of them. Biggest limitation with disease ontology is a good taxonomy for the causal organisms.

Link to TO paper on CROP workshop page.

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?

• Need to submit list of speakers by November 1, 2012.

PJ will check with DW about Gramene involvement

PRO-PO-GO meeting, May 15, 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), Chris Mungall (Berkeley) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)