POC Conf. Call 10-9-12

POC meeting, Webex Conference Call; Date: Tuesday Oct 9th, 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_10-2-12?

Back to POC Meetings Minutes

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=68952927&rKey=8ea2a20393db7805

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SIA v0.2.1 Released

Note the update to v0.2.1 already. I solved a nagging issue and enhanced the data storage structure today. If you downloaded v0.2 yesterday, please upgrade to v0.2.1 before continuing to try out SIA. Thanks! - JP

Justin Preece has packaged and uploaded a new version of SIA for Mac and Linux (Windows still in progress). This version is fit for public consumption, although it is still very much beta software with lots of opportunity for improvement. Several technical issues have been fixed and a few small enhancements have been made.

• Our lab site post: http://jaiswallab.cgrb.oregonstate.edu/software#SIA
• Downloads: http://files.cgrb.oregonstate.edu/Jaiswal_Lab/sia/v0.2.1/

It would be great if folks on today's call with access to Linux and Mac machines could give the installation instructions a test drive. Feel free to let me know if anything seems amiss. If you want to report any bugs or request new features, just send an email to <sia-support@palea.cgrb.oregonstate.edu>

JP will coordinate the appropriate PO emails and web site announcements with Lol. Thanks!

Update from Cornell

Ale has been in communication with Bob Turgeon and got comments from him on phloem terms. fill in details...

Change to gametophyte development stage

This change is urgent, because we need to address this in the manuscript in prep.

gametophyte development stage (PO:0028003) is currently defined as "A whole plant development stage that has as primary participant a whole plant during the interval between meiosis or apospory and its death or fertilization."

I think the last part about fertilization is misleading, because it suggests that the gametophyte stage could end in any plant with fertilization. Many gametophytic plants continue to live (and nourish the sporophyte) long after fertilization. In seed plants, the gametophyte does not exactly die after fertilization, but is transformed. I suggest we add something to the comment to help explain this, but keep the definition simpler.

New proposed definition: A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between meiosis or apospory and its death.

New addition to comment (rest stays the same): In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.

Fruit development stages for whole plants

whole plant fruit development stage (PO:0025500)

New term

proposed defintion: A sporophyte reproductive stage that begins when a fruit (PO:0009001) enters its fruit initiation stage (PO:0025503) on a whole plant (PO:0000003) that does not have any other fruits as part, and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

Comment: Includes whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.

whole plant fruit formation stage (PO:0007042)

postponed to future meeting

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (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 iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit development stages during its life. 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. Although the use of synonyms like 07-milk stage in rice properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.

Is it better to use whole plant fruit formation stage has_part fruit formation stage (new term, see below) or fruit formation stage part_of whole plant fruit formation stage?? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.

whole plant fruit ripening stage (PO:0007010)

postponed to future meeting

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

comment: Succeeds a whole plant fruit formation stage. 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 ripening stage (PO:0025502). Although individual fruits are undergoing ripening (which is a type of senescence) during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, followed by a sporophyte senescent stage (PO:0007017), as in case (1). A semelparous species may have one fruit ripening stage for each whole plant fruit developments stage (PO:0025500), followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, a plant may have multiple fruit development stages and in the sporophyte reproductive stage (PO:0007130) after all fruit has ripened, without entering dormancy or senescence, as in case (3). 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 whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of stages like dough stage properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.

Is it better to add whole plant fruit ripening stage has_part fruit ripening stage or fruit ripening stage has_part whole plant fruit ripening stage? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.

New fruit development stages

fruit development stage (PO:0001002)

def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).

comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:0025500) or its subclasses.

New proposed subclasses

still need to create SF tracker items and add xref to terms

fruit formation stage (PO:0025501)

Proposed def.: A fruit development stage (PO:0001002) that being with the formation of the plant zygote (PO:0000423) that is contained in that fruit and ends when its fruit ripening stage (PO:0025502) begins.

comment: A fruit formation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage applies to an individual fruit (PO:0009001). For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).

new subclasses of fruit formation stage

These are the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits. I also added a new stage for fruit initiation.

fruit initiation stage (PO:0025503): A fruit formation stage (PO:0025501) that begins with the formation of the plant zygote (PO:0000423) that is contained in that fruit (PO:0009001) and ends when the plant cells (PO:0009002) in the fruit begin to divide or expand (add GO terms).

Comment: The fruit initiation stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage ends as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).

Apply similar changes as for PO:0025501. Copy comment to PO:0025501.

fruit size up to 10% stage (PO:0025504): A fruit formation stage (PO:0025501) that begins after a fruit initiation stage (PO:0025503), and ends when the fruit (PO:0009001) has reached 10% of its final size.

Comment: Begins as soon as plant cells (PO:0009002) in a developing fruit begin to divide or expand. Succeeds a fruit initiation stage (PO:0025503) and proceeds a fruit size 10 to 30% stage (PO:0025505). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage up to 10% (PO:0007032).

fruit size 10 to 30% stage (PO:0025505): A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 10% to 30% of its final size.

Comment: Succeeds a fruit size up to 10% stage (PO:0025504) and proceeds a fruit size 30 to 50% stage (PO:0025506). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 10 to 30% (PO:0007009).

fruit size 30 to 50% stage (PO:0025506): A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 30 to 50% of its final size.

Comment: Succeeds a fruit size 10 to 30% stage (PO:0025505) and proceeds a fruit size 50 to 70% stage (PO:0025507). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 30 to 50% (PO:0007029).

fruit size 50 to 70% stage (PO:0025507): A fruit formation stage (PO:0025501) that spans the interval when a fruit (PO:0009001) has reached 50 to 70% of its final size.

Comment: Succeeds a fruit size 30 to 50% stage (PO:0025505) and proceeds a fruit size 70% to final size stage (PO:0025508). This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 50 to 70% (PO:0007007).

fruit size 70% to final size stage (PO:0025508): A fruit formation stage (PO:0025501) that spans begins when a fruit (PO:0009001) has reached 70% of its final size and ends when a fruit has reached its final size and a fruit ripening stage (PO:0025502) begins.

Comment: Succeeds a fruit size 50 to 70% stage (PO:0025507) and proceeds a fruit ripening stage. This term can only be used if the final size of the fruit is known. This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage 70% to final size (PO:0007027).

fruit ripening stage

Proposed def.: A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).

Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).

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

See SF tracker for FF.00 fruit size 10% and sibling terms

postponed to future meeting

At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.

What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.

FF.00 fruit size up to 10% stage (PO:0007032)

proposed new name and definition:

whole plant fruit formation stage up to 10%: A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% 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 is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504).

FF.01 fruit size 10 to 30% stage (PO:0007009)

proposed new name and definition:

whole plant fruit formation stage 10 to 30%: A whole plant fruit formation stage (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 is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505).

FF.02 fruit size 30 to 50% stage (PO:0007029)

proposed new name and definition:

whole plant fruit formation stage 30 to 50%: A whole plant fruit formation stage (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 is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506).

FF.03 fruit size 50 to 70% stage (PO:0007007)

proposed new name and definition:

whole plant fruit formation stage 50 to 70%: A whole plant fruit formation stage (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 is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).

FF.04 fruit size 70% to final size stage (PO:0007027)

proposed new name and definition:

whole plant fruit formation stage 70% to final size: A whole plant fruit formation stage (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: Succeeded by a whole plant fruit ripening stage (PO:0007010). 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 is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).

related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79

Add 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 whole plant fruit ripening stage (PO:0007010)

postponed to future meeting

The current definitions are very vague and circular! For now, propose 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 at some point.

FR.00 beginning of fruit ripening stage (PO:0007036)

current def.: The stage at which fruit maturation begins.

proposed new name and definition:

whole plant beginning of fruit ripening stage: 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:

whole plant early fruit ripening stage: 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.

whole plant mid fruit ripening stage: 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.

whole plant late fruit ripening stage: 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.

whole plant fruit ripening complete stage: 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

Upcoming meetings and Presentations 2012-2013:

Phenotype RCN meeting, Oct 26-29th 2012

Asilomar, CA

LC is going and has been working with LM to compile EQ statments to describe ~100 rice mutants. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.

The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs.

PAG 2013, San Diego, CA; January 12th - 16th, 2013

• Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6

We will be running a workshop focusing on:

Applications of Ontologies for Plant and Animal Genomics

Three speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud.

• PJ present the Ref Plant Ontology Vision?

• Would like to invite someone from Textpresso and AgriGO as these are applications that would attract a number of people.

from 9/4- PJ: Suggestions- someone from GO in Berkeley, e.g. Nigam Shaw

• 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.

Deadline for computer demo- Nov 1st

I would imagine a SIA demo would be appropriate. - JP

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.

possible venue for CROP white paper?

PRO-PO-GO meeting, May 2013

Location: Buffalo, NY

Tentative Dates: May 8-9th or May 15-16th, 2013.

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]

Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

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