POC Conf. Call 10-16-12

POC meeting, Webex Conference Call; Date: Tuesday Oct 16th, 2012 10am PDT/1pm EDT

In attendance:

POC members: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Ramona Walls (NYBG)

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=69148902&rKey=02baa0c6ebef843d

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=69148902&rKey=43711462fbe1ed02

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-9-12? No additions, deletions, or changes.

Back to POC Meetings Minutes

Update from Cornell

Since last week, we have done 12 slides and 159 images

I need to finish a couple of manuscripts for my other two grants due at the end of this month, but after that I have already separate a block of time for editing slides.

-Update of schedule:

• In the field from December 1 to the 22, no email access
• In New Zealand from January 9th to 24th (no or very limited access after Jan 15th)

PJ will work with MAG to create a mirror of the image database at OSU in early November. Images are ready to share at any time.

MAG has been adding key words and RW adds PO ids where appropriate.

phloem terms

Bob Turgeon sent comments on the definitions for companion cells. RW will add his comments to the SF tracker item.

SIA v0.2.1 Released

JP has packaged and uploaded a new version (v0.2.1) 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!

PO "Aspect" vs. "Ontology Branch"

BS was concerned about the heading "Aspect" on the PO term pages, because it has a very specific meaning in library science. We should change it to say "Ontology branch". May need to wait for a release, because it is part of the database.

GO still uses "ontology". They should perhaps switch that as well.

Updated to "Ontology Branch" on po-dev on the term pages and "Filter tree view" in browser.

Can be updated on live and beta sites once it is approved.

The use of "Aspect" is widely adopted throughout our system. In June 2012, RW went through a number of the webpages and changed the references to "ontology" to "Aspect", so those papges will have to be updated as well. In addition, column 9 on the association file is "Aspect. Not sure is this is an issue. Go still uses 'Ontology' on their browser"

New fruit development stages for individual fruits

Last week we agreed to add a term for fruit development stage (PO:0001002).

view on dev browser

We had some discussion of whether or not a seed development was part of fruit development, or a separate but interdependent process. Even though some fruits will not develop without seed development, they are still separate processes.

Should change comment of fruit developments stage to say it may depend on and occur concurrently with a seed development stage.

New proposed subclasses

fruit formation stage (PO:0025501)

We worked on this term a bit last week. Here is a modified definition, based on our discussion.

Proposed def.: A fruit development stage (PO:0001002) that begins immediately after the formation of the first plant zygote (PO:0000423) contained in the relevant fruit (PO:0009001) and ends the initiation of the fruit ripening stage (PO:0025502) of that fruit.

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. For the development stage of a whole plant (PO:0000003), use whole plant fruit formation stage (PO:0007042).

Should add a reference PO:0004505 fertilized ovule stage, is_a seed development stage. Say something like the fruit formation begins immediately after the first fertilized ovule stage in a seed that is contained in the relevant fruit.

The definition above was modified as we were discussing it.

Should reference fertilization in GO. We have used and will use a lot of GO processes for defining stages, so creating links will be an ongoing process.

new subclasses of fruit formation stage

These are similar to the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits. Includes a new stage for fruit initiation, which is probably not needed for whole plants.

fruit initiation stage (PO:0025503): A fruit formation stage (PO:0025501) that begins immediately after the formation of the first plant zygote (PO:0000423) contained in the relevant fruit (PO:0009001) and ends when the plant cells (PO:0009002) in the fruit begin to divide or expand.

Comment: The fruit initiation stage may begin without fertilization or formation of a plant zygote (PO:0000423) in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This stage may be very brief. 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).

Add comment as per fruit formation stage.

What about fruits that don't grow after fertilization? I guess they go right to ripening stage? Do we need a comment to this effect? Maybe say it ends when cells start to divide or expand or senesce, if it can go directly into the ripening stage.

Many species, for example those with achenes, have fruits that don't grow after fertilization, but do have ripening processes and go directly from the initiation stage to the ripening stage.

Note from last week: We need to coordinate with GO about terms like "growth".

fruit size up to 10% stage (PO:0025504): A fruit formation stage (PO:0025501) that begins when the plant cells (PO:0009002) in a fruit (PO:0009001) begin to divide or expand, and ends when the fruit has reached 10% of its final size.

Comment: 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).

Maybe add to comment of these terms that they "are not relevant for fruits that do not grow after fertilization". This is referring to fruits that put energy into the development of the see but not the ovary wall.

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 a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).

Changes were made to the definition above.

Link to GO page for fruit ripening. Note that we already worked on this term with GO.

Note that I have not yet proposed any subclasses for this term. Also, I have not yet addressed development stages for any of the parts of fruits, such as pericarp, which could be used to help define more specific stages for the ripening of the whole fruit.

The subclasses for whole plant fruit ripening stages are very vague and have circular definitions. Suggest that PO work on stages of individual fruit ripening and then tackle the whole plant ripening stages.

Could consider using percent cutoffs (as with sizing) for fruit ripening. How do you define 10% or 50% ripe, though? It is most important to map species-specific values to terms like early, middle, and late fruit ripening stage.

Fruit development stages for whole plants

whole plant fruit development stage (PO:0025500)

We didn't have time to discuss these this week, but the definitions below incorporate the concerns and discussions from earlier meetings.

Continued from POC Conf. Call 10-9-12

new proposed defintion: A sporophyte reproductive stage that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) that is not currently participating in a whole plant fruit development stage begins a fruit initiation stage (PO:0025503), 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: A whole plant fruit development stage begins with the beginning of whole plant fruit formation stage (PO:0007042) and ends with the end of a whole plant fruit ripening stage (PO:0007010). A whole plant fruit development stage can be thought of as a fruiting cycle for a whole plant that begins when the plant starts to produce fruit and ends when all of the fruit on the plant are ripe, unless the plant enters a sporophyte senescent stage or sporophyte dormant stage before all the fruit is ripe. 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. Some plants retain their fruit after ripening and through dormancy, and thus may begin a new whole fruit development stage while fruits from the previous whole plant fruit development stage are still present.

whole plant fruit formation stage (PO:0007042)

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) that is not currently participating in a whole plant fruit development stage begins a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (PO:0007010).

Comment: Precedes a whole plant fruit ripening stage (PO:0007010). 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 formation 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.

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

On next week's agenda: POC_Conf._Call_10-23-12#Subclasses_of_whole_plant_fruit_formation_stage_.28PO:0007042.29

whole plant fruit ripening stage (PO:0007010)

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 (PO:0007042). 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 fruit ripening (GO:0009835), 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, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages 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 synonyms like "10-dough stage in sorghum" 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.

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

On next week's agenda: POC_Conf._Call_10-23-12#Subclasses_of_whole_plant_fruit_ripening_stage_.28PO:0007010.29

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

• 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?

website and registration are now open: Biocuration 2013

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)

Next meeting scheduled for POC_Conf._Call_11-6-12 at 10am PDT/1pm EDT

No meeting next week.