POC Conf. Call 10-2-12

POC meeting, Webex Conference Call; Date: Tuesday Oct 2nd, 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=68762282&rKey=e8c8ec38d231d79d

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68762282&rKey=8b2c0631206a46f

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_9-25-12? Not additions, deletions, or changes.

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Ramona's last day :-(

As most of you know, Ramona is leaving the NYBG to work for iPlant. Her last day at the Garden will be Wednesday, October 17th. She will be available afterwards to complete work on the manuscripts in progress (paper on plant anatomical entities and paper on development stages for Physiologia Plantarum).

Update from Cornell

Ale has been in communication with Bob Turgeon and got comments from him on phloem terms. He had some questions and Ale will have more details next week, as well as some updated definitions.

Fruit development stages for whole plants

whole plant fruit formation stage

Was 5 fruit formation stage (PO:0007042).

At the POC meetings on 8-14-12 and 9-4-12, we agreed that this term was originally created to describe a whole plant development stage during which fruit is being formed. We agreed to change the name and definition accordingly. Also discussed on 9-25-12.

New proposed name: whole plant fruit formation stage

New proposed def.: 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 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 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. Although the use of stages like milk or particular fruit sizes (see synonyms) properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.

has_part fruit development stage (PO:0001002) This could be made more specific, after we add specific types of fruit development stages.

As specified in the PO definition of fruit, initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then we can refer to those stages in the definition of this stage.

This definition will probably change slightly as we work on the new and revised terms for fruit development stages (for example, we may change definition to refer to new stages called fruit initiation stage and fruit ripening stage), but can we accept the new name and provisional definition?

whole plant fruit ripening stage

Was 6 ripening stage (PO:0007010).

At the POC meetings on 9-4-12, we agreed that this term was originally created to describe a whole plant development stage during which fruit is ripening. We agreed to change the name and definition accordingly.

New proposed name: whole plant fruit ripening stage.

New proposed def.: A sporophyte reproductive stage (PO:0007130) that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) is begins the process of ripening (GO:0009835) and ends when (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, whichever comes first.

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). 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 annual 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 perennial species may have one fruit ripening stage for each growing season, followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, the plant may remain 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 development stage (PO:id) has ended. Although the use of stages like dough or particular ripening stages (see synonyms) properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.

has_part fruit development stage (PO:0001002) (This could be made more specific, after we add specific types of fruit development stages.)

subset for angiosperms

This definition may change slightly as we work on the new and revised terms for fruit development stages.

Name changes

We have removed the numbers from the names of 5 fruit formation stage (PO:0007042) and 6 ripening stage (PO:0007010) (see above). Suggest that we change the names of their sibling terms, to be consistent in not numbering them:

3 inflorescence detectable stage (PO:0007047) change name to whole plant inflorescence detectable stage

4 flowering stage (PO:0007016) change name to whole plant flowering stage.

Also suggest minor changes to the definition of PO:0007016, whole plant flowering stage:

Current def.: The stage at which any flower(s) on the plant are open.

Comment: This stage refers to the whole plant.

New proposed def.: A sporophyte reproductive stage (PO:0007130) during which a flower (PO:0009046) on a whole plant (PO:0000003) is open.

Comment: This term is to be used for a stage of development of a whole plant. For the stages of development of an individual flower, see flower development stage (PO:0007615).

This definition needs work (e.g., not all flowers open), so this change is just for triage. We can come back to it later.

We have already done extensive work on the definition of 3 inflorescence detectable stage.

Change to gametophyte development stage

postponed until next week

Flower app under development at NYBG

If we have time at this week's meeting, RW can preview the app we are developing for our outreach component.

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)