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.
Back to POC Meetings Minutes
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).
RW will be moving to iPlant to work as a "Scientific Analyst" interfacing between the plant scientist community and the on programmers and developers and infrastructure at iPlant to help meet challenges in cyber infrastructure. Focusing on Plant Ecology within the TOL division to bring in large datasets. e.g. Traitnet
Plan on who will be continuing the work at NYBG- TBA
RW is interested in keeping in touch and helping the PO interact with iPlant and others. Example Sandy Knapp is interested in writing a grant about ontologies for plant taxonomy, which will depend upon the PO. RW will contact SK and introduce PJ, PO could provide a letter of support. RW will be helpful in future integrations with iPlant as cROP is developed. Ontologies are needed to connect the resources there.
Also; Soltis- Open Tree of Life - possible development of a taxonomy ontology? Needs stable ids.
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.
Manuscripts in prep
LC will send around PAE paper draft in the next few days. Would like to have it submitted next week.
RW will have draft of PSDS paper ready in a few days, but we checked deadline and we can wait until mid-November to submit. RW should wait until after the PAE paper has been circulated before sending around the PSDS paper. We will still need to have the PSDS paper close to finished by the end of October, because RW won't have much time to work on it after October.
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.
revise comment to say something like "Although the use of synonyms like milk stage or fruit size 10% (get exact names)..."
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?
Again we discussed whether or not this terms should apply to populations of plants, but most felt strongly that this term should only apply to individual plants.
Even on an individual plant, one fruit may start to ripen, but none of the others follow (for non-climateric fruits that are not ethylene dependent).
We could define the fruit ripening stage as starting when half of the fruits start to ripen,
Maybe say "Of the first fruit of an individual plant". We already know that it applies to a single whole plant, because it is subtype of whole plant development stage.
Four issues: typical single plant, single plants with atypical development, typical populations, population of plants with atypical development. To deal with all of these, we need to first define the term well for a single plant.
One can still describe this for populations by saying something like 50% of the plants in a population are at the fruit ripening or fruit formation stage.
Problem with using 50% of fruits are ripe is that it is not useful for indeterminate plants. If we leave it at the first fruit, than it is clear no matter what type of plant.
Some dissatisfaction with "growing season". Maybe we need a term in the PO like fruiting cycle.
Take out comment about annuals only having one fruiting per season, because many have more than one.
Begins with the first fruit of a "fruiting cycle". Perhaps the solution is to create a parent term "whole plant fruit development stage" and let plants have more than one of those during its life, all nested within a single sporophyte reproductive stage. Each whole plant fruit development stage have only one whole plant fruit formation stage and one whole plant fruit ripening stage.
We need to develop the individual fruit development stages in conjunction with these terms.
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) 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.
rephrase "ends when either: ..." or maybe say "ends with the earliest of either...
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.
One problem is that sometimes the fruit doesn't ripen until well after the plant begins to senesce or go dormant. May need to put something this effect in the comment and point out that the individual fruits can still go on ripening afterwards.
There are cases when a single fruit starts to ripen, but nothing happens to the rest of the fruits until later, when the rest of the ripening kicks in. We may want to define the beginning as something like "When the first fruit starts to ripen in a way which, in case there are other fruit, the majority of the other fruits start to ripen continuously therewith.
We should mention in the comment that this stage begins when the fruit formation stage ends.
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.
These name changes are okay.
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.
This refers to anthesis. Maybe better to say that it is when the pollen is ready to be released or stigmas are receptive.
Maybe better to define it as when flowers are present.
Should anthesis be in GO? Probably anthesis is a stage, not a process, so it should stay in PO.
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:
- To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
- To identify potentially fruitful applications which such enhanced coordination might bring
- To enhance the Protein Ontology treatment of plant-related proteins
- To address coordination issues between the GO and PO, for example as concerns treatment of development stages
- 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)
