POC Conf. Call 10-2-12
POC meeting, Webex Conference Call; Date: Tuesday Oct 2nd, 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_9-25-12?
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 for Plant Phys and paper on development stages for Physiologia Plantarum).
Fruit development stages for whole plants
under construction
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.
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 beginning 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.
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, 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) 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) (This could be made more specific, after we add specific types of fruit development stages.)
subset for angiosperms
The definition needs some work to clarify when this stage ends, particularly for perennials. We should also add a comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.We expect that this definition will change slightly as we work on the new and revised terms for fruit development stages.
Name changes
We have changed 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 stag:
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.
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 statemnts 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 othologs.
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
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.
from 9/4- PJ will check with DW about Gramene involvement
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 Dates TBD: Will probably be a Wednesday and Thursday around the 2nd or 3rd week of May. Should avoid Memorial Day Weekend (May 24-27th).
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)
