POC Conf. Call 9-25-12

POC meeting, Webex Conference Call; Date: Tuesday Sept 25th, 2012 10am PDT/1pm EDT

In attendance:

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

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

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_9-04-12?

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=68559652&rKey=2372f53c53e0133c

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68559652&rKey=c5053bcfd32d7d2e

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Recent Meeting reports

NSF Plant Genome PIs Meeting

Arlington, VA, September 6-7, 2012

PJ presented a 2 pager and poster

Genome Informatics 2012

September 6th-9th Robinson College, Cambridge, UK

JP attended and submitted a poster representing the PO

• made contact with Remco Ursem (bioinformatics @ Rijk Zwaan - Dutch vegetable and seed company); he is interested in PO
• conference was tilted towards biomedical and mammalian research
• lots of buzz about the ENCODE release and its implications for changing research methods in other organisms

  ENCODE Summary Paper

  "The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions."

• interesting talks:
  • Josh Stein (Gramene) - iPlant Discovery Environment (data cloud and analysis applications)
  • Dick McCombie - next-gen sequence assembly for plants, emphasis on merging data from multiple sequencing platforms (long-read MiSeq and PacBio, short-read HiSeq) prior to assembly
  • Pavel Pezner: new de Bruijn graph assembly model utilizing an extra dimension of network relatedness (represented by color); built for single-cell assembly
  • a couple of talks about single-cell sequencing; there seems to be growing interest in that approach

PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012

For more information see the wiki page: Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012

Crop Plant Trait Ontology Workshop OSU, Sept. 13-15th, 2012

The Plant Ontology and the Trait Ontology, along with EBI/TransPlant, GARNet (BBSRC) and the Generation Challenge Program hosted the Crop Plant Trait Ontology Workshop from September 13th-15th 2012 at Oregon State University. Co-organized with representatives from SGN, SOYbase, maizeGDB and many other groups.

Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and representatives from two plant agribusinesses- Syngenta and Monsanto, gathered in Corvallis for a workshop on the latest developments in and broad discussion of the need for a coordinated effort to develop and extend the plant and trait ontologies to describe the anatomy and traits of agronomic importance to major crops cultivated world wide.

The goal of this workshop was to widen the awareness and participation of the plant breeding community in the use of ontologies, and to create a semantic framework for meaningful cross-species queries using a common reference ontology for plants.

• Guest speakers Melissa Haendel; (Ontology Development Group, OHSU Library and Barry Smith (OBO Foundry)

• Participants engaged in hands-on activities, learning to use the ontology editor OBO-Edit and working in small groups to classify plant trait term requests which had been submitted.

Outcomes:

-preparing a short new item for circulation

-preparing a "vision/white paper" to focus on the ref plant onotlogy concept

-follow up meeting will occur at PAG 2013, along with Ontology workshop

-Many new and enhanced collaborations

Update from Cornell

Link to CU-PAC site

From Ale: added 29 slides and 549 photos (some of these are already in CUPAC server, but the ones done last two weeks are not, we will upload the rest during this week)

RW visited Cornell and MAG and RW started adding keywords in the beginning of Sept, and came up with a way to add PO's to all the images then link them to the PO pages, but it will probably be a few weeks before Kevin is able to implement the links.

News: The website is up again (but was not available during the call). Cornell had a major servers crash the last two weeks and it took them several days to figure out what it was wrong.

MAG will be talking with PJ about having a technician work on labeling the images using the SIA tool

Update on SIA

• JP reported that they are making progress fixing the bugs with the file switching memory management problem.
• Getting ready to make the next release 1.2, will be available on the the Jaiswal lab website.
• Bug tracker is set up through the Jaiswal Lab tracker- this will be available to outside users through email- more details TBA

Cont. from last meeting:

Upper level term: 5 fruit formation stage (PO:0007042)

current def.: Formation of the seed-bearing structure after flowering.

new name and definition, from last meeting:

whole plant fruit formation stage (PO:0007042): 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) (could be more specific about this, after we add specific types of fruit development stages)

subset for angiosperms

Discussion and comments:

Maybe refer to initiation of first fruit ripening, instead of fruit ripening stage?

Some discussion of this as a population measure: If you want to apply this to a population, you may choose the point when, e.g., 50% of the plants have initiated fruit. BS suggested that this should be defined for an individual plant, and have population terms defined separately.

Initiation of the first fruit begins with fertilization (formation of zygote). This can be defined more clearly in fruit development stages, then refer to those in these definitions.

For gymnosperms, we could have terms like whole plant strobilus development stage. Seed development stage should apply to gymnos as well as angiosperms.

Do we want a parent for both of these terms: "whole plant fruit development stage"? This would match more closely to fruit development stage (PO:0001002).

Upper level term: 6 ripening stage (PO:0007010)

current def.: Maturation of the fruit.

proposed new name and definition from last meeting:

whole plant fruit ripening stage (PO:0007042): 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) (could be more specific about this, after we add specific types of fruit development stages)

subset for angiosperms

GO:ripening is defined as a type of senescence. Should the term ripening be used only for fleshy fruits? Fruit drying also probably involves cell death, so perhaps it is type of ripening as well.

Add comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.

Note: the different fruits on a plant may be in different stages, but the whole plant can only be in one stage.

When does the ripening stage end? For annuals, ripening stage is followed by senescence of whole plant in annuals, but for perennials, maybe different. We need to incorporate this into the definition.

PJ: Some pear varieties do not ripen on the plant. Have to be picked and treated. In that case, the plant never enters the whole plant fruit ripening stage, but the individual fruits to.

We be good to tie this to seed development. Make the connection as part of the fruit development stages, and then link fruit stages to whole plant stages. Seeds may regulate development of fruit. Interaction between progeny and maternal tissue.

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.

Will 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

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:

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)