POC Conf. Call 11-15-11

POC meeting, Webex Conference Call; Date: Tuesday Nov 15th, 2011 10am (PST)

In attendance:

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

Absent: Pankaj Jaiswal (OSU), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-8-11? no additions, deletions, or change

Back to POC Meetings Minutes

Schedule for Nov 22 call: results of the doodle poll Lol will send email with time for meeting.

PSDSO revisions: Plant structure development stages

We have some open user requests which are holding up the addition on annotations:

eg. Requests for terms for Cotton seed hairs (seed trichomes), Open since 07-28-2010, from AgBase curators

Existing terms:

* seed trichome (PO:0004511): exact synonym: seed hair

Def'n: A trichome that develops from seed coat epidermis and is often long with putative dispersal function. [source: POC:Curators]

is_a trichome, which is_a plant structure

"and is often long with putative dispersal function" should go to the comment.

*seed development stage (PO:0001170):

Current def'n: Stages of seed development, from fertilization to the dry or quiescent state. [source: TAIR:ki]

Proposed new def'n: A plant structure development stage that begins with fertilization and ends with seed maturation.

Comment: Only used for seed plants. Some seeds may enter a period of dormancy after seed development is complete.

is_a plant structure development stage; part_of sporophyte phase; subset for gymnosperms and angiosperms; add relation: seed participates_in seed development stage

New proposed def.: A plant structure development stage that has as participant a seed.

The seed can be defined as a mature ovule. We should work on the definition of seed, but seed trichome development stages will not be subtypes of seed development stage. Trichome development stages are more important for now.

Suggested term definitions and ontology structure

from AgBase curators (8-31-2010, huiwang7)

They proposed adding the new terms:

seed hair development stage (PO:000xxxx), which would be:

• [part_of] seed hair initiation stage: The earliest histological evidence of seed hair initiation, ie, a change in the orientation of cell

division in the ovule epidermises occurs at or just before anthesis. (

• [part_of]seed hair elongation stage: A period of rapid elongation of hair initials without cell division for 16-25 days.

• [part_of]seed hair secondary wall biosynthesis stage: A phase of the massive amounts of secondary cell wall cellulose synthesis.

• [part_of]seed hair maturation stage: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA).

Relevant citations:

Ruan YL, 2003, Plant Cell 15:952-964 [Source:PMID: 12671090]

Lee JJ, 2007,Annals of Botany 100:1391-1401 [Source:PMID: 17905721]

from Lee et al: "Cotton fibre development is delineated into four distinct and overlapping developmental stages: fibre initiation, elongation, secondary wall biosynthesis and maturation."

See link to Timeline of STD

Proposed new terms and definitions:

• Feedback from the AgBase curators indicate that they are more interested in this as a trichome development stage than as a seed development stage, thus we propose adding the following terms:

• seed trichome development stage (PO:000xxxx): A plant structure development stage during which one or more seed trichomes develop.

Comment: part of seed development stage synonym: seed hair development stage

(is_a plant structure development stage; part_of seed development stage; add seed trichome participates_in seed trichome development stage) synonym: seed hair development stage

• seed trichome initiation stage (PO:000xxxx): A seed trichome development stage when the earliest histological evidence of seed trichome initiation appears.

comment:A change in the orientation of cell division in the ovule epidermises occurs at or just before anthesis.

synonym: seed hair initiation stage

• seed trichome elongation stage (PO:000xxxx): A period of rapid elongation of hair initials without cell division for 16-25 days.

synonym: seed hair elongation stage

• seed trichome secondary wall biosynthesis stage(PO:000xxxx): A phase of the massive amounts of secondary cell wall cellulose synthesis.

synonym: seed hair secondary wall biosynthesis stage

• seed trichome maturation stage (PO:000xxxx): A period of seed hair maturation from 50 to 60 days post-anthesis (DPA).

synonym: seed hair maturation stage

We will try adding a general term for trichome development stage. Then seed, leaf, etc. trichome stages would be subtypes of this.

We will have to try out the different structures, to see whether it is better to then have things like initiation stage, elongation stage as subtypes of the general term or of each type of trichome.

Need to look at what different types of trichome development stages will need. Will depend on how comparable the development stages of trichomes are across plants.

BS was concerned about making separate sets of terms for every type of trichome. We could end up making a separate set of development stages for every structure in the PAO. Need to see what terms people are actually annotating too

One example is from MAG: We should check the development of seed trichomes for other species such as those of Bombacaeae (Chorisia). Milkweed (Asclepias) is another.

Initiation of all trichomes is the same except for in roots, but root hair cell is already separate from trichome. All trichomes go through some type of elongation or expansion.

These stages may not be discrete -- e.g., secondary wall biosynthesis could be occurring while elongation is going on. However, even though the processes overlap, we need to have beginnings and ends for all stages, and we need to provide guidance to annotators about which term to use if they are overlapping. One possibility is to make each stage end when the next process begins, even if the process that marked the beginning of the first stage is still going on.

We need to be careful not to blur the line between stages and GO processes. We can define stages as the period of time when the GO processes occur.

A stage always has one primary participant; it includes everything that happens during a given period of time; it is part of the life of a plant. We define them as having a beginning and end, but we have to be careful about saying they have a discrete boundary (even a single cell division takes a little time).

Current leaf trichome stages are quite different. Will have to try to align the two types.

These are also referred to as GO Biological processes:

• GO:0090376 seed trichome differentiation: The process in which a relatively unspecialized epidermal cell acquires the specialized features of a seed trichome. A seed trichome is a trichome that develops from seed coat epidermis and is often long with putative dispersal function. [GOC:tb, PMID:17905721]

4 part_of child terms:

• GO:0090377 seed trichome initiation: The process in which the developmental fate of an epidermal cell becomes restricted such that it will develop into a seed trichome, causing a change in the orientation of cell division in the ovule epidermis at or just before anthesis. (Source: PMID:17905721). Comment: These processes continue up to 3 days post-anthesis (DPA) in Gossypium spp.

• GO:0090378 seed trichome elongation: The process in which a seed trichome irreversibly increases in size in one [spatial] dimension or along one axis, resulting in the morphogenesis of the cell." [GOC:tb] comment: The increase in length of the seed trichome without cell division. Elongation is defined to be from 5 to 20 DPA in Gossypium spp.

• GO:0090379 secondary cell wall biogenesis involved in seed trichome differentiation: A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of inextensible cellulose- and pectin-containing cell walls that are formed between the plasma membrane and primary cell wall of seed trichomes after cell expansion is complete." [GOC:tb]

comment: The processes involved in the massive amount of secondary wall cellulose synthesis in seed trichomes continue to 30 DPA in Gossypium spp.

• GO:0090380 seed trichome maturation: A developmental process, independent of morphogenetic (shape) change, that is required for a seed trichome to attain its fully functional state." [GOC:tb]

comment: These processes continue to 60 DPA in Gossypium spp.

PSDSO revisions: vegetative, reproductive and dormant stages

Continued from POC_Conf._Call_11-1-11 and POC_Conf._Call_11-8-11

We can efficiently deal with gametophyte and sporophyte together for these:

We agreed last week we did not need "development" in all the term names

gametophyte/sporophyte dormant stage

proposed def'ns:

sporophyte dormant stage (PO:0007132): A sporophyte development stage that occurs during the interval between the suspension of physiological activity and its reactivation.

gametophyte dormant stage (PO:0025342):A gametophyte development stage that occurs during the interval between the suspension of physiological activity and its reactivation.

We agreed to use dormant in the term name, and include 'dormancy" as a synonym. We need to review what occurs during dormancy- suspension of growth and cell division.

No additional work was done on these this week.

gametophyte/sporophyte vegetative stage

proposed def'n:

gametophyte vegetative stage (PO:0025340, new): A gametophyte development stage that occurs during the interval between spore germination and the formation of gametangia.

sporophyte vegetative stage (PO:0007134, existing - was vegetative stage): A sporophyte development stage that occurs during the interval between the first division of the zygote and the formation of sporangia.

This includes the embryo stage.

What about plants that go in and out of the reproductive stage, like perennials? Are they always in reproductive stage, once they have made sporangia?

After an extensive discussion, we decided it was better to define vegetative stage as ending once reproductive structures are formed, even if the plant goes through later periods without production of those structures. Once a plant reaches the reproductive stage, it stays in that until it senesces or dies. This makes it easier to define stages that do not overlap. There is no restriction that a plant in the reproductive stage cannot undergo further vegetative growth.

Need to add a comment that the plant may enter senescence stage or dies before becoming reproductive. Can give example of Appalachian gametophyte fern (Vittaria appalachiana).

How will this affect annotations? For existing species (e.g., maize, At, rice), it is easy, because they are annuals. Incoming species like grape are perennial, but grapes generally don't go in and out of reproductive stages.

Most annotations are to individual parts of plants, rather than whole plant. However, they do use whole plant growth stages. For example, annotation for leaf that was sampled during the whole plant growth stage during which the inflorescence is elongating.

Need to make a tracker for embryonic stage and look at other stages in gymnosperms like proembryo stage. See link to book in last week's minutes.

We also need to have a term for zygotic stage. A sporophyte development stage between syngamy and the first cell division.

Will need to look at existing subtypes of vegetative and reproductive growth in sporophytes, and add stages requested by Cosmoss for subtypes of gametophyte stage.

gametophyte/sporophyte reproductive stage

gametophyte reproductive stage (PO:0025341, new): A gametophyte development stage that occurs during the interval between the initiation of gametangia and the onset of senescence.

At the POC meeting on 11-8-11, we discussed having the gametophyte reproductive stage end with fertilization, but maybe the gametophyte lives on after this. It seems unlikely that is will always be the case that senescence of the gametophyte begins with fertilization.

sporophyte reproductive stage (PO:0007130, existing - was reproductive stage): A sporophyte development stage that occurs during the interval between the initiation of sporangia and the onset of senescence.

Collaborations

Wood anatomy and Forest Trees

Wood anatomy: PO will work with a group of scientists to develop ontology terms to describe wood anatomy.

From Jill Wegrzyn at UC Davis: The forest tree community (and in particular the conifers), are interested in collaborating with the Plant Ontology project to develop terms specific to our communities. I currently coordinate efforts on the TreeGenes database (http://dendrome.ucdavis.edu) and will be leading efforts to integrate ontologies into our existing database.

Three Goals:

• wood development and timecourse- formation
• terms for wood structure in the PAO
• Terms to describe wood quality and phenotype, traits

LC set up a wiki page to organize the Info for this meeting, see: Wood_Anatomy goal is to do this by the middle of February.

An email was sent out to all the interested people asking for input on who to invite from our list of potential experts and on deciding where and when to do it. Waiting for replies....

Upcoming meetings and Presentations 2011/2012:

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011

RW registered and submitted abstract (Media:PO_abstract_PGBatCSHL2011.pdf). This presentation should involve the larger analysis for the PO paper with the data from Physco and grape etc.

Will be a poster. Can also set up laptop in the poster room to give demo.

Sematic web conference focused on life science

JP will attend the SWAT4LS meeting in December. Folks such as TW from NCBO will be there.

PAG 2012

January 14-18, 2012, San Diego, California

PO will be represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. We have 5 speakers and time at the end for a panel discussion.

PJ will give the introductory remarks at the Ontology workshop, and hopefully take part in the Panel Discussion.

For more info, see the PAG 2012 Ontology workshop wiki page.

• LC is also presenting in the Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm) and in the Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).

• LC will also do a computer demo for the PO, unless one of the Justins is there and wants to do it.

• The PO will take part in an Outreach booth organized by MaizeGDB.

Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

Call for abstracts is now open: Need to clarify the deadlines

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation)

2. Poster only

3. Workshop only

• Submission deadline November 30, 2011

• Notification of acceptance February 3, 2012

Instructions

There are seven topic sessions from which submitters are invited to select:

  1. Ontologies, standards and best practices, including gold standard datasets.
  2. Protein annotation; sequences, structures and pathways.
  3. Community annotation and Wikis.
  4. Genomics and metagenomics data curation.
  5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
  6. Literature collection, text mining and curation.
  7. Tools to assist curation, including automated pipelines. 

There are four submission tracks:

  1. Paper, with consideration for oral presentation
  2. Talk
  3. Workshop
  4. Poster 

PJ planning to attend and will be running a biocuration workshop, LC and RW can go, DWS will be away,

'From 9-27-11: PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide.

Annual meeting of the Society for the Preservation of Natural History Collections SPNHC 2012

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012)

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

22-25 July 2012; Graz, Austria.

Conference Web site: http://purl.bioontology.org/ICBO/

We also have the opportunity to organize an anatomy workshop as well along with CM and MH- need to decide about this soon

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts.

Could also consider organizing a phenotype ontology workshop.

Relevant dates

31 December 2011: Workshop and tutorial proposal submission deadline

25 January 2012: Notification of acceptance of workshops and tutorials

31 January 2012: Paper submission deadline

28 February 2012: Notification of paper acceptance

15 March 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline

15 April 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance

30 June 2012: Deadline for all camera-ready copies for the proceedings

We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?

Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX