POC Conf. Call 11-22-11

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POC meeting, Webex Conference Call; Date: Tuesday Nov 22nd, 2011 11:30am (PST)/ 2:30pm (EST)

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-15-11?

Back to POC Meetings Minutes

Summary of where annotations are in the current PGDSO:

On the 11-15-11 call, BS raised a valid concern that we could end up making a separate set of development stages for every structure in the PAO. He suggested that we review which stage terms people are actually annotating to.

There is an easy means to do that on the live browser: click on the "pie chart symbol"

For example (Note these are not all direct annotations):

Annotations on plant growth and development stage

Largest categories are flower development stages (PO:0007615), #48,062; leaf development stages(PO:0001050),#45,957 and Seed dev stage (PO:0001170): #46,318.

plant structure development stage

Largest categories are flower organ development stages (PO:0007600): ~84% (#46,676) and embryo development stages (PO:0007631): ~81% (#44,878).

This analysis can be extended down to any of the individual terms.

I found this viewer for the pie charts to be a little flaky so I created a table: File:PGDSO Annotation summary - Plant Structure Dev Stage.pdf

PDSO Revisions: Plant structure development stages

trichome/seed trichome development stages

This section in progress...

Proposed new terms and definitions:

Proposed new general term:

trichome development stage (PO:000xxxx): A plant structure development stage that has as its participant a trichome.

synonyms:

Comment:

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

Comment:

synonym: seed hair development stage


  • seed trichome initiation stage (PO:000xxxx): A seed trichome development stage which begins with the onset of seed trichome intiation (GO:0090377)and terminates with the onset of seed trichome elongation (GO:0090378).


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


existing term: leaf trichome development stage (PO:0007039):

Proposed new def'n: A trichome development stage during which one or more leaf trichomes develop.

comment:


  • Is it 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.

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. ref?

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.

Define stages as the period of time when the GO processes occur.


GO Biological processes

  • 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.


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.


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

Whole plant development stages

Review of definitions we discussed last week.

gametophyte/sporophyte vegetative stage

proposed definitions:

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

comment: A gametophyte may begin to senesce or die from other causes before producing gametangia. Some plants, such as the fern Vittaria appalachiana, may never produce gametangia, and remain in the vegetative stage indefinitely. Vegetative growth can also occur during the reproductive stage.

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 a sporangium.

comment: A sporophyte may begin to senesce or die from other causes before producing sporangia. Developmental vegetative growth (GO:0080186) can also occur during the reproductive stage.

gametophyte/sporophyte reproductive stage

proposed definitions:

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

comment: A whole plant may continue developmental vegetative growth (GO:0080186) after it has entered the reproductive stage, and it may revert to a condition in which it is no longer producing gametantia, but once it has initiated a single gametangium, it remains in the reproductive stage until senescence or death by some other cause.


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

comment: A whole plant may continue developmental vegetative growth (GO:0080186) after it has entered the reproductive stage, and it may revert to a condition in which it is no longer producing sporangia, but once it has initiated a single sporangium, it remains in the reproductive stage until senescence or death by some other cause.

gametophyte/sporophyte dormant stage

under construction

dormancy process (GO:0022611): The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity. (They also have a term for seed dormancy.)

proposed definitions:

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

comment: During the sporophyte dormant stage, a sporophyte participates in a dormancy process (GO:0022611). The dormant stage is a response to environmental conditions, such as extreme heat, drought, or cold. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed or other plant structure, although dormancy of other plant structures such as buds is an essential part of the sporophyte dormant stage.

Sporophyte dormant stage involves the formation of dormant buds. These may be above ground (in woody plants), underground (in plants with tubers, bulbs, or corms) or at ground level (in herbaceous plants without tubers, bulbs, or corms). In herbaceous plants (e.g., perennials), dormancy involves the death of all or most of the shoot system.

Evidence of the end of dormancy is the resumed growth of buds and/or the growth of vascular cambium.


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

comment: During the gametophyte dormant stage, a gametophyte participates in a dormancy process (GO:0022611). The dormant stage is a response to environmental conditions, such as extreme heat, drought, or cold. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures.


References:

Vegis; Dormancy in Higher Plants ARPP 1964

paper on sporophyte dormancy in a bryophyte

Dormancy of gemmae in a liverwort: DOI: 10.1034/j.1600-0706.2001.940314.x. In this case, the gemma is a whole plant.

Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?

gametophyte/sporophyte senescent stage

Work on these terms is ongoing. Will present new definitions and GO proposal for senescence at a future meeting.

embryo stage and plant embryo

embryo stage

We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed embryo stage and made is_a sporophyte vegetative stage.

proposed def.:

embryo stage (PO:0007631): A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.

Comment: The embryo stage generally starts after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.

plant embryo

Now that we have a working term for embryo stage, we can define plant embryo in terms of the stage.

existing def. plant embryo (PO:0009009): A whole plant in the early part of a sporophytic phase after the first cell division.

proposed def. plant embryo (PO:0009009): A whole plant that participates in the embryo stage (PO:0025369).

comment (basically the same as existing comment): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.

-change from participates_in sporophyte development stage to participates_in embryo stage

zygote stage

We already have a term "A zygotic stage" (PO:0001097), is_a embryo stage. This was renamed zygote stage and made is_a sporophyte development stage.

proposed def. zygote stage (PO:0001097):A sporophyte development stage that occurs during the interval between syngamy and the first cell division.

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:

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 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.

SPNHC 2012

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

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/

  • The consensus with CM, MH and DOS was not to organize an Anatomy Ontology Workshop this year.

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

Next meeting scheduled for Tuesday, Nov. 29, 2011 at 10am PST/1pm EST

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