POC Conf. Call 11-29-11

POC meeting, Webex Conference Call; Date: Tuesday Nov 29th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-22-11?

Back to POC Meetings Minutes

Hot News: Demo of the new PO Web Service

JP will give us a demo; see link to PO Dev for review: add link as available...

PDSO Revisions: Plant structure development stages

Wrapping up the trichome/seed trichome development stages

seed trichome development stages

New or revised terms and definitions:

New general development term:

trichome development stage (PO:0025368): A plant structure development stage that has as primary participant a trichome. [source: POC:Curators]

PAO terms:

• trichome (PO:0000282): A unicellular or multicellular plant structure that forms a non-sclerified outgrowth from the epidermis. [source: POC:Curators]

modified comment: This class is the union of unicellular trichome [narrow synonym of trichome cell (PO:0008030)] and multicellular trichome (PO:0025162). A trichome can vary in length and shape and may be branched or unbranched. It may be glandular or non-secretory.

• seed trichome (PO:0004511): A trichome that develops from seed coat epidermis. [source: POC:Curators] (removed "and is often long with putative dispersal function")

New child terms:

• seed trichome development stage (PO:0025369): A trichome development stage that has as primary participant a seed trichome. [source: POC:Curators]

Comment: Seed trichome development stage consists of the following sub stages: seed trichome initiation stage (PO:0025370), seed trichome elongation stage (PO:0025371), seed trichome secondary wall biosynthesis stage(PO:0025372) and seed trichome maturation stage (PO:0025373).

synonym: seed hair development stage (exact)

BS: Add as a comment: "The STDS consists of the following processes in this order....and list the GO BP terms". Put the GO term and # in each comment.

• seed trichome initiation stage (PO:0025370 new): A seed trichome development stage which occurs during the interval between the onset of seed trichome initiation (GO:0090377) and the onset of seed trichome elongation (GO:0090378). (LC:test)

The GO Ids should go in the comment

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

synonym: seed hair initiation stage (exact)

These references to GO are a bit different that the one in cell, in which GO:cell is the genus in the definition.

Keep definition more or less as is, but put GO ids in the comment.

Do we need to say " between the onset of the process of seed trichome initiation...". Consensus was that it is not necessary.

• seed trichome elongation stage (PO:0025371 new): A seed trichome development stage which begins with the onset of seed trichome elongation (GO:0090378) and terminates with the onset of seed trichome secondary cell wall biogenesis (GO:0090379). (LC:test)

Comment: In Gossypium, seed trichome initials undergo a period of rapid elongation without cell division for 16-25 days.

synonym: seed hair elongation stage (exact)

Reword definition as per seed trichome initiation stage. Add to comment that although the seed trichome elongation stage ends when when the process of secondary wall biosynthesis begins, the process of seed trichome elongation may continue.

• seed trichome secondary wall biosynthesis stage(PO:0025372 new): A seed trichome development stage which begins with the onset of seed trichome secondary cell wall biogenesis (GO:0090379)and terminates with the onset of seed trichome maturation (GO:0090380).(LC:test)

comment:

synonym: seed hair secondary wall biosynthesis stage

• seed trichome maturation stage (PO:0025373 new): A seed trichome development stage which encompasses the process of seed trichome maturation (GO:0090380).(LC:test)

comment: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA). synonym: seed hair maturation stage (exact)

It seems that the seed trichome maturation process in GO is poorly defined and overlaps with the seed trichome secondary wall biosynthesis stage. BS suggested we should suggest an improvement to the GO terms that will make it more clear. Need to look at the literature on seed trichome development in cotton and other species and determine what is really going on.

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.

• 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.

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

reference from MAG:

Betancur,et al (2010). Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton Fiber. Journal of Integrative Plant Biology, 52, 205-220. link

leaf trichome development stage (PO:0007039):

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

Moved leaf trichome development stage (PO:0007039) to be is_a trichome development stage. new def'n: A trichome development stage that has as primary participant a leaf trichome. (POC:Curators)

The existing children of leaf trichome development are:

PO:0007056 : 1 pattern formation [0]

PO:0007058 : 2 endoreduplication [0]

PO:0007059 : 3 branch formation [0]

PO:0007135 : 4 growth directionality [0]

We need to look at these and the related GO terms.

• Cotton Fibre Genomics project

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

Work on these terms is ongoing. Will present new definitions at a future meeting.

If we have time to work on these this week, see additional notes at Items_for_future_meetings#Dormant_stages.

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.

Plant Anatomical Spaces

LC pointed out that we have annotation on several of these terms: for example:

• axil (PO:0025224): (1)
• micropyle (PO:0020025): (1),
• stomium (PO:0020101): (2),
• seed micropyle (PO:0006334):(1)

There are also a couple of annotations on cuticle (PO:0000022).

Most of these annotations should be on the structures surrounding the spaces, not on the spaces (or substance, in the case of the cuticle) themselves. We should probably modify the comments to alert annotators to this.

Collaborations

Wood Anatomy and Forest Trees

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

Please see the Wood_Anatomy wiki page for more information.

Three Goals:

• Develop terms for wood structure in the PAO
• Develop terms and ontology structure for wood formation,the time course of development
• Terms to describe wood quality and phenotype, traits- go into TO?

Update and status: Consensus agreement that we should hold the meeting at the NYBG during the period from the last week of January to mid Feb and invite these experts to attend:

• Frederic Lens: (new faculty at Netherlands Centre for Biodiversity Naturalis)
• Barb Lachenbruch link
• Elisabeth Wheeler (paleobotanist and wood anatomist at NC State
• Rachel Spicer Connecticut College

Along with Jill Wegrzyn of the TreeGenes Database at UCDavis.

We should send a letter of inquiry to these folks and fix a date. Maybe it would be more appropriate for the letter to come from NYBG?

LC is happy to assist with the drafting of the letter and arrangements from this end.

FNA

See previous minutes for details of the mappings (POC_Conf._Call_11-1-11#FNA)

We had a conference call with FNA on Nov 18th, 2011.

Next steps:

• add 364 synonyms to existing terms - many of these are plural forms
• fix several errors that were discovered while doing the mappings (minor things, like definitions of ariloid versus strophiole).
• add 143 unique new terms, plus their synonyms

-FNA provides definitions, so this will be relatively easy

• work with FNA to create an official mapping file

-FNA will provide unique IDs for their terms. This is needed especially for FNA terms that have the same name but different meaning.

-FNA terms that map to >1 PO term should have multiple lines in the mapping file. Whenever the FNA term matches a general term plus its subtypes, should only map to the general term. They can use reasoner to infer mapping to more specific subtypes. We can create some new general terms like "organ apex".

-Some of their terms that are just too general for PO. For these, when HC does the next round of text mining, she will pull out more meaning from context, e.g., use the term leaf base instead of just base.

• begin work on phenotype/character terms, including the 101 from this list plus all of the FNA character terms

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) which will be presented as a poster.Can also set up laptop in the poster room to give demo.

RW and LC are working with CM to do some Phenolog analysis, may be included in the poster.

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.

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