POC Conf. Call 11-22-11

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

In attendance:

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

Absent: Justin Elser (OSU), Justin Preece (OSU), Dennis Stevenson (NYBG), 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_11-15-11? no additions, deletions, or changes

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

This shows the distribution of annotations between "whole plant growth stage (PO:0007033)" and "Plant structure development stage (PO:0007021)"

plant structure 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.

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

This can guide us for which parts of the PDSO to work on next, after we get through the upper level. We looked at some of the stage terms for vegetative growth, such as leaf production stage (PO:0007133), which has a large number of child terms of the form: LP.01 one leaf visible to LP.20 twenty leaves visible. Many of these stages have many of the maize gene models associated with them.

PSDS Revisions: Plant structure development stages

trichome/seed trichome development stages

At the 11-15-11 meeting, we decided to test one approach- 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 and to define the stages as the period of time when the GO processes occur.

seed trichome development stages

Proposed new terms and definitions:

Proposed new general term:

trichome development stage (PO:0025368 new): A plant structure development stage that has as its participant a trichome.(LC:test)

synonyms: none at this point

Comment: none at this point

new proposed definition: A plant structure development stage that has as primary participant a trichome.

Has_participant does not exclude the possibility of other participants. What we really want to imply is that this is the major or primary participant.

Unfortunately, we can't use both participates_in and has_participates in (because it causes circularity in AmiGO).

BS prefers that we use has_participant, because for any given entity, whether or not it participates in a process may occur by accident, but the has_participant relation is more integral to the process.

We had a discussion of the definitions of trichome and seed trichome. Instead of saying that the seed trichome is often long, we should put the comment on trichome: "trichomes can vary in length and shape and may be branched or unbranched."

We also looked at the def'n of leaf trichome: A phyllome trichome that is part of a leaf epidermis. synonym: narrow: phyllid trichome

• seed trichome development stage (PO:0025369 new): A trichome development stage during which one or more seed trichomes develop.(LC:test)

new proposed definition: A trichome development stage that has as primary participant a seed trichome.

Comment: Add to comment "Seed trichome development stage consists of ... (subtypes).

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.

This tells users what order the stages go in, without having to number them. Although we can keep the numbers in existing stages, for new ones like this where there aren't that many, we can try not numbering them.

"It would be nice if we could offer PSDS as a time line." -- We can do this to some extent (in the future) by using the precedes/preceded_by and succeeds/succeeded_by relations.

synonym: seed hair development stage (exact)

• 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.

Should add the GO term "developmental vegetative growth (GO:0080186)" to the comment.

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.

All present were in favor of these definitions

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.

All present were in favor of these definitions

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.

Definitions should be modified to include intrinsic or natural dormancy, rather than as a response to environmental conditions, such as extreme heat, drought, or cold.

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.

BS: suggest if you could divide the comments into the specific taxa- users could read what they need- alternate comments

Suggested new def'n: plant embryo stage (PO:0007631): A sporophyte vegetative stage that has as its primary participant a plant embryo.

BS: Always use has_participant whenever possible

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

We decided to keep the long description in the def'n of the plant embryo and make it a participant in the plant embryo stage. Can keep the long description in the comment of the stage again.

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.

Should be 'plant zygote stage' (PO:0001097): A sporophyte development stage that occurs during the interval between syngamy and the first cell division and has as participant a plant zygote.

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.

The spaces are from CARO which is based on the FMA

BS: comments about the FMA: (author Cornelius Roth): There may be actual genes that are associated with these holes or AE. May be assoc with a change during development. ' We should check the usage of these annotations and make sure they are appropriate. Are they directly on the space terms?

If so, LC should talk with TB and see why they are there. They can be corrected in the next data release, if necessary.

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.

Tabled for next meeting as PJ and DWS were not at the meeting

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

Tabled for next meeting

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