POC Conf. Call 11-29-11

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

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

Absent: Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

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

Back to POC Meetings Minutes

Streaming recording link:

https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=59721862&rKey=b749b12f361bc149 Download recording link:

https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=59721862&rKey=c0a0fdccc81bc195

Hot News: Demo of the new PO Web Service

JP will give us a live demo of how the new services will work

This is a link to the documentation page on PO Dev for review.

NSF Report and the OBO Foundry Application

The OBO Foundry group is still working on developing the template, but we in good shape in terms of the application. BS suggested that we should contact Melissa Haendal and let her know that we have an NSF deadline. PJ will contact her - we could invite her to come meet with us if that would help, as she is on campus a couple of days a week.

MAG will send PJ a report including the stats on the # of photographs, how many have gone to PSO.org, new undergrads aor grad students (with demographics).

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]

synonym: seed hair development stage (exact)

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).

Do we need to list the GO BP terms and # in this comment as well?

• seed trichome initiation stage (PO:0025370): A seed trichome development stage which occurs during the interval between the onset of seed trichome initiation and the onset of seed trichome elongation. [source: POC:Curators]

Synonym: exact: seed hair initiation stage

Comment: Refers to the GO Biological Process terms: seed trichome initiation (GO:0090377) and seed trichome elongation (GO:0090378).

• seed trichome elongation stage (PO:0025371): A seed trichome development stage which occurs during the interval between the onset of seed trichome elongation and the onset of seed trichome secondary wall biosynthesis. [source: POC:Curators]

Synonym: exact: seed hair elongation stage

Comment: Refers to the GO Biological Process terms: seed trichome elongation (GO:0090378) and secondary cell wall biogenesis involved in seed trichome differentiation (GO:0090379).

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

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): A seed trichome development stage which occurs during the interval between the onset of seed trichome secondary wall biosynthesis and the onset of seed trichome maturation. [source: POC:Curators]

synonym: exact: seed hair secondary wall biosynthesis stage

Comment: Refers to the GO Biological Process terms: secondary cell wall biogenesis involved in seed trichome differentiation (GO:0090379) and seed trichome maturation (GO:0090380).

• seed trichome maturation stage (PO:0025373): A seed trichome development stage which encompasses the process of seed trichome maturation. [source: POC:Curators]

Synonym: exact: seed hair maturation stage

Comment: Refers to the GO Biological Process term: seed trichome maturation (GO:0090380).

proposed comment: 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

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

• Cotton Fibre Genomics project

leaf trichome development stage (PO:0007039):

• leaf trichome development stage (PO:0007039): A trichome development stage that has as primary participant a leaf trichome. [source: GR:Chih-Wei_Tung, POC:Curators]

Comment: None

Now is_a trichome development stage.

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.

Whole plant development stages

This section still being developed....

gametophyte/sporophyte dormant stage

GO terms

GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.

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 new definition for dormancy process: A developmental process in which a dormant state is induced, maintained or broken.

Comment: A dormant state is characterized by a suspension of most physiological activity, and, in plants, by a suspension of growth.

seed dormancy (GO:0010162): The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated.

proposed new definition for seed dormancy: A dormancy process that has as participant a seed.

comment: Seed dormancy is characterized by a suspension of physiological activity that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.(work on comment)

organism dormancy (new term): A dormancy process that has as participant a whole organism.

PO terms

sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in a dormancy process (GO:0022611).

comment: This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure, although dormancy of buds is an essential part of the sporophyte dormant stage. A sporophyte dormant stage involves the formation of dormant buds. These may be above ground (in woody plants), at ground level (in herbaceous plants), or underground (in plants with tubers, bulbs, corms, or perennating rhizomes). Dormancy may be preceded by the senescence of other plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. Evidence of the end of dormancy is the resumed growth of buds and/or the growth of vascular cambium. The dormant stage is an evolved response to environmental conditions such as seasonality, extreme heat, drought, or cold.

gametophyte dormant stage (PO:0025342): A gametophyte development stage during which a gametophyte participates in a dormancy process (GO:0022611).

comment: This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage is an evolved response to environmental conditions such as seasonality, extreme heat, drought, or cold.

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.

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 (Bioinformatics) and Andrew Groover Geneticist, USDA Forest Service, Institute of Forest Genetics, Davis CA.

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.

We will put together a draft invitation letter which will come from all three Co-PIs and then people can follow up with the individual experts. DWS knows Fredich Lens well, MAG knows Rachel Spicer. LC will follow up with Barb Lachenbruch. RW will follow up with Rachel Spicer BS could do a introduction for the non-ontologists to explain what we are doing. Day 1

RW cannot be there Jan 24th through the 26th, first week of Feb is better for MAG and BS as well, and works for DWS as well.

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.

Poster presentation: "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes link

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