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

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.

Developers can access live version of PO, without having to worry about keeping downloads up to date. Matches PO terms and synonyms based on partial or complete strings. Also provides terms info like definition, etc. Also gave quick preview of annotation wiki.

PJ: should url be coming for po.org. JE: Can't go there for two reasons. Web server can't handle JSON (once we move to newer Amigo, it could go there). Our SVN is served from palea.

Will need a JSON parser plug-in to view results. Available to download on browser.

Being generated directly from database, so it is based on whatever file is on AmiGO.

Just queries terms at this point, not ontology structure.

BioPortal also has REST services. Need to check how they overlap with this.

Maybe Plantsystematic.org could use this service for providing keywords. Maybe it could also be used by Phylocode.

NSF Report and the OBO Foundry Application

The OBO Foundry group is still working on developing the template, but we are 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 or grad students (with demographics).

PSDS Revisions: Plant structure development stages

Wrapping up the trichome/seed trichome development stages

seed trichome development stages

PJ could create a new icon for the has_participant relation. LC will work with him on it

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.

This is okay.

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

Do we need a general term for seed trichome and a more specific term for seed coat trichome? Need to look into whether or not there are trichomes on seeds that don't develop from the seed coat epidermis (like maybe on wings)?

If not, we can keep the current term, but maybe should rename it 'seed coat epidermis trichome'. For the time being, we should add a comment such as: "This should really be called seed coat epidermis trichome" and if so, add specific terms for other types of trichomes.

We have the same issue with leaf trichome (which is a general term), when people need to describe trichomes on leaf lamina, petiole, etc. PJ suggested that we could create a series of more specific terms, and have the general term as a broad synonyms for all of them. Alternative is to keep the general term as a parent.

New child terms of trichome development stage:

• 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?

BS: We should make as many possible links to GO. We can add sentence to comment restating the GO processes that are also listed in the comment for trichome development stage.

• 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).

BS would like to see some qualitative account of what initiation is. Could repeat the GO BP definition of initiation in comment. Same for other stages.

• 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.

Also add old comment into comment.

• 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).

General discussion:

We could add a feature request to AmiGO to display terms in numerical order (instead of alphabetical order). Then we could get them to display in whatever order we want.

We will also probably want to add precedes/follows relations to get show the temporal order.

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.

These are more general stages for trichomes, not just for leaf trichomes.

BS: Is "pattern formation" used regularly? Not the best wording.

PJ raised an issue about lumping the types of trichomes together. The stages in : Elongation, formation of stalk, formation of head. Depends on uni- versus multi-cellular. Some expression may be specific to certain cells (e.g., only in top-most or head cell/s).

Whole plant development stages

postponed until next week

gametophyte/sporophyte dormant stage

GO terms

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

PO terms

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

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

gametophyte/sporophyte senescent stage

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

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 Elizabeth Wheeler. LC will follow up with Barb Lachenbruch. RW will follow up with Rachel Spicer

BS could do an introduction to ontologies for the non-ontologists on Day 1 and also assist primarily with goals #1 and #2 and maybe some #3.

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

no discussion this week

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:

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation) (LC would prefer a talk)

2. Poster only

3. Workshop only

• Submission deadline December 9, 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.

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