POC Conf. Call 10-11-11

POC meeting, Webex Conference Call; Date: Tuesday Oct 11th, 2011 10am (PDT)

POC members: In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Justin Elsner (OSU), Justin Preece (OSU),Marie Alejandra Gandolfo (Cornell University)

Absent: Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-4-11? There were no additions, deletions, or changes

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Status of Upcoming Release

Dbxrefs

Links to images on PlantSystematics.org

Now that we have a way customize the dbxrefs, we can add an automatic link to images on PlantSystematics.org.

We need two kinds of links: directly to individual images and to keyword search results.

KN can create a single url that will link to either a keyword or a unique image id.

We need to decide if we also want to have id numbers for keywords - if so we will need to provide a table of those (keyword/id records). RW thinks that having another set of ids would get confusing, and suggests just using keywords. Alternately, we could use the PO id# as the ID for a key word, but then we might run into problems when the same PO id maps to multiple keywords (because of synonyms).

We need to decide on an abbreviation: PSO, PlantSystematics.org (don't know if dot is allowed) or something else.

RW prefers PSO because it is easy to type, but it may cause confusion with the obsolete abbreviation for Plant Structure Ontology. Opinions?

LC: How about "PltSys:org" or something similar that would be somewhat recognizable. Maybe we should ask KN what they would prefer. The full name can be filled using the dropdown box.

JE: Why do we even need the org part? We don't for any others. My suggestion would be PltSys or PlantSystematics.

Test links: We can only put a few links in for this release. Any preferences on what they should be?

septum, replum (if we can find good image), others?

We decided to just use the name"PlantSystematics:keyword or image id" rather than using an abbreviation.

Rather than creating a separate list of numbers to identify the keywords, we decide that it will be better to have the keywords themselves as the link. These could be linked to the individual synonyms by creating the separate dbxrefs on the synonyms. Problem of possible duplication, misspelling, different forms, especially since they were entered by hand. Need a list of keywords from PS.org to check them and do the mapping to the PO. Also, how to differentiate b/n vascular and non-vascular leaf.

Additional issues of who will keep track of the mappings and maintain it. How will they link back to us, can we get the PO ids displayed on their site. All or just a subset options: MAG can add PO ids to her images she is creating- as keywords??

Will map PO terms and synonyms to the list of keywords in the PS.org database. The keywords are probably stored in the database with an internal id #. We should organize a separate meeting with KN and the group- can he share the database schema with the Justins, so see how to set this up. Will not be passed on outside the group.

We are waiting for KN to create a url to the keyword search page- will be able to test on dev for the next release

RW will work on setting up a time to discuss with KN- MWF are days he teaches at Cornell. Could do it on Tuesday or at another time.

We could add links to PS.org as dbxrefs for synonyms, for example, to differentiate between different types of flowers or fruits.

New dbxref for Fragaria annotations

For the time being, we will just have the link go to the Jaiswal lab webpage, since we do not have links to the actual data on the Genome Database for Rosaceae page

abbreviation: Jaiswal_Lab

database: Genome Database for Rosaceae

object: mRNA

example_id: Jaiswal_Lab:gene00002

generic_url: http://jaiswallab.cgrb.oregonstate.edu/

url_syntax: http://jaiswallab.cgrb.oregonstate.edu/cgi-bin/id_search.cgi?id=[example_id]

url_example: http://jaiswallab.cgrb.oregonstate.edu/cgi-bin/id_search.cgi?id=gene00002

I am not sure if this will work since there is nothing there to link to.

You can create a PO_ref for this, modify evidence code.LC and PJ will talk about after the meeting to sort it out.

Other dbxref issues

AP Web: Added new link for AP:web. Links to their home page, because their glossary is set up with frames and can't be accessed directly.

Names instead of initials: All dbxref abbreviations should now use full names instead of initial. For example, Spanish translations are now: POC:Maria_Alejandra_Gandolfo. Most have been changed, any remaining can be fixed in the next release.

Note that those names (for the translations) do not actually show up on the browser

Annotation files:

-test set of annotations are on beta browser (1st 500 lines of all the files). Please review the information on the beta browser

MaizeGDB:

We have received updated files from MS: (10-6-11. These contain the additional information in col 16 and the additional rows, but they have not been hand checked)

• po_anatomy_stock_zea_MaizeGDB.assoc
• po_anatomy_gene_zea_MaizeGDB.assoc
• po_anatomy_genemodel_zea_MaizeGDB.assoc
• po_growth_genemodel_zea_MaizeGDB.assoc

I believe these are ready to go. JP is working on annotating them with classical mapped gene set for the release. Status report?

JP downloaded the new files from MS and is working on it, annotating them with classical mapped gene set for more info see: CoGe. Completed it by the end of the call- ~800 for anatomy and ~10,000 for the growth stages. Will do a test load this afternoon.

TAIR:

TB said she would look after making any necessary changes. Their current file has some annotations to seedling and to some alt ids (need list of those from JE)

Need to move annotations from:

PO:0006469 (was 'Zea style') now: PO:0009074 style

Why are these in the TAIR file anyway??

This is on the live browser as well: Rad54

SGN

NM is working on the updates

Gramene:

Waiting for the updates, sent them the new ontology files

Need to move annotations from:

• PO:0006318 Poaceae floret > PO:0009082 floret
• PO:0006329 Poaceae floret meristem > flower meristem PO:0000229
• PO:0006384
• PO:0006441
• PO:0006442
• PO:0006444
• PO:0006445
• PO:0006446
• PO:0006449
• PO:0006450
• PO:0006451
• PO:0006452
• PO:0006455
• PO:0006456
• PO:0006457
• PO:0006462
• PO:0006463
• PO:0006464
• PO:0006465
• PO:0006472
• PO:0006497
• PO:0006508

Strawberry

These were submitted by PJ. Do we need to do anything further on these?

See note above about dbxref update.

Timeline for the October 2011 Release

We will aim to have the work on the strawberry and maize annotation files done today and go ahead with loading the full set of the ontology and annotations onto the beta browser. JE said there may be more problems with the annotation files since they have not been updated. MAG has translated the announcement in Spanish for us, can be posted on the po front page. LC will send out notifications once the release is live- hopefully in the next few days.

In progress for next release....

Physcomitrella

PJ and LC have been working with the SR and the Physcomitrella group to resolve a couple of issues.

-Need gene or gene models rather than microarray probe ids

-problem of annotating to the same tissue under different stress conditions. How can we specify this?

Asked CM @ using column 16 and terms from the EO (http://www.gramene.org/db/ontology):

On Oct 6, 2011, at 2:49 PM, Laurel Cooper wrote:

We are working on bringing in a large set of associations from the Physcomitrella genome group that consists of genes expressed under different environmental conditions. We are wondering if we can use the col 16 to capture that information by creating an annotation extension to terms from the EO (http://www.gramene.org/db/ontology).

For example, we have a set of gene expression annotations to PO structures after dehydration. What relation can we use in the annotation extension? Can we use "response_to"?

I noticed that on the GO-wiki

We need to be able to differentiate between the gene expression in the same structures under different conditions.

CM response:

You can use c16 to refine the main PO term. The key is to ask: what would the term look like if pre-coordinated?

For example, if you want to "dehydrated leaf", then c5=leaf and c16=has_quality(dehydrated) or if you have a process term "dehydration" then it could be c16=is_output_of(dehydration)

LC will create a mapping between the treatments and the potential EO terms we could do, can create the needed EO terms, if necessary. It seems the Col 16 is the right place to put this information, but we need to determine the proper relation, Col 16 refers to the plant strucuture

See the RO.obo file- put in link, a lot of variability in the use of col 16

"Assayed_under" or "Assayed_in" maybe a better alternate

Grape

LC has been working with the Grape Genome group to sort out how to submit their data. There are issues with IEA data they sent us.

They do have some RNA seq data for set of tissues:callus, leaf (I), leaf (S), root (I), root (S), stem (I).

Nicola asked me to suggest a cutoff value based on the RPKM value. What do you suggest to set to consider a gene as expressed?

Here is an example locus: IT_10s0116g00060

LC will continue to work with Nicola and find out if their RPKM values are normalized and if they have been published and how they figured out their cut-offs. We can provide a page for an explanation or create a Po-reference. LC will give Nicola a mapping for these tissues. We will just ask them to provide the annotations to these tissues.

Plans and Priorities for the next Release

• Revision of PGDSO:

At the NYBG POC Meeting, we made some great progress in setting the stage for the next round of revisions, for specifics see: Saturday_Sept_10th,_2011#Goals_for_revision_of_PGDSO:

• Physco and grape data

• Mappings to FNA

• PlantSystematics.org images

• ABRC annotations to PO and TO terms, etc

User requests open on Source Forge: PAO

should work on completing old SF requests for the upcoming release.

Examples:

• TraitNet requests

Items_for_future_meetings#TraitNet_requests

• spikelet

• stipule

Upcoming meetings and Presentations 2011/2012:

• LC out at Programming for Biology course at CSHL, Long Island, NY

October 17th - November 1st, 2011

• MAG Gone to Argentina for field work: October 18th to Nov8th, 2011

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011 Abstract Deadline: September 9, 2011...

Academic/Student No-Housing Package $720

RW registered and submitted abstract (Media:PO_abstract_PGBatCSHL2011.pdf). Will need to present a preliminary data analysis for the talk/poster.

No word yet on talk vs poster. Data analysis for presentation; This presentation should involve the larger analysis for the PO paper with the data from Physco and grape etc.

PAG 2012

January 14-18, 2012, San Diego, California

PO will host an Ontology workshop for PAG on Saturday January 14th from 10:20am-12:30pm

Use of Ontologies for Organizing Plant and Animal Genomics Data

Please see the PAG 2012 Ontology workshop wiki page.

LC is working on inviting speakers. Additional suggestions are welcome.

Important Dates:

• Registration and Abstract submissions: open on Sept 22
• Early Pre-Registration Deadline: October 31
• Travel Grants Deadline: November 1
• Abstract Submission Deadline: November 11

PJ may be tied up on Sat am, so we will not plan on him giving a talk. LC will also do a computer demo.

LC is also presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00am - 10:10am.

LC will prepare an abstract and send to MS as well

The PO will take part in an Outreach booth organized by MaizeGDB

Who is attending: LC, PJ (weekend), maybe JP, JE??

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.

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.

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:

Submission site now open. Deadline for submissions is Saturday, October 15th, 2011 at 11:59 PM PST.

RW, DWS and MAG will 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.

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. RW will put the draft plant PATO on the SVN.

• We need to have a section sponsor for the workshop proposal, DWS suggested the structural section (Head: Bruce Kirchoff), paleo section or systematists. Development and structural, genetics, and teaching sections would also be appropriate co-sponsors.

From meeting website:

When you submit your proposal, you will be asked for the following information:

• What Societies and Sections will be sponsoring the session. Please provide contact information for any persons who have approved the sponsorship
• The societies participating in Botany 2012 of which you are a member
• The names, email and street addresses of the organizers, and which of them will lead the session
• A title and description of the session
• Keywords and web links that are relevant
• Requirements, such as room type, food, special equipment or transportation, depending on the type of proposal
• An estimate of anticipated attendance
• A list of invited speakers or leaders, if relevant.

Proposal was circulated to the group- please respond by end of the week

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.