POC Conf. Call 10-4-11

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POC meeting, Webex Conference Call; Date: Tuesday Oct 4th, 2011 10am (PDT)

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections(additions/deletions, etc) needed in the minutes from the POC_Conf._Call_9-27-11?


Issues and status reports for the Upcoming Release

For more details of the changes in the upcoming release, see: Summary of Changes to PO September 2011

Updating of Dbxrefs

Our version of AmiGO has a built-in set of dbxrefs, in a Perl file, and it is not reading the current GO file.

In order to update these, this file has to be so will have to be edited manually by JE (or JP).

We decided on the POC_Conf._Call_9-27-11 to use the PO_DBXref.txt file on the SVNto store the updated dbxrefs stanzas.

  • An older version of this file is also available through the documentation page on the PO website:

LC: Do we really need to have this file PO_DBXref.txt on our website, since it is just for our internal use? If so, it should be updated. It could be a link to the SVN. 


 What parts of these stanzas does AmiGO actually use?  If JE could give us a copy of the info from the AmiGO file, we could compare the contents of the txt file and the actual functional links

Status of Dbxrefs that have been fixed:

  • Link to SF trackers (OB_SF_PO):

Link is currently in the PO_DBXref.txt file on SVN, appears to be working on beta.

For example see thallus, PO:0030027


  • MaizeGDB Links:

These look like they are working ok on the beta browser.


  • Gramene links:

The ones on the beta browser are working, not sure if the ones that were broken are there- need to load some test data on beta to make sure.

The ones changed in dbxref.txt are (as of 9-29-11, #152):

abbreviation: GR

database: Gramene: A Comparative Mapping Resource for Grains.

object: Protein

example_id: GR:P93436

generic_url: http://www.gramene.org/

url_syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id]

url_example: http://www.gramene.org/db/protein/protein_search?acc=P93436


Note: This URL actually refers to Gramene proteins. Should the stanza be renamed?


abbreviation: GR_MUT

database: Gramene: A Comparative Mapping Resource for Grains.

object: Mutants

example_id: GR_MUT:GR:0060198

generic_url: http://www.gramene.org/

url_syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]

url_example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198


Note that this URL actually refers to Gramene genes and mutants now. Should the rest of the stanza be edited and renamed?


  • Solanaceae Genome Network (SGN) links:

A couple of the links on live to SGN were also broken. We have been working wiht NM @SGN to get these straightened out.

The stanzas below were updated on the PO_DBXref.txt file on SVN, and appear to be working on beta.

However, many of the id’s from the association file, have no corresponding pages (e.g., id’s of 645 or below) and some of the id’s may not be going to the correct page.

For example, go to the Live PO page, search annotations for “LA0085” and then click on the link to go to the page for germplasm LA0085 in S. lycopersicum.

On this page, and in the association file, LA0085 has the id 4420, but if you go to http://solgenomics.net/stock/4420/view/, it is a dead link.

PO will update the link to use the new urls (see below:)

SGN should be sure that all germplasms have an ID for this url and that those id’s are correct. SGN should check and uptdate the stock/germplasm ids in all of the germplasm association file.


abbreviation: SGN_gene

database: Sol Genomics Network

object: locus identifier

example_id: SGN_gene:7740

generic url: http://solgenomics.net/

url_syntax: http://solgenomics.net/phenome/locus_display.pl?locus_id=[example_id]

url_example: http://solgenomics.net/phenome/locus_display.pl?locus_id=7740


abbreviation: SGN_germplasm

database: Sol Genomics Network

object: stock/accession/germplasm identifier

example_id: SGN_germplasm:6583

generic url: http://solgenomics.net/

url_syntax: http://solgenomics.net/stock/[example_id]/view/

url_example: http://solgenomics.net/stock/6583/view/


abbreviation: SGN_ref

database: Sol Genomics Network

object: reference identifier

example_id: SGN_ref:800

generic url: http://solgenomics.net/

url_syntax: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]

url_example: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=800

Note: One of the common links that SGN uses (pub_id=861) goes to a page with basically no information. NM is working on fixing it.


  • Links to the non-standard refs:

RW Created a PO_references page on the wiki and added a few of the PO_REF definition dbxrefs to the ontology file, for testing.

For example see: thallus (PO:0030027) working on beta browser


dbxref.txt fil

The file on SVN only has correct text for the stanzas we have changed. Can JE give RW the text that AmiGO is actually using, so she can update dbxref.txt.

Link on http://plantontology.org/docs/docs.html goes old file. Should link to SVN?

Annotation files

  • MaizeGDB

MS is working on updating the MaizeGDB annotation files that are on our SVN. They should updated by the end of the week.

PJ raised a point last week that we should have the set of Maize classical genes mapped to the maize gene models.

Since MS is really busy right now, JP is going to insert the mappings in the association files based on Schnable's mapping data files and will commit changes to the SVN. Once MS updates the association files, we can just rerun them, or let her do it at her end for later releases. This raised the issue of how to link to the dbxrefs and not end up with broken links.


From JP by email: I did some testing this evening on PO beta, swapping in classical gene names & symbols for gene model id's (GRMZ*) on maize annotations. We wanted to see what the effect(s) would be if we replaced DB Object ID (col 2) with a locus id and/or replaced DB Object Symbol (col 3) with a classical maize gene symbol provided by CoGe.

JP created two new association rows in the test load file Justin Elser has been using in Beta to test MaizeGDB uploads to test these:

MaizeGDB 12768 wx1 - PO:0006340 PMID:20110808|MaizeGDB:9021423 IEP - A waxy1 GRMZM2G099328 gene_model taxon:4577 20110914 MaizeGDB part_of(PO:0009025) MaizeGDB GRMZM2G099328 wx1 - PO:0006340 PMID:20110808|MaizeGDB:9021423 IEP - A waxy1 - gene_model taxon:4577 20110914 MaizeGDB part_of(PO:0009025)

(Don't worry about the fact that my chosen gene model id doesn't actually map to "wx1". That's irrelevant for our test.)

Next, JE reloaded his test annotation data on beta (thanks, Justin). Here are the results on the AmiGO browser:

[(replaced col 2 with the locus id for "waxy1", moved the gene model id to synonyms)]

(left the gene model id in col 2)

So the question on the table, I think, is which of these two approaches should we take? Please peruse these two pages and their links to MaizeGDB and let me know what you think. My gut feeling is that the first option (use locus id) is best for the users, but it will require add'l mapping work -- for us and for Mary -- to create an associated list of gene model id's to locus id's.


  • Gramene:

From last meeting: New annotations should be coming from Gramene in the next 1-2 weeks. PJ and LC have been in communication with KYC at Gramene and pointed them to the editor's file as the most current one. Not sure what the time line on these will be.


Others

We are also working on adding new annotation files for Physcomitrella, grape and strawberry. We will need to add DBXrefs for these sources as well.


Physcomitrella-


strawberry- will link to the Roseacea database- need link, pj will send it to us.



Grape - The original contributor, Nicola sent an additional file with the evidence code IEA (Inferred from Electronic Annotation) - thus these are based on homology to Arabidopsis, not actual assays in the grape leaf. Not a strong evidence to create annotations based on. PJ requested that they substitute the code: 'ISS'

The current file we are working on should be combined with the new one, put onto the SVN, but not loaded into the database. Gene or coding region may match, but without promoter analysis, it is too weak. PJ will talk to PlexDB to get the microarray expression data- PlexDB has ~17 grape experiments, so we could link to m/a probe ids mapped to the genes. Julie Dickerson may be able to send us a dump for the database.


We will not try to include these in this release, but will continue building it. Column 1. DB reference should be to CRIBI (sp?) link?. Column

Final Edits to be fixed:

PJ has requested that these be returned to being part_of spikelet floret, instead of spikelet. This is how most people think of them.

In order to do this (an maintain the logical consistency of the PO, lemma and palea would have to be is_a phyllome, instead of is_a flower bract.

Plan for the next few weeks:

LC will be away at a course from 10-16 to 11-2. We want to continue having meetings- RW will


Upcoming meetings and Presentations 2011/2012:

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.

PAG 2012

January 14-18, 2012, San Diego, California

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

Our proposal for an Ontology workshop for PAG has been approved. It will be on Saturday January 14th from 10:20am-12:30pm

Use of Ontologies for Organizing Plant and Animal Genomics Data


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

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

Other activities?

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,

PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide. See notes above

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.


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.

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