POC Conf. Call 9-27-11

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POC meeting, Webex Conference Call; Date: Tuesday Sept 27th, 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_9-20-11?

Tech Issues for the Upcoming Release

Inclusion of synonyms

The Spanish synonyms are now working fine, have the descriptor "(Spanish:)" preceding them.

  • Japanese synonyms?

Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO

Japanese synonyms are not currently in the editors' file. Should be added. What is the status on this?

For the release, we will highlight this new feature as we are the first ontology to offer spanish (and possibly Japanese) translations. Will send out the announcements in Spanish as well.


2. Eliminating_Zea/Poaceae_terms_from_PO

This is complete for both PAO and PGDSO, although some names and definitions in the PGDSO may change as we go forward.


3. New annotation files:

We are working on getting the new set of MaizeGDB annotations in.

Addition of new annotations for grape (LC working on) and strawberry

What is the status of the Physcomitrella annotations? PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids


We will move ahead with the release with the maizeGDB anatomy annotations (in SVN already), may need some minor fixing

There is increasing interest in the OBOEdit community to be able to include non-standard characters. They are not a problem for OE, but for AmiGo and other applications. JP will bring it up ont he next AmiGO development meeting


4. Fixing the links to the Dbxrefs



5. For more details see: Summary_of_Changes_to_PO_September_2011

Adding Dbx Refs

for MaizeGDB

See notes from the Follow_up_meeting_re:_Association_files_for_the_Kaeppler_data_set_Sept_15,_2011

We can use one database abbreviation to access all MaizeGDB pages. It uses their url for anything with a MaizeGDB id, but also works for gene model names.

File format (modified from http://www.geneontology.org/cgi-bin/xrefs.cgi - changed object to include gene model name):

abbreviation: MaizeGDB

database: Maize Genetics and Genomics Database

object: MaizeGDB Object ID Number or Gene Model Name

example_id: MaizeGDB:881225

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]

url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225


Mary will update all of the xrefs in MaizeGDB's old association files to use this abbreviation when she does her next update. Until then, we should keep the other MaizeGDB abbreviation in the dbxref file, so the links will still work.

Existing MaizeGDB stanzas are incorrectly formatted. We cannot add the new stanza to http://plantontology.org/docs/dbxref/PO_DBXref.txt without removing at least one of the old ones. Not sure what repurcussions this will have.

Gramene

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.

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.

dbxref file

Does PO's version of AmiGO read from http://plantontology.org/docs/dbxref/PO_DBXref.txt? This file seems very out of date and appears to have incorrect formatting in a number of places.


PJ will work with the JE/JP to get the Dbxrefs working.

PJ: The local file is not used. The major library of Dbxrefs is coming from GO, as part of AmiGO. For JP: when you are working with CM on the new AmiGO, need to make sure that the local installations, can amend the library of cross refs from GO with the ones from the local databse.

RW: The problem we are having is that even if we request new DBxrefs to be added to the GO file, they are not showing up in our browser. It appears that our version of AmiGO has a built-in set of refs and it is not reading the current GO file. Go is using an updated version of AmiGO, we are using a customized version of the older version. Suggestion is to have the new AmiGO read the common file.

LC will send PJ the broken Gramene links, need new ones for the new files. JP will set up meeting with JE and CM to work on this

non-standard definition dbxrefs

We have a few definition dbxrefs that don't have an isbn or pmid number. We need to create a dbxref library for these, similar to what GO uses (GO reference collection). RW can add this to the OE file. Need to look into how AmiGO interfaces with this.

Edits to complete before release: PAO

All the edits from last weeks aganda have been completed

Possible new Collaborator Group:e-monocot

Fill in some details:...

RW met with the director of the project at IBC in Melbourne. He was interested in PO.

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

  • Pricing

Academic Package $1055

Graduate/PhD Student Package $880

Corporate Package $1340

Academic/Student No-Housing Package $720

Corporate No-Housing Package $905

DWS will be away, but RW could attend


PAG 2012

January 14-18, 2012, San Diego, California

Registration and Abstract submissions open on Sept 22nd

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).

*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

From the Instructions page: For authors wishing to submit to DATABASE for the 2012 BIOCURATION VIRTUAL ISSUE:

  • Submission deadline: October 15, 2011
  • First decisions: November 15, 2011
  • Revisions deadline: December 15, 2011
  • Final decisions: January 10, 2012
  • Conference: April 2-4 2012

PJ planning to attend, LC and RW can go. Check with Pascal to confirm dates

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open

RW and DWS will look at putting in a proposal for a half day workshop.

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