Difference between revisions of "Annotation"

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[[GO-CAM May 24th, 2017]]
[[GO-CAM May 24th, 2017]]
[[GO-CAM June 14th, 2017]]

Revision as of 04:38, 14 June 2017

Group Leaders

David Hill (MGI) and Kimberly Van Auken (WB)

GO Annotation Meetings

2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010

Guidelines from Annotation Camp

Annotation Meeting Stanford, CA, Feb 2012

Migration of annotating groups to Protein2GO

Procedure for migration of protein annotations to Protein2GO

Extension of Protein2GO to non-UniProtKB Identifiers


  • Keep all curators up-to-date with ontology development and how it affects annotations

How To?

How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?

OBO-Edit can load files from the disk OR from a URL.
Choose the "File -> Load..." menu option
Choose the OBO File Adapter
Type http://www.geneontology.org/ontology/gene_ontology.obo into the filename box

To see the has_part relationships, use this URL for the extended GO version:


How to run Mike Cherry's filtering script locally before checking the GAF into SVN?

  • You need access to SVN to run the script locally. If you don't have access please write to go-admin@genome.stanford.edu
  • Familiarize yourself with SVN commands (http://geneontology.org/page/svn-help)
  • You need to check out the following files from SVN. The script will fail or will give you inaccurate reports if you don't have the current version of any of the files.

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/ontology go/ontology
username@ext.geneontology.org's password:
[this will co the entire directory]

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/gene-associations/submission go/gene-associations/submission
username@ext.geneontology.org's password:
[this will co the entire directory]

>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/software/utilities go/software/utilities
username@ext.geneontology.org's password:

> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/doc/ go/doc
username@ext.geneontology.org's password:

Now you have the necessary files to run the script in your space.

  • cd to the gene-associations/submission directory
>cd go/gene-associations/submission
>../../software/utilities/filter-gene-association.pl -e -i gene_association.sgd.gz

You should see the filtering script report once the script runs through the file.

Annotation Conference calls

  • Calls are held on the 2nd and 4th Tuesday of each month. at 4pm GMT, 8am PDT.
  • Please contact David and Kimberly if there are items you would like to add to the agenda.
  • Recurring meeting URL: https://stanford.zoom.us/j/976175422

to join via phone: enter Meeting ID 976175422 after dialing in

  • from US: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)
  • from UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717
  • from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622

LEGO calls

Meetings are every Monday 11:30AM Eastern, 4:30PM Greenwich, 8:30AM Pacific

Bluejeans recurring meeting URL: https://bluejeans.com/969313231

to join via phone: enter Meeting ID 969313231 after dialing in

  • from US: +1.408.740.7256 or +1.888.240.2560
  • from UK: +44.203.608.5256
  • from Switzerland: +41.81.588.0256

LEGO January 4, 2016

LEGO January 18, 2016

LEGO February 1, 2016

LEGO February 15, 2016

LEGO March 7, 2016

LEGO March 21, 2016

LEGO March 28, 2016

LEGO April 4, 2016

LEGO April 25, 2016

LEGO May 2, 2016

LEGO May 9, 2016

LEGO May 16, 2016

LEGO May 23, 2016

LEGO June 6, 2016

LEGO June 13, 2016

LEGO June 20, 2016

LEGO June 27, 2016

LEGO July 11, 2016

LEGO July 18, 2016

LEGO July 25, 2016

LEGO August 8, 2016

LEGO August 15, 2016

LEGO August 22, 2016

LEGO August 29, 2016

LEGO September 12, 2016

LEGO September 19, 2016

LEGO September 26, 2016

LEGO October 5, 2016

LEGO October 10, 2016

LEGO October 17, 2016

LEGO October 24, 2016

LEGO October 31, 2016

GO-CAM May 10th, 2016

GO-CAM May 24th, 2017

GO-CAM June 14th, 2017


Meetings are every Wednesday 10:00AM Eastern, 3:00PM Greenwich, 7:00AM Pacific

Bluejeans recurring meeting URL: https://bluejeans.com/969313231

to join via phone: enter Meeting ID 969313231 after dialing in

  • from US: +1.408.740.7256 or +1.888.240.2560
  • from UK: +44.203.608.5256
  • from Switzerland: +41.81.588.0256

LEGO GAF/GPAD September 28, 2016

LEGO GAF/GPAD October 5, 2016

Monthly Reports

Meeting calendar

Annotation_topics for next meeting


















Metrics of success


Annotation Issues

Issues for the Annotation Group

  1. Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)

Annotations to Catalytic activity with IPI

Annotation Quality Control Checks

Action items from March 2010 GOC meeting