Difference between revisions of "Annotation"

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(How to run Mike's filtering script locally before checking the GAF into SVN?)
(How to run Mike's filtering script locally before checking the GAF into SVN?)
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>../../software/utilities/filter-gene-association.pl -e -i gene_association.sgd.gz
 
>../../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.
 
</pre>
 
</pre>
  

Revision as of 14:02, 16 March 2015

Purpose

Group Leaders

Rachael Huntley (GOA@UniProt) and Rama Balakrishnan (SGD) with help from Kimberly (WormBase).

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

Activities

  • 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
(From:http://www.geneontology.org/newsletter/archive/200705.shtml#tip)

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

http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo

How to run Mike'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 add items you would like discussed into the agenda for the next call, or contact Rama.
  • 2015
  • Curation Consistency Rota 2015

Monthly Reports

Meeting calendar

Annotation_topics for next meeting

Annotation_31Jan10

Annotation_21Dec10

Annotation_19Oct10

Annotation_21Sept10

Annotation_17Aug10

Annotation_04Aug10

Annotation_19July10

Annotation_22June10

Annotation_08June10

Annotation_01June10

Annotation_17May10

Annotation_29Apr10

Annotation_15Apr10

Annotation_08Apr10

Annotation_22Mar10

Annotation_15Mar10

Annotation_10Apr10

Metrics of success

Process

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