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==LEGO GAF/GPAD Calls== | |||
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]] | |||
Revision as of 12:30, 27 September 2016
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
Activities
- Roadmap 2010
- Roadmap 2011
- RoadMap (PDF file - provides project goals with time line)
- Educate GOC curators about best annotation practice;
- Enforce annotation rules/policies within GOC
- Maintain the annotation/evidence code documentation
- Train/assist new groups with annotations: see How_External_Communities_can_contribute_annotations_to_the_GO_Consortium
- Educate and keep all the annotating groups up-to-date with changes in GAF format
- Annotation Extensions
- Keep all curators up-to-date with ontology development and how it affects annotations
- Chain of Evidence- Proposal to represent chain/summation of evidence in an annotation.
- Evidence Code Ontology (ECO) - Proposal to represent evidence in an ontology
- Proposal for cron tabs - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences
- Examples for phylogeny based evidence codes
- Ideas for GOC community curation tool
- Protein Complex ids as GO annotation objects
- LEGO-style annotation ideas
- Proposed Developments to the GAF annotation format
- InterPro2GO Session October 4th 2011
- MF-BP inferences
- Protein Binding clean up
- Annotation Guidance Pages
- Evidence Code proposals
- With/From field restrictions for evidence codes
- Core Consortium annotation activities
- GPAD
- Common Annotation Framework Specification
- gp2protein file
- gp2rna file
- gp_unlocalized file
- mechanisms for reducing annotation redundancy
- Annotations to Cell Fraction-type terms
- TermEnrichment: Gold Standard Data Sets
- "Response to" terms
- GAF 2.1 specs
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 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
- Annotation Call 2016 Minutes
- 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.
- Recurring meeting URL: https://bluejeans.com/993661940
to join via phone: enter Meeting ID 993661940 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
- Past Annotation Call Minutes: 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | Curation Consistency Rota 2015
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
- 2015
- 2016
LEGO GAF/GPAD Calls
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
Monthly Reports
- September 2011
- August 2011
- July 2011
- June 2011
- May 2011
- April 2011
- March 2011
- February 2011
- January 2011
- December 2010
- November 2010
- October 2010
- September 2010
- August 2010
- July 2010
- June 2010
Meeting calendar
Annotation_topics for next meeting
Metrics of success
Process
Issues for the Annotation Group
- Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)
Annotations to Catalytic activity with IPI