Annotation

Group Leaders

Rachael Huntley (GOA@UniProt) and Rama Balakrishnan (SGD) with help from Pascale (dictyBase/Ref.genome project).

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

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
  • Mock-ups of new GOC Annotation pages
• 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
  • Column 16: Cell Type
  • Column 16: Targets
• 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
• 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

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

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 Rachael or Rama.

• Past Annotation Call Minutes: 2010 | 2011 | 2012

• 2013
• Annotation Conf. Call, January 22, 2013

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

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

• Annotations removed as a result of Annotation QCs

• Moved to GAF2.0 format on the 1st June 2010

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