RefGenome9Dec08 Phone Conference (Archived)

Improving annotation documentation

Process:

• Amelia is the point person for the documentation project.
• New content driven by Kara and Pascale as they go through the trees for the RefGenome project and see the usage of the terms
• Debby and Brenley will be in charge of salvaging and consolidation of existing documentation
• everyone will send appropriate examples and counter-examples with PMIDs to the GO editorial office to add as comments to the GO terms and definitions
• All documentation will be indexed and searchable on GONUTS (Seth, Amelia)

Tree-based annotation process

(Kara and Pascale)

Annotation issues

• 'Response to x': Tanya Annotation_consistency:_'Response_to'_terms
• HTP: Emily Annotation_consistency:_HTP

1. Annotation consistency: x protein binding and with : Becky, David
2. Annotation consistency: Using IEP : Emily, Pascale, Ruth, Stacia
3. Annotation consistency: xx binding in the context of gene product  : Victoria, Pascale, David
4. Annotation_consistency:_IDA_or_IC_for_processes :Tanya Berardini, Emily Dimmer, Pascale Gaudet, Chris Mungall, Kimberly VanAuken, David Hill

Review action items

1. Everyone should add to Annotation_consistency:_'Response_to'_terms how they use the response to terms (evidence codes and typical supporting experiment)
2. Everyone who have comments about a potential HTP annotation tag should add them here: Annotation_consistency:_HTP.
3. Debby: Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.
4. Emily and Debby: Clarify GO:0006730 one-carbon compound metabolic process and GO:0019438 aromatic compound biosynthetic process - these terms were added by the HAMAP and InterPro groups. Both of those processes involve enzymes that use a folic acid derivative as a coenzyme, but Debbie didn't think that FolE (which catalyzes the first committed step in folic acid biosynthetic) should be annotated to those processes.
5. Victoria: Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.
6. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
7. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.

Next conference call

Tuesday January 13, 2009, (10 AM CDT, 8 AM PDT, 4 PM BST)

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