Difference between revisions of "Annotation Advocacy progress report for 2014"

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(Annotation Consistency)
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''Protein oligomerization terms:'' Use of these terms is inconsistent. We would like to provide guidelines on how to annotate using these terms. Options include using PRO IDs in the annotation extension field or annotating directly to a complex ID (when this facility is in place). The ontology is being overhauled in this area.
 
''Protein oligomerization terms:'' Use of these terms is inconsistent. We would like to provide guidelines on how to annotate using these terms. Options include using PRO IDs in the annotation extension field or annotating directly to a complex ID (when this facility is in place). The ontology is being overhauled in this area.
  
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'''Apoptosis'''
 
''E1, E2, E3 Ub ligase terms'': Overhaul of these terms and discussion on how to reannotate
 
''E1, E2, E3 Ub ligase terms'': Overhaul of these terms and discussion on how to reannotate
 
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'''Enzyme Regulator activity terms'''
 
'' Guidelines for annotating complexes as objects''
 
'' Guidelines for annotating complexes as objects''
 
'' Use of ECO terms for evidence ''
 
'' Use of ECO terms for evidence ''
 
'' Discussion on tracking Unpublished references'': Groups are requested to create GO_Refs for unpublished references instead of MOD specifc internal references. This will help in QC.
 
'' Discussion on tracking Unpublished references'': Groups are requested to create GO_Refs for unpublished references instead of MOD specifc internal references. This will help in QC.
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'''Other topics''': We also had Sandra Orchard and David OS talk about the IntAct Complex Portal and OWL language that is being used to model the ontologies.
  
 
==New Annotation Datasets==
 
==New Annotation Datasets==

Revision as of 16:40, 16 December 2014

Management

Rachael Huntley (UniProt-GOA)

Rama Balakrishnan (SGD)

Annotation Consistency

Annotation calls

We continue to discuss annotation issues on our biweekly annotation calls. Subjects can be anything from new annotation guidelines, quality control checks, ontology or evidence code-related discussions, tool development or updates from annotating groups.

Some of the discussion we have had this year include;

Jenkins reports: Jenkins validates GAF files for both hard and soft QC checks and generates reports. Groups are reminded via email to check the reports for their GAF files and to correct any errors.

Annotation extension: Discussion on the correct use of relationships in col-16. Consistency exercises have been provided on several calls where we discuss specific annotations using extensions with the aim of reaching a consensus on how to annotate the example.

Discussion of use of pipe vs coma in the With/From Field for IPI and IGI evidence codes

Protein oligomerization terms: Use of these terms is inconsistent. We would like to provide guidelines on how to annotate using these terms. Options include using PRO IDs in the annotation extension field or annotating directly to a complex ID (when this facility is in place). The ontology is being overhauled in this area.

Apoptosis E1, E2, E3 Ub ligase terms: Overhaul of these terms and discussion on how to reannotate Enzyme Regulator activity terms Guidelines for annotating complexes as objects Use of ECO terms for evidence Discussion on tracking Unpublished references: Groups are requested to create GO_Refs for unpublished references instead of MOD specifc internal references. This will help in QC.

Other topics: We also had Sandra Orchard and David OS talk about the IntAct Complex Portal and OWL language that is being used to model the ontologies.

New Annotation Datasets

  • Data update from PseudoCAP group (use of ISS to transfer annotations to genes from other strains of pseudomonas)
  • Assist the Synapse group at Broad Institute to make annotations for Synapse genes

Documentation

We finished porting annotation guidance webpages to the Drupal site. We are in the process of cleaning up and updating the content.

GO Helpdesk

GO helpdesk staff

Rama Balakrishnan, Rachael Huntley, Harold Drabkin, Jane Lomax, Kimberly Van Auken, Tanya Berardini, Rebecca Foulger, Prudence Mutowo-Meullenet, Poala Roncaglia, David Osumi-Sutherland.

We have recruited 4 new curators to join the GO-help rotation. A FAQ was published on the GOC website to point users to some of the common questions about GO.