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

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(Annotation Consistency)
(NEW QC checks)
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* RCAs are that older than 1 year should be removed
* RCAs are that older than 1 year should be removed
* annotations to terms that have do_no_annotate tag
* annotations to terms that have do_no_annotate tag
* binding (GO:5488) got the tag do_not_annotate.
==GO Helpdesk==
==GO Helpdesk==

Revision as of 16:51, 16 December 2014


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.

GO Wiki and SVN changes GO repository and wiki were moved to a new machine 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.


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Discussion on tracking Unpublished references: Groups are requested to create GO_Refs for unpublished references instead of MOD specifc internal references.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.

Symbiotic relationships in the ontology and how to annotate host-cell interactions.

Extracellular branch of ontology

Phase terms in Process ontology. The ontology team has introduced phase terms in the ontology to represent distinct periods when processes occur. These terms do not have relationship (is_a) to any other process terms and they all also have a do_no_annotate tag.

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


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

Annotation to Complexes as Objects

We are working on guidelines to annotate and produce annotations for complexes.

NEW QC checks

  • We now require that for each annotation, there be either a PMID or a GO_REF as reference.
  • RCAs are that older than 1 year should be removed
  • annotations to terms that have do_no_annotate tag
  • binding (GO:5488) got the tag do_not_annotate.

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.