Tasks/Priorities 2012 (Archived)

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Tasks due 1st May 2012

  1. Implementation of the JIRA project management software for the GO Consortium
  2. Common Annotation Framework. Determine the directions and deliverables for the next year.
  3. Full documentation of the minimal/ideal annotation format, including the gp2protein, gp2rna formats.

Task management requests

We need to be able to start relying on other GO-NIH funded curators for contributions. Perhaps also set up some focused working group meetings to make headway.

Other Projects

Annotation_Extension field (col-16)

1. Clear, full guidance describing the data for the annotation_extension field Some documentation is in progress here: http://wiki.geneontology.org/index.php/Annotation_Extension

Actions needed:

- draft documentation to be finished (estimated time: 5 hours)

- documentation to be agreed by the GO Consortium annotation groups. This would initially be introduced in an annotation call, then a GO list discussion

- Annotation activity (estimated time to end doc: 2 months)


2. Annotation_extension QC checks to ensure quality of data

QC checks need to be agreed and implemented to enforce the agreed format. Many of the annotation_extension fields published by groups do not meet the current format specifications QCs would need to specify the overall format of the line and take into account the appropriate domain/scope of individual relations

- QCs to be formulated (general format QC, scope/domain restrictions applied to relationship usage QC, Protege web service for more advanced checks?)

- QCs to be agreed by GO Consortium (schedule GO annotation calls)

- QCs to be implemented on GOC-submitted files by the appropriate filtering mechanism

- Annotation QC and software activity


3. Relationships ontology

- relationships used in the annotation_extension field need to be agreed by both the ontology developers and annotators as being sufficiently descriptive for both annotations and logical definitions.

- relationship ontology needs to move out of scratch

- create a web-based visual represenation of the relationship ontology?

- ontology and annotation activity


4. Display the annotation_extension field in AmiGO - discussion on appropriate web display required at a GO Consortium annotation call?

- annotation and software activity


5. Public engagement on the value of the annotation_extension data

- dedicated open call inviting go_friends folk?

- email targetting tool developers, informing them of the annotation_extension resource?

- publication showcasing the value of the annotation_extension resource?

- all managers?

Extended annotation format (increased expressivity)

Chain of evidence

http://wiki.geneontology.org/index.php/Chain_of_Evidence

  • Working group needs to be set up to determine how best to represent chains of evidence and report options back to the annotation groups.
  • Concept of Annotation ID seems increasingly as an useful concept to deal with chain of evidence and to string annotations together. This is in the context of the recent discussions on ISS from IC (new ISC evidence cod) and evidence code for inferences based on inter-ontology links

Non-redundant set of annotations

Annotating to Complexes as Objects

  • Come up with pipleline/specs to annotate Complexes as objects.
    • sort out contributes_to qualifier
    • how to propagate annotations to subunits



  1. Clean up existing documentation on wiki and move to the GO website.
  2. Create new documentation for existing file formats: annotation/mapping files, annotation guidance (already mentioned, and set as a prioritised task for this next quarter)
  3. Annotation documentation guidance; what constitutes a redundant annotation, clarification of contributes_to qualifier. Specific guidance for transcription and apoptosis.
  4. Discuss and resolve new annotation methods: annotating to protein complexes, mapping of ECO to GO ev. codes, annotation relations
  5. define pipeline for PAINT curation and GOC annotation targets - to be coordinated with PAINT folks
  6. Evidence codes. Mapping of ECO to GO evidence codes. Resolve evidence code for MF-BP, BP-CC inferences
  7. QC checks, integrating centrally created annotations (reciprocals/inferrred). We need to collaborate with the software group as to how to implement for best impact.
  8. open up CANTO in some form to the public, communication with emerging annotation groups
  9. Transition_to_OWL
  10. TermGenie templates
    1. Regulation by
    2. Chemical entity templates
    3. Process-cell component templates
  11. LEGO prototype environment
  12. formal specification of expressive annotations in OWL

Action Items from the February 2012 GO Consortium meeting

ACTION: PIs need to determine the most important items to be communicated for metrics on annotation quality/efficiency improvements. These need to be displayed separately for NIH-funded and the full GO Consortium efforts.

ACTION: an appropriate web-display for GOC users needs to be constructed, including statistics and statements on how the annotation set is changing in accordance to new format/focused annotation efforts.

ACTION: gp2protein files. More documentation needed to support users of these. Annotation groups need to engage and update their files.

ACTION: groups who annotate to ncRNAs should create a gp2rna file.