Tasks/Priorities 2012 (Archived): Difference between revisions

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- 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.
- 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.


==== Extended annotation format ====
==== Extended annotation format (increased expressivity)====


===== Chain of evidence =====
===== Chain of evidence =====
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* Working group needs to be set up to determine how best to represent chains of evidence and report options back to the annotation groups.
* 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  
* Concept of Annotation ID seems increasingly as an useful concept to deal with chain of evidence and to string annotations together
 


====Non-redundant set of annotations====
====Non-redundant set of annotations====

Revision as of 14:04, 16 March 2012

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. We need clear, full guidance describing the data that should go into this 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 (estimated time to end doc: 2 months)


2. 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 - QCs to be agreed by GO Consortium - QCs to be implemented on GOC-submitted files by the appropriate filtering mechanism

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.

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

Non-redundant set of annotations


  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