Tasks/Priorities 2012 (Archived): Difference between revisions
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# Implementation of the JIRA project management software for the GO Consortium | # Implementation of the JIRA project management software for the GO Consortium | ||
# Common Annotation Framework. Determine the directions and deliverables for the next year. | # Common Annotation Framework. Determine the directions and deliverables for the next year. | ||
# Full documentation of the minimal/ideal annotation format, including the gp2protein, gp2rna formats. | # Full documentation of the minimal/ideal annotation format, including the gp2protein, gp2rna formats. | ||
====Task management requests==== | ====Task management requests==== |
Revision as of 13:25, 13 March 2012
Tasks due 1st May 2012
- Implementation of the JIRA project management software for the GO Consortium
- Common Annotation Framework. Determine the directions and deliverables for the next year.
- 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
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
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.
- Clean up existing documentation on wiki and move to the GO website.
- Create new documentation for existing file formats: annotation/mapping files, annotation guidance (already mentioned, and set as a prioritised task for this next quarter)
- Annotation documentation guidance; what constitutes a redundant annotation, clarification of contributes_to qualifier. Specific guidance for transcription and apoptosis.
- Discuss and resolve new annotation methods: annotating to protein complexes, mapping of ECO to GO ev. codes, annotation relations
- define pipeline for PAINT curation and GOC annotation targets - to be coordinated with PAINT folks
- Evidence codes. Mapping of ECO to GO evidence codes. Resolve evidence code for MF-BP, BP-CC inferences
- QC checks, integrating centrally created annotations (reciprocals/inferrred). We need to collaborate with the software group as to how to implement for best impact.
- open up CANTO in some form to the public, communication with emerging annotation groups
- Transition_to_OWL
- TermGenie templates
- Regulation by
- Chemical entity templates
- Process-cell component templates
- LEGO prototype environment
- formal specification of expressive annotations in OWL