Annotation Advocacy progress report for 2015

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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, Annotation Extension 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:

  1. Mechanics of these annotation calls, how to make them productive, effective. We switched to using Bluejeans. We also decided to have a annotation consistency exercise every month
  2. ECO presentation by Marcus Chibucos
  3. Jenkins GAF reports
  4. Availability of RNAcentral IDs for annotating RNA gene products
  5. Behind the scenes of how data/GO annotations (GAF) are received, processed and disseminated, how to run the GAF filtering script
  6. Transferring col-16 data while doing an ISS annotation
  7. Ontology issues with ion channels (specific vs non-specific)
  8. new guidelines for creating complexes in GO to be in sync with IntAct
  9. moving SourceForge ontology tracker to github
  10. GAF 2.1 release (in this release, the with/from column can handle pipe or comma)
  11. changing the term string for transcription terms so they are more readable
  12. No more merges in the Ontology.
  13. report on how cell lines are handled by MGI
  14. review of Obsolete relations in col-16 and rehousing existing annotations
  15. New ECO term for inter-ontology inferencing pipeline
  16. update on new TermGenie templates
  17. miRNA guideline
  18. how to annotate regulation of activity (unresolved)
  19. review of col-16 documentation on github
  20. What IDs should be allowed in col-16 and column-8 (with/from)?
  21. When to tag a term with the Do Not Automatically annotate tag