QCQA call 2017-11-29

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Meeting minutes 2017-11-29

  • Suggestions for documentation: Include examples of annotations to help curators
  • Documentation needs to be accessible from the annotation tool (follow up on the suggestion to create an annotation type in Protege)
  • Suggestions by Protein2GO can be misleading (what to do? We probably need to evaluate the suggestions to see how they are being used)
  • Should look at http://build.berkeleybop.org/view/GAF/
    • Get Chris /Seth to explain
    • For active groups, discuss at some annotation meeting
    • For inactive groups - delete them automatically ?
    • Ask to get a report for each rule to see which to prioritize
  • Get a report for papers with errata/retractions ??
  • What error rate are we aiming for?
  • The aim is 100%. This varies a lot by term, etc
  • Two types of errors:

1) Incorrect annotations: “Errors” in which the general/high level branch is OK are are not considered errors. We aim to annotate in the correct branch Pragmatic aim for now is 90% (for eg when we ask for a annotation review) 2) Errors of omission: when an ‘obvious’ annotation is missing - hard to tackle Errors: often come from older annotations/older papers -> Add to guidelines to review older annotations when curating a new paper Do not manually annotate: some should be hard checks, some should just be a soft check Improve mechanism for disputes: working well Later: Implement a mechanism that GOC database can post-process annotations to flag them (or whatever mechanism) to remove them from our dataset

  • Ontology changes: It would be nice to have a tool in which we *model* the changes in slims or enrichment before committing certain ontology changes (especially when we add/remove parents)

Perhaps the way would be to look at the parent and see the difference in number of annotations

Action points

  • VAL to go through the Biocuration talk about the matrix and share common errors and examples where people felt they needed to keep the annotation
  • We will compile a list of inconsistent annotation practices (for example xxx )
  • Prioritize the development of guidelines for these
  • Ask Tony to add ORCID in EBI GPAD
  • GAF reports: http://build.berkeleybop.org/view/GAF/
    • Get Chris /Seth to explain
    • Are soft checks reported ?
    • Soft checks should be associated with a comment
    • For active groups, discuss at some annotation meeting
    • For inactive groups - delete them automatically ?
    • Ask to get a report for each rule to see which to prioritize
  • Provide a list of curators expert domains: in the contacts file


SEE ALSO

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995153/