PAINT database update pipeline

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External info

Summary Google doc

fullgo_paint_update github repo (This is the actual code that runs!)

Import EXP files

  • File location:

http://geneontology.org/gene-associations/*.gaf.gz

Import ontology

  • File location:

http://geneontology.org/ontology/go.obo

Integration with existing PAINT annotations

  • Managing differences:
    • Missing EXP evidence
      • PAINT annotations are obsoleted if derived from GO EXP evidence is now missing.
    • New exp evidence
      • Existing PAINT annotations are updated with new EXP evidence.
      • Previously obsoleted PAINT annotations are "un-obsoleted" if new EXP evidence supporting it appears.
(see for ex https://github.com/pantherdb/fullgo_paint_update/issues/10)
    • Handling obsolete and merged terms
      • obsolete terms:
        • a) has a 'replaced_by' tag
          • update GO and PAINT annotations to the new term and a message "[term] is obsoleted and replaced by [new term] so the annotation to [PTN####] is updated with new GO term" is outputted for PAINT annotations to this term.
        • b) does not have a 'replaced_by' tag
          • term and PAINT annotations are obsoleted and a message "[term] is obsoleted and no replaced term, so the annotation to [PTN####] is obsoleted" is outputted for PAINT annotations to this term
    • etc ?


  • List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface)
    • What types of messages ? obsoletes, missing EXP... what else ?
    • "[term] is obsoleted and replaced by [new term] so the annotation to [PTN####] is updated with new GO term"
    • "[term] is obsoleted and no replaced term, so the annotation to [PTN####] is obsoleted"
  • 'View omitted annotation information' -> generated on the fly ???
    • What types of messages ? tree changes information (missing nodes) - what else ?

Managing new PTHR versions