PAINT database update pipeline

Summary Google doc

https://docs.google.com/document/d/1Tx3DGLanQ1P6vBL6FWH5V5M7nVqCCCsqu-6m61jPtQ4/edit?usp=sharing

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 annotion 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 ?
• 'View omitted annotation information' -> generated on the fly ???
  • What types of messages ? tree changes information (missing nodes) - what else ?