PAINT database update pipeline

From GO Wiki
Jump to navigation Jump to search

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
    • New exp evidence

(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 -> replace to the new term b) does not have a 'replaced_by' tag -> output message xxx

    • 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 ?

Managing new PTHR versions