PAINT database update pipeline: Difference between revisions

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==External info==
[https://docs.google.com/document/d/1Tx3DGLanQ1P6vBL6FWH5V5M7nVqCCCsqu-6m61jPtQ4/edit?usp=sharing Summary Google doc]
[https://github.com/pantherdb/fullgo_paint_update fullgo_paint_update github repo] (This is the actual code that runs!)
==Import EXP files==
==Import EXP files==


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


==Import ontology==
==Import ontology==


* File location:  
* File location:
 
http://geneontology.org/ontology/go.obo


==Integration with existing PAINT annotations==
==Integration with existing PAINT annotations==
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* Managing differences:  
* Managing differences:  
** Missing EXP evidence
** Missing EXP evidence
*** PAINT annotations are obsoleted if derived from GO EXP evidence is now missing.
** New exp evidence
** New exp evidence
(see for ex https://github.com/pantherdb/fullgo_paint_update/issues/10)  
*** 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
** Handling obsolete and merged terms
- obsolete terms:  
*** obsolete terms:  
a) has a 'replaced_by' tag -> replace to the new term
**** a) has a 'replaced_by' tag
b) does not have a 'replaced_by' tag -> output message xxx
***** 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 ?  
** etc ?  


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* List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface)
* List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface)
** What types of messages ? obsoletes, missing EXP... what else ?  
** 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 ???
* 'View omitted annotation information' -> generated on the fly ???
** What types of messages ? tree changes information (missing nodes) - what else ?
** What types of messages ? tree changes information (missing nodes) - what else ?
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[[Category:Reference Genome]] [[Category:Working Groups]]
 
[[Category:PAINT]]

Latest revision as of 09:47, 9 April 2019

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