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FIx scripts that generates FB's extension_config.tsv to include the correct top term IDs for FVdv qualifiers #2450

Open vmt25 opened 3 years ago

vmt25 commented 3 years ago

The scripts use the now obsolete term 'FBdv:00007008 occurrent' as parent term to all allowed developmental qualifiers, preventing their usage in phenotype curation (see #2414)

  1. Replace 'FBdv:00007008 occurrent' with the now 4 top terms of the FBdv ontology (so that any FBdv term can be used): FBdv:00007013 age FBdv:00007024 biological process FBdv:00005259 developmental stage FBdv:00000000 Drosophila life

  2. try to automate it, so that the top or multiple top terms of the ontology are always selected even if the ontology changes - this is to future-proof it and thus prevent cases such as #2414.

  3. try to extend automation to other qualifiers/qualifier ontologies

vmt25 commented 3 years ago

An while on this, try and adapt the scripts to adopt #2004's implementation

vmt25 commented 3 years ago 
1. Replace 'FBdv:00007008 occurrent' with the now 4 top terms of the FBdv ontology (so that any FBdv term can be used):
   FBdv:00007013 age
   FBdv:00007024 biological process
   FBdv:00005259 developmental stage
   FBdv:00000000 Drosophila life

This part is done