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CCF_tools Build Status

Some simple wrapper code for testing the part/is_a relationships implicit in ASCT-b tables for validity against Uberon and CL and using these to produce OWL via ROBOT templates. One OWL file is produced following OBO standards.

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To run, you will need ROBOT installed + a python 3.8 environment with the contents of requirements.txt installed. From the command line run:

$ cd src 
$ make all

Example output file:

Example heirarchy in OWL (classes)

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Example axiom in OWL

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Example annotation of OWL axiom - showing confirmed status as valid in Uberon

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Reports

Example report listing not valid relationships https://github.com/hubmapconsortium/ccf-validation-tools/blob/master/logs/class_Kidney_log.tsv

s slabel user_slabel o olabel user_olabel
  UBERON:0001284 renal column renal column (column of Bertin) UBERON:0000362 renal medulla
  CL:0000653 glomerular visceral epithelial cell glomerular visceral epithelial cell UBERON:0006852 glomerular visceral epithelium

Translation: There is no valid (part_of or is_a) relationship between 'renal column' and 'renal medulla' or between 'glomerular visceral epithelial cell' and 'glomerular visceral epithelium'.