CCF_tools

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.

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:

• ccf_Spleen_classes.owl

Example heirarchy in OWL (classes)

Example axiom in OWL

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

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'.