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 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 | renal medulla | |
CL:0000653 | glomerular visceral epithelial cell | glomerular visceral epithelial cell | UBERON:0006852 | glomerular visceral epithelium | 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'.