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. Two OWL files are produced - one OWL file following OBO standards, and one simple RDF representation with CCF_part_of triples.
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- class_template_Kidney_partonomy.tsv
- ccf_spleen_classes.owl
- ind_template_Kidney_partonomy.tsv
- ccf_spleen_ind.owl
Example https://github.com/obophenotype/CCF_tools/blob/master/templates/class_template_Kidney.tsv.log
| s | slabel | user_slabel | o | olabel | user_olabel |
|---|---|---|---|---|---|
| UBERON:0001284 | renal column (column of Bertin) | renal column | UBERON:0000362 | renal medulla | renal medulla |
| UBERON:0001232 | collecting duct of renal tubule | Collecting Duct (Medulla) | UBERON:0001231 | nephron tubule | Tubules |
Translation: There is no valid (part_of or is_a) relationship between 'renal column' and 'renal tubule' or between 'collecting duct of renal tubule' and 'renal tubule'.
Input tables live in https://github.com/obophenotype/CCF_tools/tree/master/resources/ASCT-b_tables in tsv format.
It is sufficient to copy and paste from originals.
To add a new job, edit the Makefile to add the name of the source file (minus the .tsv file extension) to the JOBS variable:
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