Open jakebeal opened 2 years ago
Note: the sequence encoding issues go the other way as well, from 3->2
Thanks Jake! I'll check it out.
Another remapping that needs to be done: the ComponentDefinition BioPAX types needs to be remapped to Component SBO types.
How did you validate? I wrote this conversion before there was an SBOL3 validator!
We have a validator in pySBOL3, much of which is bootstrapped off of the sbol-shacl (https://github.com/SynBioDex/sbol-shacl) generated from the sbol3 ontology. You can likely pull in the shacl for validation in sbolgraph as well --- that takes care of all the "syntactic" issues, leaving the more complex rules still to implement.
Conversion from SBOL2 to SBOL3 creates files with validation errors. For example, here are the errors from conversion of this short J23101 XML file: