As discussed in #63 , this PR adds a Python script using fastobo to convert the old PSI-MOD.obo file into a propert OBO 1.4 file. I also added a Makefile to make it easier to regenerate the newstyle OBO and the OWL file when updating the editors version.
The script will basically:
Convert Remap property values into a replaced_by clause, allowing tools like robot repair to automatically replace obsolete terms with their replacement in eventual consumers of the PSI-MOD ontology.
Keep Unimod, UniProt and GNOme cross-references but fix the formatting so that they can eventually expand to full IRIs using ID spaces.
Convert other cross-references using the right xsd datatype (xsd:float for masses, xsd:string for the rest)
Remove property-values which have none values (otherwise, this can confuse parsers, e.g. because an xsd:float property like DiffAvg would have a none value)
To get it running, make sure you have Python and fastobo installed (you can get it from PyPI with `pip install fastobo).
I also fixed some typos in the editors' file (UinMod, UniMo, UnMod...)
As discussed in #63 , this PR adds a Python script using
fastoboto convert the oldPSI-MOD.obofile into a propert OBO 1.4 file. I also added aMakefileto make it easier to regenerate the newstyle OBO and the OWL file when updating the editors version.The script will basically:
Remapproperty values into areplaced_byclause, allowing tools likerobot repairto automatically replace obsolete terms with their replacement in eventual consumers of the PSI-MOD ontology.Unimod,UniProtandGNOmecross-references but fix the formatting so that they can eventually expand to full IRIs using ID spaces.xsddatatype (xsd:floatfor masses,xsd:stringfor the rest)nonevalues (otherwise, this can confuse parsers, e.g. because anxsd:floatproperty likeDiffAvgwould have anonevalue)To get it running, make sure you have Python and fastobo installed (you can get it from PyPI with `pip install fastobo).
I also fixed some typos in the editors' file (
UinMod,UniMo,UnMod...)