FoodOn Parsing problem in Python

[Anuja Tayal]

Hi

While parsing FoodOn through rdflib in python, I am getting following error

ValueError: day is out of range for month

<Graph identifier=Na3e430e5169b4b638aa47e9b4f20f991 (<class 'rdflib.graph.Graph'>)>

Can you help with the error?

Thanks and Regards

Anuja

[Damion Dooley]

If you can post a simple python script for me to run, that would be appreciated!  Unfortunately I don't have a tool at hand to spot malformed dates (protege seems to be accepting them on load/save).

Thanks,

Damion

[Damion Dooley]

Thanks for sending me the parsing script:

import rdflib
g=rdflib.Graph()
g.parse("foodon.owl",format='application/rdf+xml')

So it looks like this parses the foodon.owl file (with a few minor errors) if I load it directly from https://github.com/FoodOntology/foodon/ , the best place to get the source.  Can you load it from there please?

I'll check with Bioportal about updating their version of it.  It may require a release from our end.

[Anuja Tayal]

After uploading foodon file from GitHub, I am getting different errors

File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/xml/sax/handler.py", line 38, in fatalError

    raise exception

xml.sax._exceptions.SAXParseException: file:///Users/anujatayal/Downloads/uic-courses/food/foodon.owl:16:75: not well-formed (invalid token)

Thanks and Regards

Anuja Tayal

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[Damion Dooley]

We've made some other edits to the foodon file that might solve issues for you, if you want to try reloading foodon.owl from github?!