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using owl files from nidm-specs #94

Closed djarecka closed 6 years ago

djarecka commented 6 years ago

we should remove owl files from term and using the one from nidm-specs repo directly

djarecka commented 6 years ago

@dbkeator , @khelm - I started working on this, but I'm having problem with parsing the file from nidm-specs repo: https://github.com/incf-nidash/nidm-specs/blob/master/nidm/nidm-experiment/terms/demographics2.owl

It looks like the file is different from the one we're currently using and rdflib gives me an error even if I download it locally. Could you please check if the file has a proper syntax.

WARNING:rdflib.term:file:///Users/dorota/PyNIDM/!DOCTYPE html does not look like a valid URI, trying to serialize this will break.
WARNING:rdflib.term:file:///Users/dorota/PyNIDM/html lang="en" does not look like a valid URI, trying to serialize this will break.
*** rdflib.plugins.parsers.notation3.BadSyntax: <no detail available>
dbkeator commented 6 years ago

This may be a problem for @khelm because I've simply been using the copies of the OWL files that are in PyNIDM....

khelm commented 6 years ago

@djarecka - I don't think those demographics files are being used for anything and are legacy files. @cmaumet - is this true? I believe that you just need the nidm-experiment.owl files and the files in .../nidm-experiment/imports

djarecka commented 6 years ago

In Utils I have two files: demographics2.owl and nidm-experiment.owl (see here). I need to know where I can find them in nidm-specs and I couldn't find them in nidm-specs/nidm/nidm-experiment/imports/.

khelm commented 6 years ago

The files in the imports directory are terms that we are importing from different ontologies. The actual nidm.owl file is actually in the /nidm-experiment/terms

djarecka commented 6 years ago

I was providing wrong url, now the load_nidm_owl_files when I provide nidm-experiment.owl from nidm-specs repo. As @khelm suggested I removed demographics2.owl. See #95

dbkeator commented 6 years ago

I've removed demographics2.owl from the Util.py load_nidm_owl_files function. See https://github.com/incf-nidash/PyNIDM/pull/96