CMO completely broken right now due to parsing issues

[matentzn]

Hello!

Right now CMO cannot be processed at all:

• Broken object property:
• Many broken xrefs like <oboInOWL:xref rdf:resource="http://purl.obolibrary.org/obo/Wikipedia#_http\://en.wikipedia.org/wiki/Waist-hip_ratio"/>
• Or <oboInOWL:xref rdf:resource="http://purl.obolibrary.org/obo/MedicineNet#_http\://www.medicinenet.com"/>

As a minimum, please try to use ROBOT with the OWL release file (which is the most important one):

robot convert -i cmo.owl -f ofn -o cmo.ofn

Or open it with Protege!

[tutajm]

As suggested we have added another file in OWL functional format .ofn. The files is available here: https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.ofn

Please let us know if that fixes your problem.

PS. The .ofn file is generated from obo file just like mentioned above :-)

[matentzn]

@tutajm sorry I should have made myself clearer - we do not need a OFN release. I merely provided a test for you to run so you can fix the broken parts of CMO. What matters that all the errors in the latest CMO release are fixed, and you can test this using:

robot convert -I http://purl.obolibrary.org/obo/cmo.owl -f ofn -o cmo.ofn

CMO.owl should definitely be RDF/XML syntax, not OFN. But, from what I can see, the OFN file looks great! I spot-checked for errors and it seems all working now. THANK YOU!

[tutajm]

The files http://purl.obolibrary.org/obo/cmo.owl and http://purl.obolibrary.org/obo/cmo.obo are very old: from Feb 2019. Since then, the ontology has been updated numerous times.

The latest version of cmo ontology (updated weekly) you can always find here:
https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.owl
https://download.rgd.mcw.edu/ontology/clinical_measurement/clinical_measurement.obo

Now I'm trying to figure out how to update cmo ontology at purl.obolibrary.org.

[matentzn]

Change these two rows: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/cmo.yml#L7

!

[tutajm]

Created a pull-request to update cmo.yml. Thanks for help!