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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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omim.ttl has a broken dc:description declaration (illegal punning) #970

Closed matentzn closed 4 years ago

matentzn commented 4 years ago 
dc:description a owl:AnnotationProperty,
        owl:DatatypeProperty .

You cannot be an annotation and a data property at once!

Using this file: https://archive.monarchinitiative.org/alpha/rdf/omim.ttl

Making a quick test edit, replacing the above with just:

dc:description a owl:AnnotationProperty .

Will be sufficient.

kshefchek commented 4 years ago

these are autogenerated at the end of every dipper run from upstream ontologies, so the error is from one of these (https://github.com/monarch-initiative/dipper/blob/master/dipper/utils/GraphUtils.py#L63)

i'd like to experiment with removing this entirely, there was the idea that this is needed for scigraph but I've always wondered if scigraph or the owlapi can figure out if an object is a literal or IRI based on its type.

TomConlin commented 4 years ago

+1*10^999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999

matentzn commented 4 years ago

Dipper should not make such assumptions at all... The ontology layer should take care of that. I would be surprised if anything would change if you just removed this code.

TomConlin commented 4 years ago

+2*10^999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999

kshefchek commented 4 years ago

@matentzn this axiom comes from SEPIO in case you want to fix there as well, https://github.com/monarch-initiative/SEPIO-ontology/blob/master/src/ontology/sepio.owl#L1706

kshefchek commented 4 years ago

See this ticket for more info - https://github.com/monarch-initiative/dipper/issues/316