You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
There are a number of major syntactic issues with the CMO obo and owl releases. This causes many parsers to break, as was reported in #5.
Even in cases where parsers don't break, the results of the parse give unintended results
For example, virtually all ontology browsers and tools do not correctly interpret the definitions, because they are encoded in OBO as a property_value:
id: CMO:0003022name: hemoglobin distribution widthis_a: CMO:0000508 ! hemoglobin measurementproperty_value: created:by "sjwang" xsd:stringproperty_value: creation:date 2019-01-29T15:15:44Z xsd:stringproperty_value: hasExactSynonym "HDW" xsd:stringproperty_value: http://purl.obolibrary.org/obo/def "The distribution width of erythrocytes by their cellular (individual) hemoglobin concentrations. It is a measurement of the heterogeneity of the red cell hemoglobin concentration." xsd:string {http://www.geneontology.org/formats/oboInOWL#xref="PMID:PMID\\:3411196"}
This should be:
id: CMO:0003022name: hemoglobin distribution widthis_a: CMO:0000508 ! hemoglobin measurementcreated_by: "sjwang"creation_date: 2019-01-29T15:15:44Zsynonym: "HDW"EXACT []def: "The distribution width of erythrocytes by their cellular (individual) hemoglobin concentrations. It is a measurement of the heterogeneity of the red cell hemoglobin concentration."[PMID:3411196]
The OWL that gets generated from the current obo is both syntactically incorrect, and even when parsed, information gets missed. For example on OLS:
There are a number of major syntactic issues with the CMO obo and owl releases. This causes many parsers to break, as was reported in #5.
Even in cases where parsers don't break, the results of the parse give unintended results
For example, virtually all ontology browsers and tools do not correctly interpret the definitions, because they are encoded in OBO as a property_value:
This should be:
The OWL that gets generated from the current obo is both syntactically incorrect, and even when parsed, information gets missed. For example on OLS:
https://www.ebi.ac.uk/ols/ontologies/cmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCMO_0003022
The definition doesn't show up where it should:
It looks like at some point in the past you passed the obo through a troundtrip with a very old obo to owl converter.
If you like I can provide a PR that fixes CMO. I assume this is the source file: https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/blob/master/clinical_measurement.obo
or I can provide support to a developer to fix this
The text was updated successfully, but these errors were encountered: