andrewpatto
commented
2 years ago Hi @joeflack4 - was visiting here because I similarly was attempting to get extra properties out of OWL across into the FHIR.
With regards synonyms however - I could get 'designations' outputted.
"code": "MONDO:0002776",
"display": "external ear disorder",
"designation": [ {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular cyst"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular sinus or fistula NOS (disorder)"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular sinus or fistula"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "disease of external ear"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "external ear disease or disorder"
}, {I think possibly your 'comma splitting' syntax for the invoke is incorrect? I always assumed it meant to split the uris by comma within the shell quotes
e.g.
java -jar fhir-owl-v1.1.jar -i mondo.owl -o mondo.json \
-id mondo \
-name "Mondo" \
-content complete \
-mainNs 'http://purl.obolibrary.org/obo/MONDO_' \
-s 'http://www.geneontology.org/formats/oboInOwl#hasExactSynonym,http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym' \
-dateRegex "(?<year>\\d{4})-(?<month>\\d{2})-(?<day>\\d{2})" \
-status active \
-codeReplace '_,:'
joeflack4
lawley
Overview
I'm trying to convert Mondo from OWL to FHIR. However, synonyms are not appearing.
Example current output
Example expected output
I expect something like this. Leaving out irrelevant properties and only including 1 of the 11 synonyms here:
Reproducing
fhir-owlwith the synonym flag-s:Additional info
Examples of synonym usage in `mondo.owl
Terminal output
It appears to say that it is loading the synonyms (near the bottom). I see messages about some mappings found, but none of them appear to be related to the synonyms namespace I am using,
http://www.geneontology.org/formats/oboInOwl#.