fhir-owl
fhir-owl copied to clipboard
Published
20 hours ago •
aehrc
aehrc
Synonyms not in output
Overview
I'm trying to convert Mondo from OWL to FHIR. However, synonyms are not appearing.
Example current output
{
"code": "MONDO_0002776",
"display": "external ear disorder",
"property": [ {
"code": "imported",
"valueBoolean": false
}, {
"code": "parent",
"valueCode": "MONDO_0021205"
}, {
"code": "parent",
"valueCode": "MONDO_0002409"
}, {
"code": "root",
"valueBoolean": false
}, {
"code": "deprecated",
"valueBoolean": false
} ]
}
Example expected output
I expect something like this. Leaving out irrelevant properties and only including 1 of the 11 synonyms here:
{
"code": "MONDO_0002776",
"display": "external ear disorder",
"property": [ {
"code": "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym",
"valueString": "preauricular sinus or fistula NOS (disorder)"
}, {
...
} ]
}
Reproducing
- Download mondo: https://github.com/monarch-initiative/mondo/releases/download/v2022-07-01/mondo.owl
- Run
fhir-owlwith the synonym flag-s:
java -jar .../fhir-owl.jar -i .../mondo.owl -o .../mondo.json -s ,"http://www.geneontology.org/formats/oboInOwl#hasSynonym","http://www.geneontology.org/formats/oboInOwl#hasExactSynonym","http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym","http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym","http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"
Additional info
Examples of synonym usage in `mondo.owl
<!-- The whole class with all the synonyms -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0002776">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0000001"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0004026"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001691"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MONDO_0002409"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MONDO_0021205"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0004026"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001691"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A disease involving the external ear.</obo:IAO_0000115>
<terms:conformsTo rdf:resource="http://purl.obolibrary.org/obo/mondo/patterns/location.yaml"/>
<terms:conformsTo rdf:resource="http://purl.obolibrary.org/obo/mondo/patterns/location_top.yaml"/>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:379</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD10CM:H60-H62</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD9:380</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD9:380.9</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ICD9:744.47</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NCIT:C26972</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SCTID:49130001</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS:C0155388</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease of external ear</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disease or disorder of external ear</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">disorder of external ear</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">external ear disease</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">external ear disease or disorder</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">external ear disorder</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular sinus and fistula</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular cyst</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular cyst (disorder)</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular sinus and fistula (disorder)</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular sinus or fistula</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular sinus or fistula NOS (disorder)</oboInOwl:hasRelatedSynonym>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MONDO:0002776</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">external ear disorder</rdfs:label>
<skos:exactMatch rdf:resource="http://identifiers.org/snomedct/49130001"/>
<skos:exactMatch rdf:resource="http://linkedlifedata.com/resource/umls/id/C0155388"/>
<skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/DOID_379"/>
<skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/NCIT_C26972"/>
<skos:exactMatch rdf:resource="https://icd.codes/icd10cm/H60-H62"/>
</owl:Class>
<!-- Not primary problem of this issue; just illustrative: One of a dozen or more axioms on the class. Shows additional annotation props for a particular synonym. -->
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0002776"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">preauricular sinus or fistula NOS (disorder)</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOID:379</oboInOwl:hasDbXref>
<oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/mondo#DUBIOUS"/>
</owl:Axiom>
<!-- Not primary problem of this issue; just illustrative: The annotation prop definition used int he above axiom example. -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/mondo#DUBIOUS">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dubious synonym</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>
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#.
/Users/joeflack4/virtualenvs/mondo-on-fhir/bin/python3.10 /Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/pydevd.py --multiprocess --qt-support=auto --client 127.0.0.1 --port 55557 --file /Users/joeflack4/projects/mondo-on-fhir/mondo_on_fhir/mondo_on_fhir.py
2022-10-13 17:17:38.281 INFO 52511 --- [ main] au.csiro.fhir.owl.Application : Starting Application v1.1.0 using Java 18.0.1.1 on Elizabeths-MacBook-Pro.local with PID 52511 (/Users/joeflack4/projects/mondo-on-fhir/data/fhir-owl.jar started by joeflack4 in /Users/joeflack4/projects/mondo-on-fhir/mondo_on_fhir)
2022-10-13 17:17:38.291 INFO 52511 --- [ main] au.csiro.fhir.owl.Application : No active profile set, falling back to default profiles: default
2022-10-13 17:17:40.332 INFO 52511 --- [ main] ca.uhn.fhir.util.VersionUtil : HAPI FHIR version 5.3.0 - Rev 919c1dbddc
2022-10-13 17:17:40.343 INFO 52511 --- [ main] ca.uhn.fhir.context.FhirContext : Creating new FHIR context for FHIR version [R4]
2022-10-13 17:17:40.411 INFO 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Checking for IRI mappings in home directory /Users/joeflack4
2022-10-13 17:17:40.428 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_pr_import_owl.owl does not exist.
2022-10-13 17:17:40.428 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_wbbt_owl.owl does not exist.
2022-10-13 17:17:40.429 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_imports_omim_susc_import_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_uberon_import_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_ro_import_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_imports_cl_import_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_uberon_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_obo_ext_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_imports_uberon_import_owl.owl does not exist.
2022-10-13 17:17:40.430 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_symp_owl.owl does not exist.
2022-10-13 17:17:40.431 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_doid_import_owl.owl does not exist.
2022-10-13 17:17:40.431 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_mpath_import_owl.owl does not exist.
2022-10-13 17:17:40.431 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_go_import_owl.owl does not exist.
2022-10-13 17:17:40.432 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_pr_owl.owl does not exist.
2022-10-13 17:17:40.432 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_imports_hp_import_owl.owl does not exist.
2022-10-13 17:17:40.432 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_owl.owl does not exist.
2022-10-13 17:17:40.432 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_extra_owl.owl does not exist.
2022-10-13 17:17:40.432 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_ro_extra_owl.owl does not exist.
2022-10-13 17:17:40.432 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_chebi_import_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_trans_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_hsapdv_import_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_imports_ncbitaxon_import_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_pato_import_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_chebi_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_upheno_imports_nbo_import_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_go_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_pato_owl.owl does not exist.
2022-10-13 17:17:40.433 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_doid_imports_relations_owl.owl does not exist.
2022-10-13 17:17:40.434 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_nbo_owl.owl does not exist.
2022-10-13 17:17:40.434 WARN 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Mapping was not added because file /Users/joeflack4/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_ncbitaxon_owl.owl does not exist.
2022-10-13 17:17:40.875 INFO 52511 --- [ main] au.csiro.fhir.owl.Application : Started Application in 8.423 seconds (JVM running for 9.8)
2022-10-13 17:17:40.893 INFO 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Creating code systems
2022-10-13 17:17:40.893 INFO 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Loading ontology from file /Users/joeflack4/projects/mondo-on-fhir/mondo_on_fhir/../data/mondo.owl
2022-10-13 17:18:14.394 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading value from OWL annotation property http://www.w3.org/2000/01/rdf-schema#label
...
2022-10-13 17:18:14.782 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading value from OWL annotation property http://www.w3.org/2000/01/rdf-schema#label
2022-10-13 17:18:14.789 INFO 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Classifying ontology http://purl.obolibrary.org/obo/mondo.owl with elk
log4j:WARN No appenders could be found for logger (org.semanticweb.elk.config.ConfigurationFactory).
log4j:WARN Please initialize the log4j system properly.
2022-10-13 17:18:15.247 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading value from OWL annotation property http://www.w3.org/2000/01/rdf-schema#label
2022-10-13 17:18:15.249 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property http://purl.org/dc/elements/1.1/publisher
2022-10-13 17:18:15.249 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property http://purl.org/dc/elements/1.1/subject
2022-10-13 17:18:15.249 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property http://www.w3.org/2000/01/rdf-schema#comment
2022-10-13 17:18:15.256 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading value from OWL annotation property http://www.w3.org/2000/01/rdf-schema#label
2022-10-13 17:18:15.256 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property
2022-10-13 17:18:15.256 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property "http://www.geneontology.org/formats/oboInOwl#hasSynonym"
2022-10-13 17:18:15.256 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
2022-10-13 17:18:15.257 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"
2022-10-13 17:18:15.257 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"
2022-10-13 17:18:15.257 INFO 52511 --- [ main] au.csiro.fhir.owl.OwlProperties : Loading synonyms from OWL annotation property "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"
2022-10-13 17:18:52.681 INFO 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Writing code system to file: /Users/joeflack4/projects/mondo-on-fhir/mondo_on_fhir/../mondo.json
2022-10-13 17:18:58.947 INFO 52511 --- [ main] au.csiro.fhir.owl.FhirOwlService : Done!
Process finished with exit code 0
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 '_,:'
@andrewpatto Thanks for the suggestion! I'm guessing you are on the money. I'll give this a go and if it works I'll close this issue.
@andrewpatto 's suggestion also works for me - does it meet your requirements @joeflack4 ?
Hey @lawley the syntax of the -s flag is fine. As for my experience with it, I did just use @andrewpatto's suggestion regarding how to use the arg in a syntactically correct way, and exactSynonyms do appear as I expect (in designation)!
Remaining issues:
- Non-exact synonyms not appearing. (e.g. the
hasRelatedSynonymin my example in my original post of the issue). - Documentation: This is me being nit-picky probably, but either the documentation for the
-sflag, or in the examples, if we could show that the correct syntax is-s "<synonym_uri1>,<synonym_uri2>"rather thatn-s "<synonym_uri1>","synonym_uri2>", I'd like that.
Here's the result after my recent conversion using aehrc/fhir-owl:
{
"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"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular cyst (disorder)"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "external ear disease"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular sinus and fistula (disorder)"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "disorder of external ear"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular sinus and fistula"
}, {
"use": {
"system": "http://snomed.info/sct",
"code": "900000000000013009",
"display": "Synonym (core metadata concept)"
},
"value": "disease or disorder of external ear"
} ],
"property": [ {
"code": "imported",
"valueBoolean": false
}, {
"code": "parent",
"valueCode": "MONDO_0021205"
}, {
"code": "parent",
"valueCode": "MONDO_0002409"
}, {
"code": "root",
"valueBoolean": false
}, {
"code": "deprecated",
"valueBoolean": false
} ]
}
For comparison, here's the tentative output for this in the current version of my tool:
{
"code": "0002776",
"property": [
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "NCIT",
"code": "C26972",
"display": "external ear disorder"
}
},
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "MONDO",
"code": "design_pattern",
"display": "external ear disease or disorder"
}
},
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "MONDO",
"code": "patterns/location",
"display": "external ear disease or disorder"
}
},
{
"code": "hasRelatedSynonym",
"valueCoding": {
"system": "DOID",
"code": "379",
"display": "preauricular cyst"
}
},
{
"code": "hasRelatedSynonym",
"valueCoding": {
"system": "DOID",
"code": "379",
"display": "preauricular sinus or fistula NOS (disorder)"
}
},
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "MONDO",
"code": "patterns/location_top",
"display": "disorder of external ear"
}
},
{
"code": "hasRelatedSynonym",
"valueCoding": {
"system": "DOID",
"code": "379",
"display": "preauricular cyst (disorder)"
}
},
{
"code": "hasRelatedSynonym",
"valueCoding": {
"system": "DOID",
"code": "379",
"display": "preauricular sinus or fistula"
}
},
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "MONDO",
"code": "patterns/location_top",
"display": "disease of external ear"
}
},
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "MONDO",
"code": "patterns/location",
"display": "external ear disease"
}
},
{
"code": "hasRelatedSynonym",
"valueCoding": {
"system": "DOID",
"code": "379",
"display": "preauricular sinus and fistula (disorder)"
}
},
{
"code": "hasExactSynonym",
"valueCoding": {
"system": "DOID",
"code": "379",
"display": "preauricular sinus and fistula"
}
},
{
"code": "parent",
"valueCode": "http://purl.obolibrary.org/obo/UBERON_0001691"
},
{
"code": "parent",
"valueCode": "0002776"
},
{
"code": "parent",
"valueCode": "0002776"
}
],
"display": "external ear disorder",
"definition": "A disease involving the external ear.",
"designation": [
{
"use": {
"system": "NCIT",
"code": "C26972",
"display": "Synonym (core metadata concept)"
},
"value": "external ear disorder"
},
{
"use": {
"system": "MONDO",
"code": "design_pattern",
"display": "Synonym (core metadata concept)"
},
"value": "external ear disease or disorder"
},
{
"use": {
"system": "MONDO",
"code": "patterns/location",
"display": "Synonym (core metadata concept)"
},
"value": "external ear disease or disorder"
},
{
"use": {
"system": "MONDO",
"code": "patterns/location_top",
"display": "Synonym (core metadata concept)"
},
"value": "disorder of external ear"
},
{
"use": {
"system": "MONDO",
"code": "patterns/location_top",
"display": "Synonym (core metadata concept)"
},
"value": "disease of external ear"
},
{
"use": {
"system": "MONDO",
"code": "patterns/location",
"display": "Synonym (core metadata concept)"
},
"value": "external ear disease"
},
{
"use": {
"system": "DOID",
"code": "379",
"display": "Synonym (core metadata concept)"
},
"value": "preauricular sinus and fistula"
}
]
},