aehrc/fhir-owl

Transforms OWL ontologies into FHIR code systems.

OWL to FHIR Transformer

This Spring Boot CLI application transforms an OWL ontology into FHIR terminology resources.

Building from source

You will need Maven installed in your computer. You can build the jar file using Maven.

mvn package

Configuration

Properties

The following properties define some of the default values that are used. These can be overriden via arguments to the VM, e.g., -Dontoserver.owl.defaults.publisher=http://purl.org/dc/elements/1.1/publisher

ontoserver.owl.defaults.publisher (http://purl.org/dc/elements/1.1/publisher)

The default annotation property where the publisher of the ontology can be found.

ontoserver.owl.defaults.description (http://purl.org/dc/elements/1.1/subject,http://www.w3.org/2000/01/rdf-schema#comment)

The default annotation property where the description of the ontology can be found.

ontoserver.owl.defaults.preferredTerm (http://www.w3.org/2000/01/rdf-schema#label)

The default annotation property where the preferred term of OWL classes can be found.

ontoserver.owl.defaults.synonym (http://www.w3.org/2000/01/rdf-schema#label)

The default annotation property where the synonyms of the OWL classes can be found.

IRI mappings

The application also looks for a file named iri_mappings.txt in the classpath and uses it to load OWL ontologies that are available in the file system. This is useful to reduce the loading time of some ontologies that import large external ontologies, such as HPO. By default, the OWL API library will try to resolve any imported ontology using its IRI, which results in the ontology being downloaded from the web. The iri_mappings.txt file defines mappings between IRIs and local files, as shown here:

http://purl.obolibrary.org/obo/nbo.owl,/CSIRO/resources/ontologies/iri_maps/http___purl_obolibrary_org_obo_nbo_owl.owl

The location of the files is relative to the user's home folder.

Running

You need a JVM to run the application. The only mandatory options are -i and -o.

java -jar fhir-owl-1.0.0.jar -i [input OWL file] -o [output FHIR JSON file]

The following options are available:

Parameter	Type	Description
-c	string	Indicates which annotation property contains the concepts' codes. If the value is not set, then the IRI of the class is used. If the class is imported then the full IRI is used. If the class is defined in the ontology then the short form is used.
-codeReplace	string	Two strings separated by a comma. Replaces the first string with the second string in all local codes.
-compositional	boolean	Flag to indicate if the code system defines a post-coordination grammar.
-contact	string	Comma-separated list of contact details for the publisher. Each contact detail has the format [name|system|value], where system has the following possible values: phone, fax, email, pager, url, sms or other.
-content	string	The extent of the content in this resource. Valid values are not-present, example, fragment, complete and supplement. Defaults to complete. The actual value does not affect the output of the transformation.
-copyright	string	A copyright statement about the code system.
-d	string	Indicates which annotation property contains the concepts' displays. Default is RDFS:label.
-date	string	The published date. Valid formats are: YYYY, YYYY-MM, YYYY-MM-DD and YYYY-MM-DDThh:mm:ss+zz:zz.
-definition	string	Indicates which annotation property contains the concepts' definitions.
-description	string	The description of the code system. This option takes precedence over -descriptionProp.
-descriptionProp	string	Comma-separated list of OWL annotation properties that contain the code system description.
-experimental	boolean	Indicates if the code system is for testing purposes or real usage.
-help	none	Print the help message.
-hierarchyMeaning	string	The meaning of the hierarchy of concepts as represented in this resource. Valid values are grouped-by, is-a, part-of, and classified-with. Default is is-a.
-i	string	The input OWL file.
-id	string	The technical id of the code system. Required if using PUT to upload the resource to a FHIR server.
-identifier	string	Comma-separated list of additional business identifiers. Each business identifer has the format [system]|[value].
-includeDeprecated	boolean	Include all OWL classes, including deprecated ones.
-jurisdiction	string	Comma-separated list of jurisdictions for the codesystem. Each jurisdiction must have the format [system|code|display], with values retrieved from the FHIR Jurisdiction ValueSet.
-labelsToExclude	string	Comma-separated list of class labels to exclude.
-language	string	The language of the content. This is a code from the FHIR Common Languages value set.
- mainNs	string	Comma-separated list of namespace prefixes that determine which classes are part of the main ontology.
-n	string	Used to specify the computer-friendly name of the code system. This option takes precedence over -nameProp.
-nameProp	string	A property to look for the computer-friendly name of the code system in the OWL file. If this option is not specified or the specified property is not found, then the RDFS:label property is used by default. If no label can be found using the property then the ontology IRI is used.
-o	string	The output FHIR JSON file.
-publisher	string	The publisher of the code system. This option takes precedence over -publisherProp.
-publisherProp	string	Comma-separated list of OWL annotation properties that contain the code system publisher.
-purpose	string	Explanation of why this code system is needed.
-s	string	Comma-separated list of annotation properties on OWL classes that contain the concepts' synonyms.
-status	string	Code system status. Valid values are: draft, active, retired and unknown.
-t	string	A human-friendly name for the code system.
-url	string	Canonical identifier of the code system. If this option is not specified then the ontology’s IRI will be used. If the ontology has no IRI then the transformation fails.
-v	string	Business version. If this option is not specified then the ontology’s version will be used. If the ontology has no version then the version is set to ‘NA’.
-valueset	string	The value set that represents the entire code system. If this option is not specified then the value will be constructed from the URI of the code system.
-versionNeeded	boolean	Flag to indicate if the code system commits to concept permanence across versions.
-r	string	The reasoner to use. Valid values are: elk and jfact. Default value is elk.
-useFhirExtension	boolean	Flag to indicate if the last part of an IRI ending in .owl should be replaced with .fhir.
-dateRegex	string	A regular expression used to extract the date of the code system from the configured attribute in the ontology. It should have the following three named groups: year, month and day. The three groups will be concatenated to form a version of the form YYYYMMDD. This is useful if the ontology version is a URI that contains a date but only the date wants to be used as the version of the code system.

Examples

The Human Phenotype Ontology was transformed using the following command:

java -jar fhir-owl-v1.1.0.jar -i hp.owl -o hp.json -id hpo -name "HumanPhenotypeOntology" -t "Human Phenotype Ontology" -content complete -mainNs http://purl.obolibrary.org/obo/HP_ -descriptionProp http://purl.org/dc/elements/1.1/subject -status active -codeReplace _,: -useFhirExtension -dateRegex "(?<year>\\d{4})-(?<month>\\d{2})-(?<day>\\d{2})" -s http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

You can browse the output here.

The Sequence Ontology was transformed using the following command:

java -jar fhir-owl-1.0.0.jar -i so-simple.owl -o so-simple.json -id so -name "Sequence Ontology" -status active -codeReplace "_,:" -s "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" -mainNs "http://purl.obolibrary.org/obo/SO_" -labelsToExclude "wiki,WIKI"

You can browse the output here.

fhir-owl's Issues

maven build failure

[INFO] Scanning for projects...
[INFO]
[INFO] -------------------------< au.csiro:fhir-owl >--------------------------
[INFO] Building FHIR OWL 1.1.0-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ fhir-owl ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ fhir-owl ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 9 source files to ./fhir-owl/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] ./fhir-owl/src/main/java/au/csiro/fhir/owl/FhirOwlService.java:[32,24] cannot find symbol
  symbol:   class PostConstruct
  location: package javax.annotation
[ERROR] ./fhir-owl/src/main/java/au/csiro/fhir/owl/FhirOwlService.java:[101,4] cannot find symbol
  symbol:   class PostConstruct
  location: class au.csiro.fhir.owl.FhirOwlService
[INFO] 2 errors
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  2.289 s
[INFO] Finished at: 2020-03-03T14:49:16-05:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project fhir-owl: Compilation failure: Compilation failure:
[ERROR] ./fhir-owl/src/main/java/au/csiro/fhir/owl/FhirOwlService.java:[32,24] cannot find symbol
[ERROR]   symbol:   class PostConstruct
[ERROR]   location: package javax.annotation
[ERROR] ./fhir-owl/src/main/java/au/csiro/fhir/owl/FhirOwlService.java:[101,4] cannot find symbol
[ERROR]   symbol:   class PostConstruct
[ERROR]   location: class au.csiro.fhir.owl.FhirOwlService
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

Question about design (content retention)

I was looking at the documentation for fhir-owl and also looking at some of the output it generates and comparing with obographs. The big difference I saw is that by default, fhir-owl leaves out most content/properties/relationships unless you specifically ask it to include something (and currently, there are a lot of possible properties and relationships that are not supported, because they have to be specifically added to the CLI and implemented). On the other hand, Obographs seems to transform everything in OWL to a JSON representation.

My thought was that this is a preferable approach: to convert all the content we possibly can from OWL to FHIR. I'm wondering if fhir-owl has chosen not to do this specifically as a design decision, or if there is another reason why the output is currently much more minimalistic (i.e. it was easier to design fhir-owl the way it currently is for MVP purposes)?

Another reason I'm asking this is because my team has a use case for getting OWL/OBO into FHIR, but we would like to convert as much content as possible to FHIR, adding extension elements where necessary. I'm wondering if the fhir-owl team is open to moving the design from the current, more minimalistic approach, to a more "everything goes" style?

Customizing CodeSystem properties heirarchyMeaning and jurisdiction are unsupported. Setting contacts does not add them to the transform output.

Add support for translating Data Property and Object Properties into CodeSystem Properties.

Add flags to determine if Data Properties and Object Properties should be extracted from the OWL source into concept Properties

Add flag to support adding filters corresponding to these properties.

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

1. Download mondo: https://github.com/monarch-initiative/mondo/releases/download/v2022-07-01/mondo.owl
2. Runfhir-owl with 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

Add -filter arg to allow adding filters

To support $find-matches operations, filters need to be added to the CodeSystem resource. Support adding filters while doing a transform from FHIR to OWL.