Table 7 The SSSOM mapping, SPARQL query, and the result of the proof-of-concept use case for getting all patients with biological sex and gender attributes .

prefix skos: http://www.w3.org/2004/02/skos/core#

prefix umls: http://www.nlm.nih.gov/research/umls/

prefix fhir: http://hl7.org/fhir/

prefix omop: https://ohdsi.github.io/CommonDataModel/

SELECT ?s ?p ?o

WHERE {

omop:gender_concept_id skos:narrowMatch* ?p.

?s ?p ?o

}

# Get all patients who has 'Gender' attribute

prefix skos: http://www.w3.org/2004/02/skos/core#

prefix umls: http://www.nlm.nih.gov/research/umls/

SELECT ?s ?p ?o

WHERE {

 # Ensure it is 'gender'-related conept.

 umls:Gender skos:narrowMatch* ?p.

 ?s ?p ?o

 }

http://example.org/patient/omop_patient_01

https://ohdsi.github.io/CommonDataModel/gender_concept_id

https://athena.ohdsi.org/search-terms/terms/8507

http://example.org/patient/omop_patient_02

https://ohdsi.github.io/CommonDataModel/gender_concept_id

https://athena.ohdsi.org/search-terms/terms/8532

http://example.org/patient/cdisc_patient_01

https://www.cdisc.org/sdtm_sex

http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20197

http://example.org/patient/cdisc_patient_02

https://www.cdisc.org/sdtm_sex

http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16576

http://example.org/patient/cdisc_patient_03

https://www.cdisc.org/sdtm_sex

http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17998

http://example.org/patient/pheno_patient_01

https://phenopacket-schema.readthedocs.io/karyotypic_sex

https://phenopacket-schema.readthedocs.io/XX

http://example.org/patient/pheno_patient_02

https://phenopacket-schema.readthedocs.io/karyotypic_sex

https://phenopacket-schema.readthedocs.io/XY

http://example.org/patient/pheno_patient_09

https://phenopacket-schema.readthedocs.io/karyotypic_sex

https://phenopacket-schema.readthedocs.io/XYY

http://example.org/patient/pheno_patient_10

https://phenopacket-schema.readthedocs.io/karyotypic_sex

https://phenopacket-schema.readthedocs.io/XXX

http://example.org/patient/pheno_patient_11

https://phenopacket-schema.readthedocs.io/karyotypic_sex

https://phenopacket-schema.readthedocs.io/XXXX

http://example.org/patient/pheno_patient_12

https://phenopacket-schema.readthedocs.io/karyotypic_sex

https://phenopacket-schema.readthedocs.io/XO

http://example.org/patient/fhir_patient_06

http://hl7.org/fhir/administrative_gender

http://hl7.org/fhir/administrative-gender#male

http://example.org/patient/fhir_patient_07

http://hl7.org/fhir/administrative_gender

http://hl7.org/fhir/administrative-gender#female

http://example.org/patient/omop_patient_03

https://ohdsi.github.io/CommonDataModel/observation_concept_id_as_gender

https://loinc.org/LA22878-5

http://example.org/patient/omop_patient_04

https://ohdsi.github.io/CommonDataModel/observation_concept_id_as_gender

https://loinc.org/LA22879-3

http://example.org/patient/openehr_patient_04

https://ckm.openehr.org/ckm/archetypes/administrative_gender

http://hl7.org/fhir/administrative-gender#male

http://example.org/patient/openehr_patient_05

https://ckm.openehr.org/ckm/archetypes/administrative_gender

http://hl7.org/fhir/administrative-gender#female