Table 8  The SSSOM mapping, SPARQL query, and the result of the proof-of-concept use case for getting all patients with sex attributes and female values.

umls:female

 skos:narrowMatch http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender#F,

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

 loinc:LA22879-3,

 ncit:C16576,

 pheno:XX,

 pheno:XXX,

 pheno:XXXX,

 pheno:XO.

# Get patients whose sex is female (not gender female)

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/

PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#

SELECT ?s ?p ?o

WHERE {

umls:female skos:narrowMatch*/rdf:type* ?o.

umls:sex skos:narrowMatch* ?p.

?s ?p ?o

}

http://example.org/patient/fhir_patient_02

http://hl7.org/fhir/birth_sex

http://terminology.hl7.org/CodeSystem/v3-AdministrativeGender#F

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_02

https://www.cdisc.org/sdtm_sex

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

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_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