Table 6 The SSSOM mapping, SPARQL query, and the result of the proof-of-concept use case for getting all patients with sex attributes.

From: Cross-Standard Health Data Harmonization using Semantics of Data Elements

(a) Mappings between representations

(b) SPARQL query

umls:sex

 skos:narrowMatch fhir:birth_sex,

  cdisc:sdtm_sex,

  omop:gender_concept_id,

openehr:sex_assigned_at_birth,

  pheno:sex,

  pheno:karyotypic_sex.

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/

SELECT ?s ?p ?o

WHERE {

 umls:sex skos:narrowMatch* ?p.

 ?s ?p ?o

 }

(c) Query results

Subject

Predicate

Object

http://example.org/patient/fhir_patient_01

http://hl7.org/fhir/birth_sex

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

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/fhir_patient_03

http://hl7.org/fhir/birth_sex

http://terminology.hl7.org/CodeSystem/v3-NullFlavor#OTH

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

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