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The Swiss BioRef ontology

Metadata

URI
https://biomedit.ch/rdf/sphn-ontology/swissbioref#
Version URI
https://biomedit.ch/rdf/sphn-ontology/swissbioref/2022/2/
Imports
https://biomedit.ch/rdf/sphn-ontology/sphn/2021/2
https://biomedit.ch/rdf/sphn-resource/gmdn-bioref/2022-04-26/2
https://biomedit.ch/rdf/sphn-resource/gudid-bioref/20211101/3
License
https://creativecommons.org/licenses/by-nc-sa/4.0/
SPHN RDF Schema
RDF (turtle)
Swiss BioRef RDF Schema
RDF (turtle)
External Terminologies in RDF
BioMedIT Portal (with Switch edu-ID)

Description

The RDF schema describing concepts defined in the Swiss BioRef dataset

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Annotation Properties
  5. Namespaces
  6. Legend

Classes ↑

Swiss BioRef Conceptc # Classes

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#SwissbiorefConcept
Description

Concepts defined by the Swiss BioRef dataset
Children
(Sub-classes) 		Medical Devicec
Terminologyc
Agec

Agec # Classes

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#Age
Description

time elapsed after birth of the individual
Meaning binding
(Equivalent-classes)		 LOINC 30525-0 | Age |c
SNOMED 397669002 | Age (qualifier value) |c
Parents
 Swiss BioRef Conceptc
Property
(In the domain of) 		Cardinality Class or Datatype Restriction
has age unitop
 0 .. * SPHN | Unit |c
has age determination date timedp
 0 .. * xsd:dateTimec
has age valuedp
 0 .. * xsd:floatc
has age typeop
 0 .. * LOINC 35659-2 | Age at specimen collection |c or LOINC 30972-4 | Age at onset of adverse event |c
Restrictions None
Used in
(In the range of)		 has subject ageop

Medical Devicec # Classes

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#MedicalDevice
Description

product intended for medical use when the main effect is not achieved by a medicinal product; medical devices include, but are not limited to, implants, instruments, devices, in vitro diagnostics
Meaning binding
(Equivalent-classes)		 SNOMED 49062001 | Device (physical object) |c
Parents
 Swiss BioRef Conceptc
Children
(Sub-classes) 		Laboratory analyzerc
Property
(In the domain of) 		Cardinality Class or Datatype Restriction
has medical device type identifier codeop
 0 .. * SNOMED 272181003 | Clinical equipment and/or device (physical object) |c or https://biomedit.ch/rdf/sphn-resource/gmdn-bioref/GMDN-BIOREFc
has medical device product identifier codeop
 0 .. * https://biomedit.ch/rdf/sphn-resource/gudid-bioref/GUDID-BIOREFc
Restrictions None

Laboratory analyzerc # Classes

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#LabAnalyzer
Description

Laboratory analyzer used to assess biosamples, e.g., an analyzer device or testkit (each stand-alone, or as combination of parent device and testkit)
Parents
 Medical Devicec
Property
(In the domain of) 		Cardinality Class or Datatype Restriction
has laboratory analyzer product identifier codeop
 0 .. * https://biomedit.ch/rdf/sphn-resource/gudid-bioref/GUDID-BIOREFc
has laboratory analyzer type identifier codeop
 0 .. * https://biomedit.ch/rdf/sphn-resource/emdn/EMDNc or https://biomedit.ch/rdf/sphn-resource/gmdn-bioref/GMDN-BIOREFc
Restrictions None
Used in
(In the range of)		 has lab result deviceop
has lab result testkitop

Terminologyc # Classes

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#Terminology
Description

Terminology class for grouping external resources used in the Swiss BioRef project
Meaning binding
(Equivalent-classes)		 SPHN | Terminology |c
Parents
 Swiss BioRef Conceptc
Children
(Sub-classes) 		https://biomedit.ch/rdf/sphn-resource/gudid-bioref/GUDID-BIOREFc
https://biomedit.ch/rdf/sphn-resource/gmdn-bioref/GMDN-BIOREFc
Used in
(In the range of)		 has codeop

Object Properties ↑

has age typeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasAgeType
Description

type of age, e.g. at sample collection, at diagnosis, or onset of adverse event
Super-properties Swiss BioRef attribute objectop
Domain(s) Agec
Value set (Range) LOINC 35659-2 | Age at specimen collection |c LOINC 30972-4 | Age at onset of adverse event |c LOINC 63932-8 | Age at diagnosis |c

has age unitop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasAgeUnit
Description

specifies the unit of the age value, e.g., years (a) or months (mo)
Super-properties Swiss BioRef attribute objectop
Domain(s) Agec
Value set [Child Of] (Range) SPHN | Unit |c

has codeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasCode
Description

code, name, coding system and version of an element
Super-properties Swiss BioRef attribute objectop
Value set (Range) SPHN | Terminology |c Terminologyc SPHN | Code |c

has lab result deviceop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasLabResultDevice
Description

laboratory analyzer used to assess the biosample used in this lab test
Super-properties Swiss BioRef attribute objectop
Domain(s) SPHN | Lab Result |c
Range Laboratory analyzerc

has lab result lab test codeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasLabResultLabTestCode
Is Defined By SNOMED 15220000 | Laboratory test (procedure) |
Description

code of the lab test (set of analyses of interest in Swiss BioRef project)
Super-properties has codeop
Domain(s) SPHN | Lab Result |c
Value set (Range) LOINC 11558-4 | pH of Blood |c LOINC 22748-8 | Cholesterol in LDL [Moles/volume] in Serum or Plasma |c LOINC 59261-8 | Hemoglobin A1c/Hemoglobin.total in Blood by IFCC protocol |c LOINC 4544-3 | Hematocrit [Volume Fraction] of Blood by Automated count |c LOINC 2069-3 | Chloride [Moles/volume] in Blood |c LOINC 789-8 | Erythrocytes [#/volume] in Blood by Automated count |c LOINC 14979-9 | aPTT in Platelet poor plasma by Coagulation assay |c LOINC 22664-7 | Urea [Moles/volume] in Serum or Plasma |c LOINC 14927-8 | Triglyceride [Moles/volume] in Serum or Plasma |c LOINC 15074-8 | Glucose [Moles/volume] in Blood |c LOINC 1742-6 | Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma |c LOINC 83071-1 | 25-Hydroxyvitamin D3+25-Hydroxyvitamin D2 [Moles/volume] in Serum or Plasma by Immunoassay |c LOINC 69419-0 | Cholesterol in LDL [Moles/volume] in Serum or Plasma by Direct assay |c LOINC 20448-7 | Insulin [Units/volume] in Serum or Plasma |c LOINC 14743-9 | Glucose [Moles/volume] in Capillary blood by Glucometer |c LOINC 14749-6 | Glucose [Moles/volume] in Serum or Plasma |c LOINC 786-4 | MCHC [Mass/volume] by Automated count |c LOINC 5902-2 | Prothrombin time (PT) |c LOINC 1988-5 | C reactive protein [Mass/volume] in Serum or Plasma |c LOINC 11557-6 | Carbon dioxide [Partial pressure] in Blood |c LOINC 30239-8 | Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma by With P-5'-P |c LOINC 14682-9 | Creatinine [Moles/volume] in Serum or Plasma |c LOINC 68438-1 | 25-Hydroxyvitamin D3+25-Hydroxyvitamin D2 [Moles/volume] in Serum or Plasma |c LOINC 1920-8 | Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma |c LOINC 6690-2 | Leukocytes [#/volume] in Blood by Automated count |c LOINC 14646-4 | Cholesterol in HDL [Moles/volume] in Serum or Plasma |c LOINC 20564-1 | Oxygen saturation in Blood |c LOINC 2947-0 | Sodium [Moles/volume] in Blood |c LOINC 785-6 | MCH [Entitic mass] by Automated count |c LOINC 1743-4 | Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma by With P-5'-P |c LOINC 39469-2 | Cholesterol in LDL [Moles/volume] in Serum or Plasma by calculation |c LOINC 787-2 | MCV [Entitic volume] by Automated count |c LOINC 718-7 | Hemoglobin [Mass/volume] in Blood |c LOINC 6298-4 | Potassium [Moles/volume] in Blood |c LOINC 11556-8 | Oxygen [Partial pressure] in Blood |c LOINC 777-3 | Platelets [#/volume] in Blood by Automated count |c LOINC 1744-2 | Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma by No addition of P-5'-P |c LOINC 32623-1 | Platelet mean volume [Entitic volume] in Blood by Automated count |c LOINC 62238-1 | Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI) |c LOINC 5894-1 | Prothrombin time (PT) actual/Normal |c LOINC 14647-2 | Cholesterol [Moles/volume] in Serum or Plasma |c LOINC 59826-8 | Creatinine [Moles/volume] in Blood |c LOINC 788-0 | Erythrocyte distribution width [Ratio] by Automated count |c LOINC 46418-0 | INR in Capillary blood by Coagulation assay |c LOINC 2075-0 | Chloride [Moles/volume] in Serum or Plasma |c LOINC 88112-8 | Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma by No addition of P-5'-P |c LOINC 2823-3 | Potassium [Moles/volume] in Serum or Plasma |c LOINC 2951-2 | Sodium [Moles/volume] in Serum or Plasma |c LOINC 6301-6 | INR in Platelet poor plasma by Coagulation assay |c

has lab result testkitop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasLabResultTestkit
Description

testkit used to assess the biosample used in this lab test
Super-properties Swiss BioRef attribute objectop
Domain(s) SPHN | Lab Result |c
Range Laboratory analyzerc

has laboratory analyzer product identifier codeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasLaboratoryAnalyzerProductIdentifierCode
Description

code, name, coding system and version of the unique device identifier (UDI) of the laboratory analyzer device to identify it on the level of manufacturer and model
Super-properties has medical device product identifier codeop
Domain(s) Laboratory analyzerc
Value set [Child Of] (Range) https://biomedit.ch/rdf/sphn-resource/gudid-bioref/GUDID-BIOREFc

has laboratory analyzer type identifier codeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasLaboratoryAnalyzerTypeIdentifierCode
Description

code, name, coding system and version describing the type of laboratory analyzer device
Super-properties has medical device type identifier codeop
Domain(s) Laboratory analyzerc
Value set (Range) https://biomedit.ch/rdf/sphn-resource/emdn/EMDNc https://biomedit.ch/rdf/sphn-resource/gmdn-bioref/GMDN-BIOREFc

has medical device product identifier codeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasMedicalDeviceProductIdentifierCode
Description

code, name, coding system and version used to describe the medical device product identifier
Super-properties has codeop
Domain(s) Medical Devicec
Value set [Child Of] (Range) https://biomedit.ch/rdf/sphn-resource/gudid-bioref/GUDID-BIOREFc

has medical device type identifier codeop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasMedicalDeviceTypeIdentifierCode
Is Defined By SNOMED 260846005 | Type of device (attribute) |
LOINC 66464-9 | Medical device type [PhenX] |
Description

code, name, coding system and version used to describe the type of medical device
Super-properties has codeop
Domain(s) Medical Devicec
Value set (Range) SNOMED 272181003 | Clinical equipment and/or device (physical object) |c https://biomedit.ch/rdf/sphn-resource/gmdn-bioref/GMDN-BIOREFc https://biomedit.ch/rdf/sphn-resource/emdn/EMDNc

has subject ageop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasSubjectAge
Description

age of subject related to Biosample, Biobanksample or FOPHDiagnosis
Super-properties Swiss BioRef attribute objectop
Domain(s) SPHN | FOPH Diagnosis |c SPHN | Biobanksample |c SPHN | Biosample |c
Range Agec

Swiss BioRef attribute objectop # OPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#swissbiorefAttributeObject
Description

Swiss BioRef object attribute defined by the dataset

Datatype Properties ↑

has age determination date timedp # DPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasAgeDeterminationDateTime
Description

datetime of determination of age
Super-properties Swiss BioRef attribute datatypedp
Domain(s) Agec
Data type xsd:dateTimec

has age valuedp # DPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasAgeValue
Description

age value of the respective concept
Super-properties Swiss BioRef attribute datatypedp
Domain(s) Agec
Data type xsd:floatc

has numeric lab result valuedp # DPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#hasLabResultValue
Description

numeric result of the laboratory test
Super-properties sphn:hasLabResultValue
Domain(s) SPHN | Lab Result |c
Data type xsd:floatc

Swiss BioRef attribute datatypedp # DPs

URI https://biomedit.ch/rdf/sphn-ontology/swissbioref#swissbiorefAttributeDatatype
Description

Swiss BioRef datatype attribute defined by the dataset

Annotation Properties ↑

licenseap # APs

URI http://purl.org/dc/terms/license

Namespaces ↑

default (:)
https://biomedit.ch/rdf/sphn-ontology/swissbioref#
brick
https://brickschema.org/schema/Brick#
csvw
http://www.w3.org/ns/csvw#
dc
http://purl.org/dc/elements/1.1/
dcam
http://purl.org/dc/dcam/
dcat
http://www.w3.org/ns/dcat#
dcmitype
http://purl.org/dc/dcmitype/
dcterms
http://purl.org/dc/terms/
doap
http://usefulinc.com/ns/doap#
foaf
http://xmlns.com/foaf/0.1/
odrl
http://www.w3.org/ns/odrl/2/
org
http://www.w3.org/ns/org#
owl
http://www.w3.org/2002/07/owl#
prof
http://www.w3.org/ns/dx/prof/
prov
http://www.w3.org/ns/prov#
qb
http://purl.org/linked-data/cube#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
sdo
https://schema.org/
sh
http://www.w3.org/ns/shacl#
skos
http://www.w3.org/2004/02/skos/core#
sosa
http://www.w3.org/ns/sosa/
sphn
https://biomedit.ch/rdf/sphn-ontology/sphn#
ssn
http://www.w3.org/ns/ssn/
time
http://www.w3.org/2006/time#
vann
http://purl.org/vocab/vann/
void
http://rdfs.org/ns/void#
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
dpAnnotation Properties
pProperties
niNamed Individuals