Naming conventions

Versions of external resources used in the context of the SPHN infrastructure are uniquely identified with a code composed of the resource short name and the version number of the resource. This code should be used whenever it is necessary to identify the exact version of the resource being referenced.

Naming conventions for coding systems and versions

short name

full name

coding system and version

examples

ATC

Anatomical Therapeutic Chemical classification

ATC-[YEAR]

ATC-2020

CHOP

Swiss Classification Of Procedures

CHOP-[YEAR]

CHOP-2019

EMDN

European Medical Device Nomenclature

EMDN-[VERSION]

EMDN-1.1

EDQM

European Directorate of the Quality of Medicines & Health Care Standard Terms

EDQM-[VERSION]

EDQM-1.2.0

GMDN

Global Medical Device Nomenclature

GMDN

GMDN

GTIN

Global Trace Item Number

GTIN

GTIN

GUDID

Global Unique Device Identification Database

GUDID

GUDID

ICD-10-GM

International Statistical Classification of Diseases and Related Health Problems

ICD-10-GM-[YEAR]

ICD-10-GM-2018

ICD-O-3

International Classification of Diseases for Oncology

ICD-O-3.[REVISION]

ICD-O-3.0; ICD-O-3.1; ICD-O-3.2

ICPC

International Classification of Primary Care

ICPC-[VERSION]-[YEAR]

ICPC-2-2003

L4CHLAB

LOINC for Swiss Laboratories

L4CHLAB-[YEAR].[#]

L4CHLAB-2019.1

LOINC

Logical Observation Identifier Names and Codes

LOINC-[VERSION]

LOINC-2.67

MedDRA

Medical Dictionary for Regulatory Activities

MedDRA-[VERSION]

MedDRA-23.1

NANDA

NANDA Nursing Diagnoses

NANDA-[YEAR-YEAR]

NANDA-2018-2020

ORPHA

Orphanet nomenclature of rare diseases

ORPHA-[YEAR-MONTH]

ORPHA-2021-07

SNOMED CT

Systematized Nomenclature of Medicine Clinical Terms

SNOMED-CT-[YEAR-MONTH-DAY]

SNOMED-CT-2021-01-31

UCUM

Unified Code for Units of Measure

UCUM

UCUM

UID

Swiss unique enterprise identification number

UID

UID

HGNC

HUGO Gene Nomenclature Committee

HGNC-[YEAR-MONTH-DAY]

HGNC-2022-11-07

Ensembl

Ensembl genome database project

Ensembl-[VERSION]-[YEAR-MONTH]

Ensembl-108-2022-10

NCBI Taxon

NCBI Taxonomy Database

NCBI-Taxon

NCBI-Taxon

UniProtKB

UniProt Knowledgebase

UniProtKB-[YEAR-MONTH]

UniProtKB-2022-04

ClinVar

ClinVar - ClinGen | Clinical Genome Resource

ClinVar-[YEAR-MONTH]

Clinvar-2022-10

RefSNP

NCBI dbSNP Reference SNP catalog

RefSNP-[YEAR-MONTH]

RefSNP-2022-04

GENO

Genotype Ontology

GENO-[YEAR-MONTH-DAY]

GENO-2022-03-05

SO

Sequence Ontology

SO-[YEAR-MONTH-DAY]

SO-2021-11-22

ISCN

International System for Human Cytogenomic Nomenclature

ISCN-[YEAR]

ISCN-2022

NCBI GenBank

NCBI GenBank Database

NCBI-GenBank-[VERSION]-[YEAR-MONTH-DAY]

NCBI-GenBank-251-2022-08-15

NCBI Gene

NCBI Gene Database

NCBI-Gene-[YEAR-MONTH-DAY]

NCBI-Gene-2022-11-22

HGVS

Human Genome Variation Society notation

HGVS-[VERSION]

HGVS-20.05

SPDI

Sequence Position Deletion and Insertion notation

SPDI

SPDI

The sections below highlights the different namespaces (ontology and version IRIs) given for each external terminologies provided in the Terminology Service. In addition, the IRI used for encoding the actual codes are also expressed in the section IRI for codes. The version of the terminology being used in the different SPHN RDF schemas is highlighted in the Version IRI.

ATC namespace

Ontology IRI:

https://biomedit.ch/rdf/sphn-resource/atc/

Version IRI (available from version 2016 to 2022):

https://biomedit.ch/rdf/sphn-resource/atc/2022/1 (imported in SPHN 2022.1 and 2022.2)

https://biomedit.ch/rdf/sphn-resource/atc/2021/3 (imported in SPHN 2021.1 and 2021.2)

https://biomedit.ch/rdf/sphn-resource/atc/2020/1

https://biomedit.ch/rdf/sphn-resource/atc/2019/1

https://biomedit.ch/rdf/sphn-resource/atc/2018/1

https://biomedit.ch/rdf/sphn-resource/atc/2017/1

https://biomedit.ch/rdf/sphn-resource/atc/2016/1

IRI for codes (to be used by data providers when annotating data):

https://www.whocc.no/atc_ddd_index/?code=

CHOP namespace

Ontology IRI: https://biomedit.ch/rdf/sphn-resource/chop/

Version IRI (available from version 2016 to 2022):

https://biomedit.ch/rdf/sphn-resource/chop/2022/4 (imported in SPHN 2022.1)

https://biomedit.ch/rdf/sphn-resource/chop/2021/4

https://biomedit.ch/rdf/sphn-resource/chop/2020/4

https://biomedit.ch/rdf/sphn-resource/chop/2019/4

https://biomedit.ch/rdf/sphn-resource/chop/2018/4

https://biomedit.ch/rdf/sphn-resource/chop/2017/4

https://biomedit.ch/rdf/sphn-resource/chop/2016/4

IRI for codes (to be used by data providers when annotating data):

https://biomedit.ch/rdf/sphn-resource/chop/

ICD-10-GM namespace

Ontology IRI:

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/

Version IRI (available from version 2014 to 2022):

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2022/2 (imported in SPHN 2022.1 and 2022.2)

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2021/2 (imported in SPHN 2021.1 and 2021.2)

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2020/2

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2019/2

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2018/2

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2017/2

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2016/2

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2015/2

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2014/2

IRI for codes (to be used by data providers when annotating data):

https://biomedit.ch/rdf/sphn-resource/icd-10-gm/

LOINC namespace

Ontology IRI:

https://biomedit.ch/rdf/sphn-resource/loinc/

Version IRI (available from version 2.69 to 2.72):

https://biomedit.ch/rdf/sphn-resource/loinc/2.72/1 (imported in SPHN 2022.1 and 2022.2)

https://biomedit.ch/rdf/sphn-resource/loinc/2.71/1

https://biomedit.ch/rdf/sphn-resource/loinc/2.69/1 (imported in SPHN 2021.1 and 2021.2)

IRI for codes (to be used by data providers when annotating data):

https://loinc.org/rdf/

SNOMED CT namespace

Ontology IRI:

http://snomed.info/sct/900000000000207008#

Version IRI (available from version 01.2021 to 01.2022):

http://snomed.info/sct/900000000000207008/version/20220207 (imported in SPHN 2022.1 and 2022.2)

http://snomed.info/sct/900000000000207008/version/20210805

http://snomed.info/sct/900000000000207008/version/20210304 (imported in SPHN 2021.1 and 2021.2)

IRI for codes (to be used by data providers when annotating data):

http://snomed.info/id/

UCUM namespace

Ontology IRI:

https://biomedit.ch/rdf/sphn-resource/ucum/

Version IRI:

https://biomedit.ch/rdf/sphn-resource/ucum/2021/1 (imported in SPHN 2022.1, 2022.2 2021.1 and 2021.2)

IRI for codes (to be used by data providers when annotating data):

https://biomedit.ch/rdf/sphn-resource/ucum/

HGNC namespace

Ontology IRI:

https://biomedit.ch/rdf/sphn-resource/hgnc/

Version IRI:

code:

https://biomedit.ch/rdf/sphn-resource/hgnc/20221107 (imported in SPHN 2023.1)

IRI for codes (to be used by data providers when annotating data):

https://biomedit.ch/rdf/sphn-resource/hgnc/

GENO namespace

Ontology IRI:

http://purl.obolibrary.org/obo/GENO_

Version IRI:

http://purl.obolibrary.org/obo/geno/releases/2022-08-10 (imported in SPHN 2023.1)

IRI for codes (to be used by data providers when annotating data):

http://purl.obolibrary.org/obo/GENO_

SO namespace

Ontology IRI:

http://purl.obolibrary.org/obo/SO_

Version IRI:

http://purl.obolibrary.org/obo/so/2021-11-22 (imported in SPHN 2023.1)

IRI for codes (to be used by data providers when annotating data):

http://purl.obolibrary.org/obo/SO_