Naming conventions
Versions of external resources used in the context of the SPHN infrastructure and that are not provided in RDF 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. This applies to resources not provided in RDF.
short name |
full name |
coding system and version |
examples |
---|---|---|---|
ClinVar - ClinGen | Clinical Genome Resource |
ClinVar-[YEAR-MONTH] |
Clinvar-2022-10 |
|
European Directorate of the Quality of Medicines & Health Care Standard Terms |
EDQM-[VERSION] |
EDQM-1.2.0 |
|
Ensembl genome database project |
Ensembl-[VERSION]-[YEAR-MONTH] |
Ensembl-108-2022-10 |
|
Global Medical Device Nomenclature |
GMDN |
GMDN |
|
Global Trace Item Number |
GTIN |
GTIN |
|
Global Unique Device Identification Database |
GUDID |
GUDID |
|
Human Genome Variation Society notation |
HGVS-[VERSION] |
HGVS-20.05 |
|
International Classification of Diseases for Oncology |
ICD-O-3.[REVISION] |
ICD-O-3.0; ICD-O-3.1; ICD-O-3.2 |
|
International Classification of Primary Care |
ICPC-[VERSION]-[YEAR] |
ICPC-2-2003 |
|
International System for Human Cytogenomic Nomenclature |
ISCN-[YEAR] |
ISCN-2022 |
|
LOINC for Swiss Laboratories |
L4CHLAB-[YEAR].[#] |
L4CHLAB-2019.1 |
|
Medical Dictionary for Regulatory Activities |
MedDRA-[VERSION] |
MedDRA-23.1 |
|
NANDA Nursing Diagnoses |
NANDA-[YEAR-YEAR] |
NANDA-2018-2020 |
|
NCBI GenBank Database |
NCBI-GenBank-[VERSION]-[YEAR-MONTH-DAY] |
NCBI-GenBank-251-2022-08-15 |
|
NCBI Gene Database |
NCBI-Gene-[YEAR-MONTH-DAY] |
NCBI-Gene-2022-11-22 |
|
NCBI Taxonomy Database |
NCBI-Taxon |
NCBI-Taxon |
|
NCBI dbSNP Reference SNP catalog |
RefSNP-[YEAR-MONTH] |
RefSNP-2022-04 |
|
Sequence Position Deletion and Insertion notation |
SPDI |
SPDI |
|
Swiss unique enterprise identification number |
UID |
UID |
|
UniProt Knowledgebase |
UniProtKB-[YEAR-MONTH] |
UniProtKB-2022-04 |
Namespace of terminologies used in SPHN
The sections below highlights the different namespaces (ontology and version IRIs) given for each external terminologies provided in the Terminology Service as an RDF file. 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
Versions from 2016 to 2024 are provided in the Terminology Service.
Ontology IRI:
https://biomedit.ch/rdf/sphn-resource/atc/
Version IRI (available from version 2016 to 2023):
https://biomedit.ch/rdf/sphn-resource/atc/2023/1
(imported in SPHN 2023.2)
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)
[…]
IRI for codes (to be used by data providers when annotating data):
https://www.whocc.no/atc_ddd_index/?code=
CHOP namespace
Versions from 2013 to 2024 are provided in the Terminology Service.
Ontology IRI:
https://biomedit.ch/rdf/sphn-resource/chop/
Version IRI (available from version 2016 to 2023):
https://biomedit.ch/rdf/sphn-resource/chop/2023/4
(imported in SPHN 2023.2)
https://biomedit.ch/rdf/sphn-resource/chop/2022/4
(imported in SPHN 2022.1)
[…]
IRI for codes (to be used by data providers when annotating data):
https://biomedit.ch/rdf/sphn-resource/chop/
ICD-10-GM namespace
Versions from 2013 to 2024 of BFS are provided in the Terminology Service.
Ontology IRI:
https://biomedit.ch/rdf/sphn-resource/icd-10-gm/
Version IRI (available from version 2014 to 2023):
https://biomedit.ch/rdf/sphn-resource/icd-10-gm/2023/3
(imported in SPHN 2023.2)
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)
[…]
IRI for codes (to be used by data providers when annotating data):
https://biomedit.ch/rdf/sphn-resource/icd-10-gm/
LOINC namespace
Versions 2.69 to 2.74 are provided in the Terminology Service.
Ontology IRI:
https://biomedit.ch/rdf/sphn-resource/loinc/
Version IRI (available from version 2.69 to 2.74):
https://biomedit.ch/rdf/sphn-resource/loinc/2.74/1
(imported in SPHN 2023.2)
https://biomedit.ch/rdf/sphn-resource/loinc/2.73/1
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
Versions from January 2021 to January 2023 of the SNOMED CT International are provided. Since 2024, SPHN uses the SNOMED CT Swiss extension.
Ontology IRI:
http://snomed.info/sct/900000000000207008#
Version IRI (available from version 01.2021 to 12.2022):
http://snomed.info/sct/900000000000207008/version/20221231
(imported in SPHN 2023.2)
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/2023/1
*(imported in SPHN 2023.2)
https://biomedit.ch/rdf/sphn-resource/ucum/2021/1
(imported in 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 2023.2)
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 2023.2)
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 2023.2)
IRI for codes (to be used by data providers when annotating data):
http://purl.obolibrary.org/obo/SO_