The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
- Prefix
dbsnp- Keywords
- genetic polymorphism genetic variation genetic variation databases genome life science repository sequence snp variant
- Links
- Homepage
- Publications
- https://bioregistry.io/pubmed:33095870
- 2006 Database resources of the National Center for Biotechnology Information
- 2001 dbSNP: the NCBI database of genetic variation
- https://bioregistry.io/pubmed:10592272
Identifier Standards
- Pattern for Local Unique Identifiers
-
Local unique identifiers in dbSNP should match this
regular expression:
^rs\d+$ - Example Local Unique Identifier
- rs121909098 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from dbSNP should match
this regular expression:
^dbsnp:rs\d+$ - Example CURIE
- dbsnp:rs121909098
Contacts
- Contact
-
Kim Dixon Pruitt
0000-0001-7950-1374
- Identifier Space Owner
-
National Center for Biotechnology Information
Ontology
A summary of the relations in the Semantic Farm schema can be found here.
- Provided By
- snp2tfbs
- In Collection (3)
- FHIR External Terminologies Synapse.org external links NFDI4Health Collection
Mappings to External Registries
Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 15 mappings to external registries with 8 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
dbSNP
|
|
| Cellosaurus | cellosaurus.resource |
dbSNP
|
|
EDAM
|
edam.data |
1106
|
|
FAIRsharing
|
fairsharing |
FAIRsharing.edxb58
|
|
| GO | go.resource |
dbSNP
|
|
| HL7 | hl7 |
6.284
|
|
Integbio
|
integbio |
nbdc00206
|
|
Identifiers.org namespace
|
miriam |
dbsnp
|
|
| N2T | n2t |
dbsnp
|
|
| NCBI | ncbi.resource |
dbSNP
|
|
| Prefix Commons | prefixcommons |
dbsnp
|
|
re3data
|
re3data |
r3d100010652
|
|
| TogoID Ontology | togoid |
Dbsnp
|
|
UniProt
|
uniprot.resource |
DB-0013
|
|
Wikidata
|
wikidata.property |
P6861
|
Providers
A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).
The local unique identifier rs121909098 is used to demonstrate the providers
available for dbSNP. Some providers may use a different example, which is displayed in the table below.
A guide for curating additional providers can be found
here.
| Provider Name | Provider Code | URI |
|---|---|---|
| dbSNP | dbsnp |
https://www.ncbi.nlm.nih.gov/snp/rs121909098 |
| Bioregistry | bioregistry |
https://bioregistry.io/dbsnp:rs121909098 |
| Identifiers.org namespace | miriam |
https://identifiers.org/dbsnp:rs121909098 |
| Name-to-Thing | n2t |
https://n2t.net/dbsnp:rs121909098 |
Extra Providers
Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.
| Provider Name | Provider Code | URL |
|---|---|---|
| Bio2RDF | bio2rdf |
http://bio2rdf.org/dbsnp:rs121909098 |
| SNP2TFBS | sib |
https://epd.expasy.org/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=rs121909098 |