The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.

Prefix

refseq

Alternative Prefixes

REFSEQ_PROT

Keywords

computational biology dna genetics life science protein rna

Links

Homepage

Contact

Kim Dixon Pruitt   0000-0001-7950-1374

Pattern for Local Unique Identifiers

Local identifiers in Reference Sequence Collection should match this regular expression:
^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$

Example Local Unique Identifiers

NP_012345   Resolve
WP_029104145.1   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Reference Sequence Collection should match this regular expression:
^refseq:(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$

Example CURIEs

refseq:NP_012345
refseq:WP_029104145.1

Publications

• 2024 NCBI RefSeq: reference sequence standards through 25 years of curation and annotation
• 2015 Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
• 2006 NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

References

GitHub Issue https://github.com/biopragmatics/bioregistry/issues/545

Contributors

• contributor Sebastian Lobentanzer   0000-0003-3399-6695   slobentanzer

A summary of the relations in the Bioregistry schema can be found here.

Has URI collision with (bioregistry.schema:0000016 )

This resource shares one or more URI format strings with NCBIProtein .

Therefore, when generating an extended prefix map, refseq, its CURIE prefix synonyms, and its URI prefix synonyms are merged into the record for NCBIProtein . If you believe that these are two distinct semantic spaces and should not be merged, please open a new issue on the Bioregistry issue tracker for discussion.

In Collection

FHIR External Terminologies

The metaregistry provides mappings between the Bioregistry and other registries. There are 11 mappings to external registries for this resource with 7 unique external prefixes.

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 NP_012345 is used to demonstrate the providers available for Reference Sequence Collection. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.