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

cdna/est cell/organelle computational biology deoxyribonucleic acid dna genetics genome genome/gene life science protein ribonucleic acid rna sequence sequence databases sequencing assay transcript

Links

Homepage

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

https://bioregistry.io/pubmed:22121212

https://bioregistry.io/pubmed:18927115

2006 NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

https://bioregistry.io/pubmed:10592200

References

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

Pattern for Local Unique Identifiers

Local unique 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

Contact

Kim Dixon Pruitt   0000-0001-7950-1374

Identifier Space Owner

National Center for Biotechnology Information

Contributor

contributor Sebastian Lobentanzer   0000-0003-3399-6695   slobentanzer

A summary of the relations in the Semantic Farm 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 Semantic Farm issue tracker for discussion.

In Collection (2)

FHIR External Terminologies Synapse.org external links

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 11 mappings to external registries 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. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

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