NCBI Gene

Identifier

ncbi_gene

License

Public domain

Citation

Brown GR, Hem V, Katz KS, et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 2015;43(Database issue):D36-D42. doi:10.1093/nar/gku1055.

Overview

NCBI Gene provides stable, gene-centric records across the tree of life.

This namespace contains current identity records and summaries, GeneRIF functional statements and interactions, discontinued-GeneID history, selected gene relationships, directed orthology pairs, sequence-accession mappings and genomic placements, NCBI-to-Ensembl matches, Gene Ontology annotations, PubMed links, genomic neighbors, RefSeq-to-UniProtKB protein mappings, and OMIM and MedGen associations for human genes and phenotypes.

Use genes to resolve an NCBI GeneID, symbol, synonym, or external identifier; use summaries for NCBI’s summary text, gene_rifs for literature-backed functional statements, interactions for source-attributed interaction records, interaction_sources to interpret interaction identifiers, and history to resolve discontinued GeneIDs.

Use accessions for reported RNA, protein, genomic, and mature-peptide accessions and placements; filter its non-null refseq_status rows when only RefSeq records are wanted.

Use ensembl_relationships, ensembl_assemblies, go_annotations, pubmed_links, neighbors, and refseq_uniprot_mapping for their corresponding reported associations.

Use relationships, orthologs, and the OMIM tables for reported cross-gene and gene-to-phenotype associations.

Tables

• ncbi_gene.accessions — NCBI Gene mappings to genomic, RNA, protein, and mature-peptide sequence accessions.
• ncbi_gene.ensembl_assemblies — NCBI annotation releases and assemblies compared with Ensembl releases and assemblies, one row per taxon in the current comparison report.
• ncbi_gene.ensembl_relationships — NCBI’s best RefSeq-to-Ensembl RNA and protein feature matches, one row per reported match.
• ncbi_gene.gene_rifs — Literature-backed Gene Reference Into Function (GeneRIF) statements for individual NCBI Gene records.
• ncbi_gene.genes — Current NCBI Gene identity, nomenclature, and cross-reference records, one row per GeneID.

gene_symbol is NCBI’s default symbol and is not necessarily an HGNC symbol. synonyms are alternate symbols, while other_designations are alternate descriptive names. db_xrefs contains external database identifiers as db and normalized id pairs.

• ncbi_gene.go_annotations — Gene Ontology annotations reported by NCBI Gene, one row per GeneID, GO term, and representative evidence code.
• ncbi_gene.history — NCBI Gene records for discontinued GeneIDs, one row per discontinued GeneID.

gene_id is the current replacement GeneID when NCBI provides one; it is null when the discontinued record has no replacement.

• ncbi_gene.interaction_sources — Metadata for the source namespaces used by NCBI GeneRIF interaction identifiers.
• ncbi_gene.interactions — Source-attributed molecular interaction records with up to two interactants and an optional resulting complex.
• ncbi_gene.neighbors — Genomic placements and nearby NCBI Gene records for genes on top-level or curated genomic sequences.
• ncbi_gene.omim_gene_relationships — Curated relationships between OMIM gene entries and NCBI Gene records.
• ncbi_gene.omim_medgen_relationships — Curated relationships from OMIM phenotype entries to MedGen clinical-genetics concepts and, when known, associated NCBI Gene records.
• ncbi_gene.orthologs — Directed NCBI Gene orthology pairs, one row per primary GeneID and ortholog GeneID pair.
• ncbi_gene.pubmed_links — NCBI Gene-to-PubMed links, one row per taxonomy, GeneID, and PubMed identifier combination.
• ncbi_gene.refseq_uniprot_mapping — NCBI RefSeq protein to UniProtKB protein mappings, one row per reported accession pair.
• ncbi_gene.relationships — Selected NCBI Gene relationships, one row per directed pair of GeneIDs.
• ncbi_gene.summaries — Current NCBI summary text for live genes that have a summary, one row per NCBI GeneID.

summary_source identifies the provider of the summary text when NCBI supplies one.