NCBI Gene Reference Ingest Guide¶
Source Information¶
InfoRes ID: infores:ncbi-gene
Description: NCBI Gene is a database maintained by the National Center for Biotechnology Information (NCBI) that provides authoritative, integrated information about genes across a wide range of species. A gene record may include official nomenclature and symbols, gene descriptions, Reference Sequences (RefSeqs), genomic maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. This ingest uses NCBI Gene as the authoritative source of gene identity and basic gene properties (symbol, full name, description) for human, mouse, and rat.
Citations: - National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2024 Dec]. Available from: https://www.ncbi.nlm.nih.gov/
Data Access Locations: - NCBI FTP Site: https://ftp.ncbi.nih.gov/gene/DATA/
Data Provision Mechanisms: file_download
Data Formats: tsv
Data Versioning and Releases: NCBI Gene data is updated regularly. Gene information files are available as current snapshots from the FTP site.
Ingest Information¶
Ingest Categories: node_property_only_provider, primary_knowledge_provider
Utility: "NCBI Gene provides authoritative gene information for human, mouse, and rat genes, including official gene symbols, and descriptions critical for gene normalization and identification in biomedical knowledge graphs."
Scope: "This ingest focuses on human (NCBITaxon:9606), mouse (NCBITaxon:10090), and rat (NCBITaxon:10116) genes only from the gene_info.gz file. All gene records for these species are included to provide comprehensive gene coverage."
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| gene_info.gz | https://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz | Tab-delimited file containing gene information for all NCBI species, filtered to human, mouse, and rat genes |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| gene_info.gz | Gene records for human (taxon ID 9606), mouse (taxon ID 10090), and rat (taxon ID 10116) only | tax_id, GeneID, Symbol, description, Full_name_from_nomenclature_authority |
Filtered Content¶
| File Name | Filtered Records | Rationale |
|---|---|---|
| gene_info.gz | All gene records for species other than human, mouse, and rat | This ingest focuses specifically on human, mouse, and rat genes as these are the primary model organisms of interest for biomedical research and translation. |
Future Content Considerations¶
node_property_content: Consider expanding to include additional model organisms (e.g., zebrafish, fly, worm, yeast) if needed for broader comparative genomics support - Relevant files: gene_info.gz (additional taxon IDs)
node_property_content: Consider adding additional gene properties such as map_location, chromosome, synonyms, or dbXrefs for richer gene annotation
Additional Notes: ['The NCBI Gene ingest provides foundational gene nodes that serve as authoritative identifiers and basic properties for downstream integration with other biomedical data sources.']
Target Information¶
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:Gene | NCBIGene | Gene nodes include official gene symbols, descriptions, full names. |
Future Modeling Considerations¶
spoq_pattern: Future iterations could include gene-to-gene orthology relationships or gene-to-pathway associations if such data becomes available from NCBI Gene
Additional Notes: ['This ingest creates comprehensive gene nodes for human, mouse, and rat that serve as foundational entities for biomedical knowledge graphs, providing authoritative gene identifiers and basic properties.', 'This is a node-only ingest: it produces biolink:Gene nodes and no edges. As a result, no edge_type_info is applicable.']
Provenance Information¶
Contributors: - Generated following NCBI Gene documentation and requirements for human, mouse, and rat gene coverage