NCBI Gene
NCBI Gene is the gene database of the National Center for Biotechnology Information, part of the US National Library of Medicine. It gives each gene a stable ID with its official symbol, aliases, map location and a written summary. Through ScholarMuse, an agent calls lookup_gene_protein with a symbol or gene name and gets the matching NCBI Gene record merged with Ensembl and UniProt data.
ScholarMuse tools: lookup_gene_protein. Each successful call uses credits.
Ask your agent
What your agent gets back
Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from NCBI Gene.
lookup_gene_protein
The tool returns one merged record. These are the parts filled from NCBI Gene. Field names are paths inside `data`.
- ids.ncbiGene
- NCBI Gene ID
- symbol
- Official gene symbol
- name
- Full gene name
- aliases
- Other symbols for the gene, up to 12
- organism
- Scientific name of the organism
- summary
- NCBI gene summary, cut at 2,000 characters
- chromosome
- Chromosome the gene is on
- cytoband
- Map location, for example 17q21.31
- location
- NCBI coordinates, only when Ensembl has no record
- links.ncbiGene
- URL of the gene page at NCBI
What it covers
- Gene records from NCBI Gene: ID, official symbol, full name, aliases, organism, chromosome, map location and summary.
- Any organism can be requested by NCBI taxon id. Common model organisms (human, mouse, rat, zebrafish, fruit fly, worm, yeast and others) can be requested by name. The default is human.
- Only current gene records are searched (the query is limited to live records in the chosen organism).
Limits
- One gene per call. The tool keeps the best match: exact symbol first, then full gene name, then all fields.
- An organism name outside the built-in list is rejected. Pass its NCBI taxon id instead.
- No sequences, transcripts, variants or literature links are returned. The summary is cut at 2,000 characters and aliases at 12.
- A UniProt accession or Ensembl gene id is resolved at those sources first. The NCBI Gene record is then attached only if it can be matched through UniProt's cross-reference or the gene symbol.
How ScholarMuse reaches NCBI Gene
The connector calls NCBI E-utilities directly: esearch on the gene database to find the gene in one organism, then esummary for the record. An NCBI API key is sent when one is configured. Without it the same data comes back, with requests spaced further apart (680 ms instead of 210 ms).
Gene searches are cached for up to 1 day and gene records for up to 7 days, so a recent edit at NCBI can take that long to appear.
API key: the upstream API can be called without one, so you do not add one.
Licence and attribution
Licence: Public domain (NCBI/NLM data usage policies apply)
Gene data from NCBI Gene, National Library of Medicine (ncbi.nlm.nih.gov/gene).
Records that come from NCBI Gene carry this licence and attribution. When you cite the data in a paper, follow NCBI Gene's own citation guidance.
