| name | ncbi-gene-search |
| description | Use this skill to search NCBI Gene by symbol and organism, then fetch compact official Entrez Gene summaries. Do not use it for variant interpretation, transcript-level modeling, or bulk offline annotation. |
Purpose
Resolve a gene symbol through NCBI E-utilities and return concise Gene database summaries.
When to use
- You need an official Entrez Gene identifier for a symbol and species.
- You want a quick NCBI summary before a larger genomics workflow.
When not to use
- You need transcript-level coordinates or large-batch annotation.
- You need clinical interpretation or variant effect prediction.
- You need offline execution.
Inputs
- Gene symbol
- Optional species, maximum result count, email, and output path
Outputs
- JSON payload containing the query, matched Gene IDs, and compact gene summaries
Requirements
- Python 3.10+
- Network access to
eutils.ncbi.nlm.nih.gov
Procedure
- Run
python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol BRCA1 --species "homo sapiens" --retmax 1 --out skills/genomics/ncbi-gene-search/assets/brca1_gene_summary.json.
- Inspect the
genes list for gene_id, symbol, description, organism, and map_location.
- Use the NCBI gene ID in downstream lookup or literature workflows when needed.
Validation
- Command exits successfully.
search.ids contains at least one Gene ID for a known symbol.- The first result has a non-empty
symbol and organism.
Failure modes and fixes
- No hits: confirm the symbol and organism spelling.
- Unexpected species: make the organism explicit with
--species.
- Too many matches: lower
--retmax and review the returned summaries.
Safety and limits
- Metadata lookup only.
- This skill does not perform variant interpretation or clinical classification.
Example
python3 skills/genomics/ncbi-gene-search/scripts/search_ncbi_gene.py --symbol TP53 --species "homo sapiens" --retmax 1
Provenance
Related skills
ensembl-gene-lookupncbi-pubmed-search
