NCBI

Access NCBI's suite of databases — Gene, PubMed, Nucleotide, Protein, and more — via the ncbi_search and ncbi_fetch tools.

TOOLncbi_search

Search any NCBI database using Entrez query syntax. Returns structured records.

Parameter	Type	Description
database *	string	`gene`, `pubmed`, `nucleotide`, `protein`, `snp`, `clinvar`.
query *	string	Entrez query string, e.g. `BRCA1[Gene] AND Homo sapiens[Organism]`.
maxResults	integer	Records to return (default 10, max 100).
sort	string	`relevance` or `date`.

Gene search

from smartsbio import SmartsBio

client = SmartsBio(api_key="sk_live_...")

result = client.tools.run(
    tool_id="ncbi_search",
    input={
        "database": "gene",
        "query": "BRCA1[Gene Name] AND Homo sapiens[Organism]",
        "maxResults": 1,
    },
)
gene = result["results"][0]
print(f"Gene ID  : {gene['id']}")
print(f"Symbol   : {gene['symbol']}")
print(f"Name     : {gene['name']}")
print(f"Location : chr{gene['chromosome']}:{gene['start']}-{gene['stop']}")
print(f"Summary  : {gene['summary'][:300]}")

PubMed literature search

from smartsbio import SmartsBio

client = SmartsBio(api_key="sk_live_...")
ws_id = client.workspaces.list()[0].id

result = client.tools.run(
    tool_id="ncbi_search",
    input={
        "database": "pubmed",
        "query": "IDH1 R132H glioma AND 2020:2025[PDAT]",
        "maxResults": 10,
        "sort": "date",
        "workspace_id": ws_id,
        "output_format": "bibtex",
        "output_path": "literature/",
    },
)
print(f"Total hits : {result['total_hits']}")
for p in result["articles"][:5]:
    print(f"  PMID {p['pmid']}  ({p['year']})  {p['title'][:65]}...")

# Download BibTeX
bib = client.files.download(result["output_path"], workspace_id=ws_id, dest="./refs/")
print(f"BibTeX saved to {bib}")

Nucleotide sequence fetch

Download a nucleotide record by accession and save the FASTA to your workspace.

from smartsbio import SmartsBio

client = SmartsBio(api_key="sk_live_...")
ws_id = client.workspaces.list()[0].id

# Fetch NM_007294 (BRCA1 mRNA, RefSeq)
result = client.tools.run(
    tool_id="ncbi_fetch",
    input={
        "database": "nucleotide",
        "accession": "NM_007294",
        "format": "fasta",
        "workspace_id": ws_id,
        "output_path": "sequences/",
    },
)
print(f"Length : {result['sequence_length']} bp")
print(f"Path   : {result['file_path']}")

# Download FASTA
fasta = client.files.download(result["file_path"], workspace_id=ws_id, dest="./sequences/")
print(f"FASTA saved to {fasta}")