ncbi_esearch
Search NCBI databases (Gene, PubMed, ClinVar, etc.) via E-utilities esearch API. Improve result completeness by using mandatory field tags in queries.
Instructions
Search NCBI databases using E-utilities esearch API.
⚠️ CRITICAL FOR COMPREHENSIVE RESULTS ⚠️ ALWAYS use NCBI field tags for Gene, ClinVar, and similar databases! Without field tags, you may miss 70-80% of relevant results.
MANDATORY FIELD TAGS FOR GENE DATABASE: • [Organism] - Taxonomic filtering (e.g., "Homo sapiens[Organism]", "Archaea[Organism]") • [Gene Name] - Gene symbols (e.g., "TP53[Gene Name]", "nifH[Gene Name]") • [All Fields] - Broad keyword search (e.g., "nitrogenase[All Fields]")
IMPACT OF FIELD TAGS (Gene Database): • Without field tags: ~300 results (20-30% recall) ❌ • With field tags: ~1,300 results (100% recall) ✅ • Performance loss: Missing field tags = 70-80% data loss!
Args:
database: NCBI database name (alias: db). Supported values:
- "gene" or "ncbigene": NCBI Gene database ⚠️ FIELD TAGS CRITICAL
- "taxonomy": NCBI Taxonomy (organism information)
- "clinvar": ClinVar (genetic variants) ⚠️ FIELD TAGS CRITICAL
- "medgen": MedGen (medical genetics concepts)
- "mesh": MeSH (Medical Subject Headings)
- "pubmed": PubMed (biomedical literature)
- "pccompound": PubChem Compound
- "pcsubstance": PubChem Substance
- "pcassay": PubChem BioAssay
query: Search query with NCBI field tags and boolean operators (alias: term)
max_results: Maximum number of results to return (default: 20)
start_index: Starting index for pagination (default: 0)
sort_by: Optional sort order (e.g., "relevance", "pub_date" for PubMed)
search_field: Optional specific field to search in
db: Alias for database.
term: Alias for query.
Returns: Formatted search results with database-specific IDs
Examples - GENE DATABASE (CRITICAL): ✅ CORRECT (finds ~1,300 archaeal nifH genes, 100% recall): database="gene" query="Archaea[Organism] AND (nifH[Gene Name] OR nitrogenase[All Fields])"
❌ WRONG (finds only ~300 genes, 23% recall):
database="gene"
query="archaea AND nifH"
Problem: Missing [Organism] and [Gene Name] field tags!
✅ CORRECT (human genes):
database="gene"
query="Homo sapiens[Organism] AND TP53[Gene Name]"
❌ WRONG (incomplete results):
query="human AND TP53"Examples - OTHER DATABASES: MeSH: database="mesh", query="asthma[MeSH Terms]" PubMed: database="pubmed", query="CRISPR[Title/Abstract] AND gene editing" Taxonomy: database="taxonomy", query="Escherichia coli[Scientific Name]" ClinVar: database="clinvar", query="BRCA1[Gene Name] AND pathogenic[Clinical Significance]" PubChem: database="pccompound", query="aspirin[All Fields]"
Learn more: https://www.ncbi.nlm.nih.gov/books/NBK3837/
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| database | No | ||
| query | No | ||
| max_results | No | ||
| start_index | No | ||
| sort_by | No | ||
| search_field | No | ||
| db | No | ||
| term | No |