ncbi_esearch
Search NCBI databases for gene, variant, or literature records with field-tag optimized queries to capture up to 100% of relevant results.
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!
EXAMPLE (Gene): ✅ query="Archaea[Organism] AND (nifH[Gene Name] OR nitrogenase[All Fields])" ❌ query="archaea AND nifH" (missing [Organism]/[Gene Name] tags → ~23% recall)
RETURNS formatted text results carrying the database-specific IDs. On a
missing/invalid database or query it returns a single text item whose
message begins with "Error:" — check for that prefix before using the IDs.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| db | No | Alias for `database`. | |
| term | No | Alias for `query`. | |
| query | No | Search query with NCBI field tags and boolean operators (alias: `term`) | |
| sort_by | No | Optional sort order (e.g., "relevance", "pub_date" for PubMed) | |
| database | No | 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 | |
| max_results | No | Maximum number of results to return (default: 20) | |
| start_index | No | Starting index for pagination (default: 0) | |
| search_field | No | Optional specific field to search in |