BioThings MCP Server

Search genes via Lucene query, returning gene details and query metadata. **IMPORTANT:** This endpoint requires structured queries using specific field names. Simple natural language queries like "CDK2 gene" or "human kinase" will **NOT** work. You **MUST** specify the field you are querying, e.g., `symbol:CDK2`, `name:"cyclin-dependent kinase 2"`, `taxid:9606`. Use this tool when you need to *search* for genes based on criteria, not when you already know the specific gene ID. If you know the exact Entrez or Ensembl ID, use the `get_gene` tool instead for faster retrieval. **Supported Query Features (based on Lucene syntax):** 1. Simple Term Queries: `q=cdk2` (Searches across default fields) 2. Fielded Queries: `q=symbol:CDK2`, `q=name:"cyclin-dependent kinase 2"` 3. Range Queries: `q=taxid:[9606 TO 10090]` 4. Boolean Queries: `q=symbol:CDK2 AND taxid:9606` 5. Wildcard Queries: `q=symbol:CDK*` Returns gene details including symbol, name, taxid, and entrezgene.

Batch query genes by multiple terms, returning a list of gene details. Perform multiple gene searches in a single request using a comma-separated list of query terms. Unlike `query_genes`, the `query_list` parameter takes multiple **terms** (like gene IDs, symbols, names) rather than full query strings. The `scopes` parameter defines which fields these terms should be searched against. **Endpoint Usage:** - Query multiple symbols: `query_list=CDK2,BRCA1` with `scopes=symbol` - Query multiple Entrez IDs: `query_list=1017,672` with `scopes=entrezgene` - Query mixed IDs/symbols: `query_list=CDK2,672` with `scopes=symbol,entrezgene`

Fetch a specific gene by Entrez or Ensembl ID. Retrieves detailed information for a **single, specific gene** using its exact known identifier. **This is the preferred tool over `query_genes` for fetching a specific gene when you already know its standard ID (Entrez or Ensembl) and don't need complex search filters.** **Supported Identifiers:** - Entrez Gene ID: e.g., `1017` - Ensembl Gene ID: e.g., `ENSG00000123374`

Fetch multiple genes by a comma-separated list of Entrez or Ensembl IDs. Retrieves detailed information for **multiple specific genes** in a single request using their exact known identifiers. **This is the preferred tool over `query_many_genes` for fetching multiple specific genes when you already know their standard IDs (Entrez, Ensembl) and don't need complex search filters.** **Input Format:** Accepts a comma-separated list of gene IDs (Entrez or Ensembl). **Example:** `gene_ids=1017,1018` or `gene_ids=ENSG00000123374,ENSG00000134057`

Retrieve MyGene.info database metadata including stats and fields. Retrieve metadata about the underlying MyGene.info gene annotation database, **NOT** information about specific genes. **Use this tool ONLY to understand the database itself** (e.g., to discover available fields, check data versions, or get overall statistics). It **CANNOT** be used to find or retrieve data for any particular gene. **Returned Information:** - `stats`: Database statistics (e.g., total number of genes) - `fields`: Available gene annotation fields and their data types - `index`: Information about the backend data index - `version`: Data version information