biothings-mcp

biothings_query_chems

Search chemical compounds using simple or complex Lucene queries. Get compound details like formula, weight, and XLogP from PubChem.

Instructions

Search chemical compounds via Lucene query (e.g., name, formula), returning compound details and query metadata.

    Search for chemical compounds using a query string with various filtering options.
    
    **Supported Query Features:**
    1. Simple Queries: "C6H12O6" - Find compounds with molecular formula, "glucose" - Find compounds with name
    2. Fielded Queries: "pubchem.molecular_formula:C6H12O6", "pubchem.molecular_weight:[100 TO 200]"
    3. Range Queries: "pubchem.xlogp:>2", "pubchem.topological_polar_surface_area:[50 TO 100]"
    4. Boolean Queries: "pubchem.hydrogen_bond_donor_count:>2 AND pubchem.hydrogen_bond_acceptor_count:>4"
    
    Returns compound details including PubChem data like formula, weight, and XLogP.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "q": "<q>"
    },
    "name": "biothings_query_chems"
  }
}

Input Schema

Name	Required	Default
`q`	Yes
`size`	No
`skip`	No
`sort`	No
`email`	No
`fields`	No	all

Output Schema

Name	Required	Description	Default
`hits`	Yes
`took`	No
`total`	No
`max_score`	No

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.6Jun 26, 2026

TDQS

C2.8/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries full burden. It discloses that the tool performs a search and returns compound details with PubChem fields, but fails to mention rate limits, authentication, pagination behavior, or whether the operation is read-only (likely safe). It adds some context beyond the schema but is not exhaustive.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is moderately concise with a summary and list of query features. However, the repeated mention of PubChem data is somewhat redundant. It could be more streamlined.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the 6 parameters and existence of an output schema, the description covers only the query string aspect thoroughly. It fails to explain other parameters, response format, or sibling tool differentiation. The tool is moderately complex but the description leaves significant gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, requiring full compensation. The description only explains the 'q' parameter with examples; the other five parameters (size, skip, sort, email, fields) are not described at all. This is insufficient for a 6-parameter tool.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it searches chemical compounds via Lucene query and returns compound details and metadata. It specifies the resource (chemical compounds) and action (search), but does not explicitly differentiate from sibling tools like biothings_get_chems or biothings_query_genes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides extensive query syntax examples but offers no guidance on when to use this tool versus alternatives like biothings_get_chem or biothings_query_many_chems. It lacks prerequisites, context for when not to use, or differentiation from similar search tools.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.