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Get Chemical Annotation Details

mychem.chemicals.annotation
Read-onlyIdempotent

Retrieve comprehensive annotation for a single chemical compound by its InChIKey (e.g. "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"), ChEMBL ID (e.g. "CHEMBL25"), PubChem CID (e.g. "CID2244"), or DrugBank ID (e.g. "DB00945"). Returns complete annotation from 16+ integrated databases: ChEBI chemical definition, IUPAC name, and synonyms; ChEMBL clinical development phase (0–4), molecule type, ATC therapeutic classification, Lipinski Ro5 properties (MW, XLogP, HBD, HBA, PSA, rotatable bonds), black-box warning flag, and withdrawal status; PubChem structural identifiers (CID, molecular formula, molecular weight, InChI, SMILES, heavy atom count, complexity score); DrugBank approved indication, mechanism of action, drug targets with gene names and pharmacological actions; PharmGKB clinical pharmacogenomics annotation count; SIDER reported side effects; and NDC product codes. Essential for drug discovery, cheminformatics pipelines, pharmacogenomics analysis, and clinical safety review.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
fieldsNoComma-separated annotation fields to retrieve. Default: chebi.name, chebi.definition, chebi.formula, chebi.mass, chembl.pref_name, chembl.max_phase, chembl.molecule_properties, pubchem.cid, pubchem.molecular_formula, pubchem.molecular_weight, drugbank.name, drugbank.groups, pharmgkb.name. For drug targets, add "drugbank.targets". For full ChEBI annotations, add "chebi". Use "all" for complete annotation from all 16 sources including SIDER (side effects), DrugCentral (clinical info), PharmGKB (pharmacogenomics), and NDC (drug codes).
chem_idYesChemical identifier to look up. Accepts: InChIKey (primary ID, e.g. "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"), ChEMBL ID (e.g. "CHEMBL25"), PubChem CID (e.g. "CID2244"), or DrugBank ID (e.g. "DB00945"). InChIKey is the most stable identifier — obtain from mychem.search results or external databases (ChEMBL, PubChem, ChEBI).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already signal readOnly/openWorld/idempotent/non-destructive, and the description adds context beyond them: it clarifies this is a per-compound lookup and details the 16+ integrated data sources returned, including safety-relevant fields like black-box warnings and withdrawal status. No contradiction with annotations exists.

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

Conciseness4/5

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

The description is front-loaded with the core operation and identifier examples before the data-source enumeration. It is dense and long because it summarizes 16+ data sources, but each clause adds scope or use-case value; slight trimming would be possible but the length is justified by the tool's breadth.

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

Completeness5/5

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

For a read-only lookup with a generated output schema, the description plus schema covers input types, default fields, optional field expansion, and use cases. There is an in-schema pointer to mychem.search for obtaining identifiers, and the annotations cover safety, so no critical calling information is missing.

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

Parameters3/5

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

Schema description coverage is 100%; both chem_id and fields have detailed descriptions in the schema, so the tool description adds little parameter-level meaning beyond what is already structured. The description's identifier examples reinforce chem_id but do not exceed what the schema already says.

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

Purpose5/5

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

The description opens with a specific verb ('Retrieve') and resource ('comprehensive annotation for a single chemical compound'), and enumerates accepted identifier types with examples. It distinguishes from siblings like mychem.chemicals.search and batch_query by emphasizing single-compound lookup via stable IDs. The database-by-database list makes the tool's output scope unmistakable.

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

Usage Guidelines4/5

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

It explicitly names use cases ('drug discovery, cheminformatics pipelines, pharmacogenomics analysis, and clinical safety review') and the schema tells agents to obtain InChIKey from mychem.search results, which implies when to use a preceding search. It does not explicitly state when not to use this tool or name the batch_query alternative, so it stops short of a 5.

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

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