chembl-mcp-server
Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
사용해야 할까요
품질 및 안전성
A
도구 정의와 프로토콜 준수에 대한 자동 분석을 기반으로 합니다.
컨텍스트 비용
~8,961토큰 (도구 정의)
~13.6 KB일반적인 응답 크기
상당한 주의 영향 (128k 컨텍스트의 7.00%)
이는 서버의 도구가 모델의 컨텍스트에 로드될 때마다 소비되는 대략적인 토큰 수입니다. 수치가 높을수록 다른 작업에 사용할 수 있는 주의가 줄어듭니다.
설치
원클릭 설치
`claude_desktop_config.json` 파일에 다음을 추가하세요:
{
"mcpServers": {
"chembl-mcp-server": {
"command": "bun",
"args": [
"@cyanheads/chembl-mcp-server"
]
}
}
}실행 가능한 패키지
npm@cyanheads/chembl-mcp-server
0.3.2streamable-http원격 엔드포인트
https://chembl.caseyjhand.com/mcpstreamable-http할 수 있는 일
도구 목록
도구 (7)
🟢 읽기 전용🟡 쓰기🔴 삭제⚪ 알 수 없음
🟢chembl_search_molecules(query, structure, search_type, similarity_threshold, max_phase_min, ...)
Discovery entry point for compounds. Find by name / ChEMBL ID / InChIKey with the default search_type=name (supply query), or run a structure search with search_type exact | similarity | substructure (supply structure as a SMILES). At least one of query or structure is required, and structure is required for the three structure modes. Returns ChEMBL ID, preferred name, canonical SMILES, formula, MW, AlogP, Lipinski violations, QED, and max clinical phase on every row; only search_type=similarity adds a Tanimoto similarity percent. Chain molecule_chembl_id into chembl_get_bioactivities or chembl_get_drug_info. A capped result carries nextCursor — pass it back as cursor with the same filters to read the next page.
입력 스키마
{
"type": "object",
"properties": {
"query": {
"description": "Search text for search_type=name — a drug name, ChEMBL ID, or InChIKey, e.g. \"imatinib\" or \"CHEMBL25\".",
"type": "string"
},
"structure": {
"description": "SMILES string for structure search, e.g. \"CC(=O)Oc1ccccc1C(=O)O\". Required when search_type is exact/similarity/substructure.",
"type": "string"
},
"search_type": {
"default": "name",
"description": "name = text lookup (query); exact = exact structure match; similarity = Tanimoto ≥ threshold; substructure = contains the structure. All structure modes need `structure`.",
"type": "string",
"enum": [
"name",
"exact",
"similarity",
"substructure"
]
},
"similarity_threshold": {
"default": 70,
"description": "Minimum Tanimoto similarity percent for search_type=similarity (40–100; ChEMBL rejects below 40). Ignored for other modes.",
"type": "integer",
"minimum": 40,
"maximum": 100
},
"max_phase_min": {
"description": "For search_type=name, restrict to compounds at or above this max clinical phase (e.g. 4 for marketed drugs only).",
"type": "integer",
"minimum": 0,
"maximum": 4
},
"limit": {
"description": "Maximum molecules to return. Defaults to the server default (25) when omitted.",
"type": "integer",
"minimum": 1,
"maximum": 100
},
"cursor": {
"description": "Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same query/structure/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set.",
"type": "string"
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"molecules": {
"type": "array",
"items": {
"type": "object",
"properties": {
"molecule_chembl_id": {
"type": "string",
"description": "ChEMBL molecule ID, e.g. \"CHEMBL25\". Pass to chembl_get_bioactivities or chembl_get_drug_info."
},
"pref_name": {
"description": "Preferred name, e.g. \"ASPIRIN\". Null for many research compounds.",
"type": [
"string",
"null"
]
},
"canonical_smiles": {
"description": "Canonical SMILES structure. Null when no structure is recorded.",
"type": [
"string",
"null"
]
},
"standard_inchi_key": {
"description": "Standard InChIKey — chain to the pubchem server for richer chemistry. Null when absent.",
"type": [
"string",
"null"
]
},
"full_molformula": {
"description": "Molecular formula, e.g. \"C9H8O4\". Null when absent.",
"type": [
"string",
"null"
]
},
"mw_freebase": {
"description": "Molecular weight of the free base in g/mol, e.g. 180.16. Null when absent.",
"type": [
"number",
"null"
]
},
"alogp": {
"description": "Calculated AlogP lipophilicity, e.g. 1.31. Null when absent.",
"type": [
"number",
"null"
]
},
"num_ro5_violations": {
"description": "Lipinski rule-of-five violation count (0–4). Null when not computed.",
"type": [
"number",
"null"
]
},
"qed_weighted": {
"description": "QED weighted drug-likeness score, 0–1. Null when not computed.",
"type": [
"number",
"null"
]
},
"max_phase": {
"description": "Max clinical phase: 4 = marketed drug, 0 = research compound. Null when unknown. The cheap druggability signal.",
"type": [
"number",
"null"
]
},
"molecule_type": {
"description": "Molecule type, e.g. \"Small molecule\". Null when absent.",
"type": [
"string",
"null"
]
},
"similarity": {
"description": "Tanimoto similarity percent (0–100) to the query structure. Present only on search_type=similarity results; on every other search_type the key is absent, not null.",
"type": [
"number",
"null"
]
}
},
"required": [
"molecule_chembl_id",
"pref_name",
"canonical_smiles",
"standard_inchi_key",
"full_molformula",
"mw_freebase",
"alogp",
"num_ro5_violations",
"qed_weighted",
"max_phase",
"molecule_type"
],
"additionalProperties": false,
"description": "A compound matched by the search."
},
"description": "Matching compounds (up to the limit)."
},
"nextCursor": {
"description": "Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one.",
"type": "string"
},
"totalCount": {
"type": "number",
"description": "Total compounds matching before the limit was applied."
},
"truncated": {
"type": "boolean",
"description": "True when the result was capped at the limit."
},
"shown": {
"type": "number",
"description": "Number of molecules returned."
},
"cap": {
"type": "number",
"description": "The limit that was applied."
},
"notice": {
"description": "Guidance when nothing matched — echoes the query and suggests how to broaden.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `missing_input`: Neither query nor structure was supplied, or a structure search_type was chosen without a structure. Other values are possible when a failure originates below the handler.",
"examples": [
"missing_input"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"molecules",
"totalCount",
"truncated",
"shown",
"cap"
]
},
{
"required": [
"error"
]
}
]
}🟢chembl_get_bioactivities(molecule_chembl_id, target_chembl_id, standard_type, pchembl_value_min, potency_view, ...)
The flagship compound↔target bioactivity bridge: measurements for a molecule (target deconvolution / selectivity), a target (lead finding), or both together (how potently one compound hits one target). Supply at least one of molecule_chembl_id (from chembl_search_molecules) or target_chembl_id (from chembl_search_targets) — supplying both narrows to that compound–target pair, supplying neither is an error. Filter by standard_type (IC50/Ki/EC50/…), minimum potency pchembl_value_min, assay_type, and organism. Not every measurement has a derivable pchembl_value, so potency_view picks which side of that split you get: the default "potency_ranked" returns the measurements that have one, most potent first (ChEMBL sorts the rest first otherwise, which is why they are not merged), and "null_potency" returns exactly the measurements that have none. totalCount is the honest full match count across both views either way. Mixing measurement types (IC50 vs Ki) is a scientific error — set standard_type to compare like with like. A popular target carries tens of thousands of rows: results spill to a DataCanvas table (call chembl_dataframe_describe for its columns, then chembl_dataframe_query for honest aggregates across the staged set), while an inline preview answers the immediate question. Each view stages its own table (bioactivities / bioactivities_null_potency), so running both against one canvas_id lets a UNION ALL rebuild the full set. The staged table is capped at CHEMBL_MAX_SPILL_ROWS; when the cap is hit, truncated is true and the table is a bounded slice, not the complete view. The inline rows are always capped at limit, so compare that against totalCount before treating them as the whole answer. Spilling the rest requires CANVAS_PROVIDER_TYPE=duckdb; without it the inline preview is all there is.
입력 스키마
{
"type": "object",
"properties": {
"molecule_chembl_id": {
"description": "ChEMBL molecule ID (from chembl_search_molecules), e.g. \"CHEMBL941\". Supply this, target_chembl_id, or both — both narrows to that compound–target pair.",
"type": "string"
},
"target_chembl_id": {
"description": "ChEMBL target ID (from chembl_search_targets), e.g. \"CHEMBL203\". Supply this, molecule_chembl_id, or both — both narrows to that compound–target pair.",
"type": "string"
},
"standard_type": {
"description": "Restrict to one measurement type, e.g. \"IC50\", \"Ki\", \"EC50\". Set this to compare potencies validly.",
"type": "string"
},
"pchembl_value_min": {
"description": "Minimum pchembl_value (−log10 molar potency), e.g. 7 keeps sub-100 nM activities. Only valid on the potency_ranked view — the null_potency rows have no pchembl_value to compare against.",
"type": "number"
},
"potency_view": {
"default": "potency_ranked",
"description": "Which side of the pchembl_value presence split to retrieve. \"potency_ranked\" (default) returns the measurements that have a derivable pchembl_value, most potent first. \"null_potency\" returns exactly the measurements that have none — the rows the ranked view excludes, otherwise unreachable. The two partition the match set and stage to separate canvas tables.",
"type": "string",
"enum": [
"potency_ranked",
"null_potency"
]
},
"assay_type": {
"description": "Restrict to an assay type code: \"B\" (binding), \"F\" (functional), \"A\" (ADMET), \"T\" (toxicity).",
"type": "string"
},
"organism": {
"description": "Restrict to a target organism, e.g. \"Homo sapiens\" (case-insensitive exact match).",
"type": "string"
},
"limit": {
"description": "Maximum rows in the inline preview. Defaults to the server default (25). The full set still spills to the canvas.",
"type": "integer",
"minimum": 1,
"maximum": 1000
},
"canvas_id": {
"description": "Optional canvas ID from a prior call to reuse the same canvas. Each potency_view re-stages its own table, so a second query of the SAME view REPLACES (overwrites) its prior rows — it does not append — while the other view's table is left intact, which is what lets both coexist on one canvas. Omit to mint a fresh canvas.",
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$"
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"activities": {
"type": "array",
"items": {
"type": "object",
"properties": {
"activity_id": {
"type": "number",
"description": "ChEMBL activity row ID."
},
"molecule_chembl_id": {
"type": "string",
"description": "ChEMBL molecule ID of the measured compound."
},
"molecule_pref_name": {
"description": "Compound preferred name. Null for many research compounds.",
"type": [
"string",
"null"
]
},
"target_chembl_id": {
"type": "string",
"description": "ChEMBL target ID the compound was measured against."
},
"target_pref_name": {
"description": "Target preferred name. Null when unnamed.",
"type": [
"string",
"null"
]
},
"target_organism": {
"description": "Target organism, e.g. \"Homo sapiens\". Null when unspecified.",
"type": [
"string",
"null"
]
},
"assay_chembl_id": {
"type": "string",
"description": "ChEMBL assay ID — pass to chembl_get_assay for provenance."
},
"assay_type": {
"description": "Assay type code: B=binding, F=functional, A=ADMET, T=toxicity, P=physicochemical, U=unclassified. Null when absent.",
"type": [
"string",
"null"
]
},
"assay_description": {
"description": "Assay description text. Null when absent.",
"type": [
"string",
"null"
]
},
"standard_type": {
"description": "Standardized activity type, e.g. \"IC50\", \"Ki\", \"EC50\" — the comparability key. Null when absent.",
"type": [
"string",
"null"
]
},
"standard_relation": {
"description": "Standardized relation, e.g. \"=\", \">\", \"<\". Null when absent.",
"type": [
"string",
"null"
]
},
"standard_value": {
"description": "Standardized value in standard_units. Null when the measurement is missing — never 0.",
"type": [
"number",
"null"
]
},
"standard_units": {
"description": "Standardized units, e.g. \"nM\". Null when absent.",
"type": [
"string",
"null"
]
},
"pchembl_value": {
"description": "−log10(molar potency); the rank field. Null when underivable (non-standard type, censored relation).",
"type": [
"number",
"null"
]
},
"type": {
"description": "Original (pre-standardization) activity type string from upstream.",
"type": [
"string",
"null"
]
},
"value": {
"description": "Original value string from upstream — not coerced.",
"type": [
"string",
"null"
]
},
"units": {
"description": "Original units string from upstream.",
"type": [
"string",
"null"
]
},
"relation": {
"description": "Original relation string from upstream.",
"type": [
"string",
"null"
]
}
},
"required": [
"activity_id",
"molecule_chembl_id",
"molecule_pref_name",
"target_chembl_id",
"target_pref_name",
"target_organism",
"assay_chembl_id",
"assay_type",
"assay_description",
"standard_type",
"standard_relation",
"standard_value",
"standard_units",
"pchembl_value",
"type",
"value",
"units",
"relation"
],
"additionalProperties": false,
"description": "One bioactivity measurement linking a compound, target, and assay."
},
"description": "Bioactivity rows for the selected potency_view — the inline preview, or the full view when it fit without spilling."
},
"totalCount": {
"type": "number",
"description": "Total matching measurements upstream — the honest full count spanning BOTH potency views, before any preview cap. The staged/preview rows are the selected view of this."
},
"potency_view": {
"type": "string",
"enum": [
"potency_ranked",
"null_potency"
],
"description": "Which view these rows came from: \"potency_ranked\" = measurements with a derivable pchembl_value; \"null_potency\" = measurements with none. Re-call with the other value to reach the rest of totalCount."
},
"spilled": {
"type": "boolean",
"description": "True when the view exceeded the preview and was staged on the canvas."
},
"canvas_id": {
"description": "Canvas ID holding the staged table — pass to chembl_dataframe_describe to list its columns, then to chembl_dataframe_query to run SQL over them. Null when canvas is disabled or nothing spilled.",
"type": [
"string",
"null"
]
},
"table_name": {
"description": "Canvas table name holding the staged rowset, and the FROM target for chembl_dataframe_query SQL — \"bioactivities\" for potency_ranked, \"bioactivities_null_potency\" for null_potency. Null when not spilled.",
"type": [
"string",
"null"
]
},
"staged_row_count": {
"description": "Rows actually registered on the canvas table. Null when nothing spilled. Below the view total when truncated is true.",
"type": [
"number",
"null"
]
},
"truncated": {
"type": "boolean",
"description": "True when the CHEMBL_MAX_SPILL_ROWS cap was hit before the upstream view was exhausted — the staged table is a bounded slice, NOT the complete view, so aggregates over it are a sample. Narrow the filters to bring the view under the cap."
},
"canvasDisabled": {
"type": "boolean",
"description": "True when CANVAS_PROVIDER_TYPE is not duckdb, so large sets could not spill — the inline rows are a capped preview, not the full set."
},
"appliedFilters": {
"type": "object",
"properties": {
"scope": {
"type": "string",
"description": "Which IDs scoped the query: the molecule, the target, or both when it narrowed to a compound–target pair."
},
"standard_type": {
"description": "The standard_type filter applied, or null.",
"type": [
"string",
"null"
]
},
"pchembl_value_min": {
"description": "The pchembl_value_min filter applied, or null.",
"type": [
"number",
"null"
]
},
"assay_type": {
"description": "The assay_type filter applied, or null.",
"type": [
"string",
"null"
]
},
"organism": {
"description": "The organism filter applied, or null.",
"type": [
"string",
"null"
]
}
},
"required": [
"scope",
"standard_type",
"pchembl_value_min",
"assay_type",
"organism"
],
"additionalProperties": false,
"description": "Filters as the server parsed them."
},
"notice": {
"description": "Guidance when no measurements matched, or how to SQL the spilled set.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. Other values are possible when a failure originates below the handler.",
"examples": [
"missing_filter",
"contradictory_potency_filter"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"activities",
"totalCount",
"potency_view",
"spilled",
"canvas_id",
"table_name",
"staged_row_count",
"truncated",
"canvasDisabled",
"appliedFilters"
]
},
{
"required": [
"error"
]
}
]
}🟢chembl_search_targets(query, accession, gene_symbol, organism, target_type, ...)
Resolve a protein/gene/UniProt accession to the ChEMBL target ID that chembl_get_bioactivities needs for the target→leads workflow. Supply at least one of accession (UniProt, e.g. P00533), gene_symbol (e.g. EGFR), or query (free-text name); filter further by organism and target_type. Returns each target with its type, organism, and component UniProt accessions + gene symbols. A UniProt accession from the uniprot/protein server is the most precise input. A capped result carries nextCursor — pass it back as cursor with the same filters to read the next page.
입력 스키마
{
"type": "object",
"properties": {
"query": {
"description": "Free-text name match against the target preferred name, e.g. \"kinase\" or \"growth factor receptor\".",
"type": "string"
},
"accession": {
"description": "UniProt accession of a target component, e.g. \"P00533\". The most precise resolver — from the uniprot/protein server.",
"type": "string"
},
"gene_symbol": {
"description": "Gene symbol of a target component, e.g. \"EGFR\" (case-insensitive exact match).",
"type": "string"
},
"organism": {
"description": "Restrict to a source organism, e.g. \"Homo sapiens\" (case-insensitive exact match).",
"type": "string"
},
"target_type": {
"description": "Restrict to a target class, e.g. \"SINGLE PROTEIN\" or \"PROTEIN COMPLEX\".",
"type": "string"
},
"limit": {
"description": "Maximum targets to return. Defaults to the server default (25) when omitted.",
"type": "integer",
"minimum": 1,
"maximum": 100
},
"cursor": {
"description": "Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same accession/gene_symbol/query/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set.",
"type": "string"
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"targets": {
"type": "array",
"items": {
"type": "object",
"properties": {
"target_chembl_id": {
"type": "string",
"description": "ChEMBL target ID, e.g. \"CHEMBL203\". Pass to chembl_get_bioactivities as target_chembl_id."
},
"pref_name": {
"description": "Preferred target name, e.g. \"Epidermal growth factor receptor\". Null when unnamed.",
"type": [
"string",
"null"
]
},
"target_type": {
"description": "Target class: \"SINGLE PROTEIN\", \"PROTEIN COMPLEX\", \"PROTEIN FAMILY\", \"CELL-LINE\", \"ORGANISM\", etc.",
"type": [
"string",
"null"
]
},
"organism": {
"description": "Source organism, e.g. \"Homo sapiens\". Null when unspecified.",
"type": [
"string",
"null"
]
},
"components": {
"type": "array",
"items": {
"type": "object",
"properties": {
"accession": {
"description": "UniProt accession of the protein component, e.g. \"P00533\". Null when not a protein target.",
"type": [
"string",
"null"
]
},
"gene_symbols": {
"type": "array",
"items": {
"type": "string",
"description": "A gene symbol for this component, e.g. \"EGFR\"."
},
"description": "Gene symbols for this component, flattened from component synonyms. Empty when none are recorded."
}
},
"required": [
"accession",
"gene_symbols"
],
"additionalProperties": false,
"description": "One protein component of the target."
},
"description": "Protein components with UniProt accessions and gene symbols."
}
},
"required": [
"target_chembl_id",
"pref_name",
"target_type",
"organism",
"components"
],
"additionalProperties": false,
"description": "A ChEMBL target resolved from the supplied protein identifier."
},
"description": "Matching targets (up to the limit)."
},
"nextCursor": {
"description": "Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one.",
"type": "string"
},
"totalCount": {
"type": "number",
"description": "Total targets matching the filters before the limit was applied."
},
"truncated": {
"type": "boolean",
"description": "True when the result was capped at the limit."
},
"shown": {
"type": "number",
"description": "Number of targets returned."
},
"cap": {
"type": "number",
"description": "The limit that was applied."
},
"notice": {
"description": "Guidance when no target matched — echoes the filters and suggests how to broaden.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler.",
"examples": [
"missing_input"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"targets",
"totalCount",
"truncated",
"shown",
"cap"
]
},
{
"required": [
"error"
]
}
]
}🟢chembl_get_drug_info(molecule_chembl_id)
Pharmacology for a drug (molecule): mechanism(s) of action, the molecular target(s) it acts on, action type (inhibitor / agonist / …), first-approval year, and clinical indications with the max phase reached for each. Supply molecule_chembl_id (from chembl_search_molecules). Distinct from the openfda server's label/adverse-event view — this is the curated mechanism-and-indication record. A mechanism's target_chembl_id chains into chembl_get_bioactivities for compounds hitting the same target. Each list carries its own retrieval state: an empty mechanisms or indications array means the molecule has none recorded only when the matching mechanisms_status / indications_status is "complete" — "failed" means the upstream request was rejected and the array says nothing about the molecule, and "truncated" means the page cap bounded the list at fewer rows than the matching *_total_count.
입력 스키마
{
"type": "object",
"properties": {
"molecule_chembl_id": {
"type": "string",
"minLength": 1,
"description": "ChEMBL molecule ID (from chembl_search_molecules), e.g. \"CHEMBL939\" for gefitinib."
}
},
"required": [
"molecule_chembl_id"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"molecule_chembl_id": {
"type": "string",
"description": "The ChEMBL molecule ID queried."
},
"pref_name": {
"description": "Preferred drug name, e.g. \"GEFITINIB\". Null when unnamed.",
"type": [
"string",
"null"
]
},
"max_phase": {
"description": "Max clinical phase across indications: 4 = marketed. Null when unknown.",
"type": [
"number",
"null"
]
},
"first_approval": {
"description": "Year of first approval, e.g. 2003. Null when unapproved or unknown.",
"type": [
"number",
"null"
]
},
"mechanisms": {
"type": "array",
"items": {
"type": "object",
"properties": {
"target_chembl_id": {
"description": "ChEMBL target ID the mechanism acts on — chain to chembl_get_bioactivities. Null when unspecified.",
"type": [
"string",
"null"
]
},
"mechanism_of_action": {
"description": "Mechanism of action, e.g. \"Epidermal growth factor receptor erbB1 inhibitor\". Null when absent.",
"type": [
"string",
"null"
]
},
"action_type": {
"description": "Action type, e.g. \"INHIBITOR\", \"AGONIST\", \"ANTAGONIST\". Null when absent.",
"type": [
"string",
"null"
]
}
},
"required": [
"target_chembl_id",
"mechanism_of_action",
"action_type"
],
"additionalProperties": false,
"description": "One mechanism of action linked to its molecular target."
},
"description": "Mechanisms of action. Empty is authoritative only when mechanisms_status is \"complete\"."
},
"mechanisms_total_count": {
"description": "Total mechanism rows ChEMBL holds for this molecule (upstream page_meta.total_count). Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0.",
"type": [
"number",
"null"
]
},
"mechanisms_status": {
"type": "string",
"enum": [
"complete",
"truncated",
"failed"
],
"description": "Retrieval state of the mechanism list. \"complete\" = every row ChEMBL records is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of mechanisms_total_count rows. \"failed\" = the upstream request was rejected, so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry."
},
"indications": {
"type": "array",
"items": {
"type": "object",
"properties": {
"mesh_heading": {
"description": "MeSH disease heading, e.g. \"Carcinoma, Non-Small-Cell Lung\". Null when absent.",
"type": [
"string",
"null"
]
},
"efo_term": {
"description": "EFO disease term, e.g. \"non-small cell lung carcinoma\". Null when absent.",
"type": [
"string",
"null"
]
},
"max_phase_for_ind": {
"description": "Max clinical phase reached for THIS indication (1–4). Null when unknown.",
"type": [
"number",
"null"
]
}
},
"required": [
"mesh_heading",
"efo_term",
"max_phase_for_ind"
],
"additionalProperties": false,
"description": "One clinical indication with the phase reached for it."
},
"description": "Clinical indications. Empty is authoritative only when indications_status is \"complete\"."
},
"indications_total_count": {
"description": "Total indication rows ChEMBL holds for this molecule (upstream page_meta.total_count). Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0.",
"type": [
"number",
"null"
]
},
"indications_status": {
"type": "string",
"enum": [
"complete",
"truncated",
"failed"
],
"description": "Retrieval state of the indication list. \"complete\" = every row ChEMBL records is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of indications_total_count rows. \"failed\" = the upstream request was rejected, so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry."
},
"notice": {
"description": "Disclosure of anything the two lists do not say for themselves: a list whose upstream fetch failed (so its emptiness means nothing), a list the page cap bounded, or — only when both lists came back complete and empty — that the molecule may be a research compound rather than a drug.",
"type": "string"
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode."
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"molecule_chembl_id",
"pref_name",
"max_phase",
"first_approval",
"mechanisms",
"mechanisms_total_count",
"mechanisms_status",
"indications",
"indications_total_count",
"indications_status"
]
},
{
"required": [
"error"
]
}
]
}🟢chembl_get_assay(assay_chembl_id)
Assay provenance behind a bioactivity row: description, type (binding / functional / ADMET / toxicity), the target it measures, organism, and ChEMBL's 1–9 confidence score (9 = direct assay on the protein target, lower = homologous or indirect). Supply assay_chembl_id from a chembl_get_bioactivities row. Call this to judge whether two measurements are comparable before ranking them together.
입력 스키마
{
"type": "object",
"properties": {
"assay_chembl_id": {
"type": "string",
"minLength": 1,
"description": "ChEMBL assay ID from a bioactivity row's assay_chembl_id, e.g. \"CHEMBL674637\"."
}
},
"required": [
"assay_chembl_id"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"assay_chembl_id": {
"type": "string",
"description": "The ChEMBL assay ID queried."
},
"description": {
"description": "Assay description text. Null when absent.",
"type": [
"string",
"null"
]
},
"assay_type": {
"description": "Assay type code: B=binding, F=functional, A=ADMET, T=toxicity, P=physicochemical, U=unclassified. Null when absent.",
"type": [
"string",
"null"
]
},
"assay_type_description": {
"description": "Human-readable assay type, e.g. \"Binding\". Null when absent.",
"type": [
"string",
"null"
]
},
"target_chembl_id": {
"description": "ChEMBL target ID the assay measures — chain to chembl_search_targets/chembl_get_bioactivities. Null when unassigned.",
"type": [
"string",
"null"
]
},
"organism": {
"description": "Assay organism. Null when unspecified.",
"type": [
"string",
"null"
]
},
"confidence_score": {
"description": "ChEMBL confidence score, 1–9 (9 = direct single-protein assay; lower = homologous/indirect). Null when unscored.",
"type": [
"number",
"null"
]
},
"confidence_description": {
"description": "Human-readable confidence description, e.g. \"Direct single protein target assigned\". Null when absent.",
"type": [
"string",
"null"
]
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode."
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"assay_chembl_id",
"description",
"assay_type",
"assay_type_description",
"target_chembl_id",
"organism",
"confidence_score",
"confidence_description"
]
},
{
"required": [
"error"
]
}
]
}🟢chembl_dataframe_query(canvas_id, sql)
Run a read-only SQL SELECT over the bioactivity rows chembl_get_bioactivities spilled to a canvas — rank, group, dedupe, and aggregate across the FULL set, not the inline preview. Reference each staged table by the name chembl_get_bioactivities returned — bioactivities for its potency_ranked view, bioactivities_null_potency for null_potency; discover the staged tables and their columns with chembl_dataframe_describe. Compute honest aggregates here (e.g. SELECT molecule_chembl_id, MEDIAN(pchembl_value) AS med FROM bioactivities WHERE standard_type = 'IC50' GROUP BY 1 ORDER BY 2 DESC). Two independent bounds apply, each reported on its own field: truncated is true when the SQL result exceeded the canvas row cap, and rendered_rows says how many of the returned rows the markdown table holds once its character budget is reached (below row_count on a wide or long result). Page past either bound with SQL LIMIT/OFFSET — append e.g. LIMIT 500 OFFSET 500 and re-call; offsets reach rows beyond the canvas row cap. Requires CANVAS_PROVIDER_TYPE=duckdb.
입력 스키마
{
"type": "object",
"properties": {
"canvas_id": {
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$",
"description": "Canvas ID returned by chembl_get_bioactivities (spilled: true)."
},
"sql": {
"type": "string",
"description": "A read-only SELECT against the staged tables. Reference tables by the names chembl_get_bioactivities returned."
}
},
"required": [
"canvas_id",
"sql"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"rows": {
"type": "array",
"items": {
"type": "object",
"propertyNames": {
"type": "string"
},
"additionalProperties": {}
},
"description": "Result rows (capped at the canvas row limit). Each row is a column→value map."
},
"row_count": {
"type": "number",
"description": "Number of rows materialized in this response."
},
"rendered_rows": {
"type": "number",
"description": "How many of those rows the markdown table in content[] holds. Below row_count when the rendered table reached its character budget — a rendering bound, INDEPENDENT of truncated: a response can be truncated:false and still render fewer rows than row_count. Re-run the same SQL with LIMIT/OFFSET to read the rows past it."
},
"truncated": {
"type": "boolean",
"description": "True when the SQL result exceeded the canvas row cap and was truncated — the engine bounding the result set itself, not the rendering. Independent of rendered_rows; page past it with LIMIT/OFFSET."
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: Called while CANVAS_PROVIDER_TYPE is not duckdb, so no canvas exists. Other values are possible when a failure originates below the handler.",
"examples": [
"canvas_disabled"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"rows",
"row_count",
"rendered_rows",
"truncated"
]
},
{
"required": [
"error"
]
}
]
}🟢chembl_dataframe_describe(canvas_id)
List the tables and columns staged on a canvas by chembl_get_bioactivities — inspect before calling chembl_dataframe_query to write correct SQL. Returns each table with its row count, kind (table | view), and column names + types. Requires CANVAS_PROVIDER_TYPE=duckdb.
입력 스키마
{
"type": "object",
"properties": {
"canvas_id": {
"type": "string",
"pattern": "^[A-Za-z0-9_-]{10}$",
"description": "Canvas ID returned by chembl_get_bioactivities (spilled: true)."
}
},
"required": [
"canvas_id"
],
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false
}출력 스키마
{
"type": "object",
"properties": {
"tables": {
"type": "array",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Canvas-local table name, e.g. \"bioactivities\"."
},
"kind": {
"type": "string",
"enum": [
"table",
"view"
],
"description": "Whether the entry is a base table or a registered view."
},
"row_count": {
"type": "number",
"description": "Number of rows in the table (materialized COUNT for views)."
},
"columns": {
"type": "array",
"items": {
"type": "object",
"properties": {
"name": {
"type": "string",
"description": "Column name, e.g. \"pchembl_value\"."
},
"type": {
"type": "string",
"description": "Column type tag, e.g. \"DOUBLE\", \"VARCHAR\", \"BIGINT\"."
}
},
"required": [
"name",
"type"
],
"additionalProperties": false,
"description": "One column available for SQL."
},
"description": "Columns available for SQL on this table."
}
},
"required": [
"name",
"kind",
"row_count",
"columns"
],
"additionalProperties": false,
"description": "One staged table or view on the canvas."
},
"description": "Tables and views staged on the canvas."
},
"error": {
"description": "Present when the call failed. Absent on success.",
"type": "object",
"properties": {
"code": {
"type": "integer",
"minimum": -9007199254740991,
"maximum": 9007199254740991,
"description": "JSON-RPC error code for this failure."
},
"message": {
"type": "string",
"description": "Human-readable description of what went wrong."
},
"data": {
"type": "object",
"properties": {
"reason": {
"type": "string",
"description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: Called while CANVAS_PROVIDER_TYPE is not duckdb, so no canvas exists. Other values are possible when a failure originates below the handler.",
"examples": [
"canvas_disabled"
]
},
"recovery": {
"description": "Actionable next step for the caller.",
"type": "object",
"properties": {
"hint": {
"type": "string"
}
},
"required": [
"hint"
],
"additionalProperties": {}
},
"retryable": {
"description": "Whether retrying may succeed.",
"type": "boolean"
}
},
"additionalProperties": {}
}
},
"required": [
"code",
"message"
],
"additionalProperties": {}
}
},
"$schema": "https://json-schema.org/draft/2020-12/schema",
"additionalProperties": false,
"anyOf": [
{
"not": {
"required": [
"error"
]
},
"required": [
"tables"
]
},
{
"required": [
"error"
]
}
]
}커뮤니티
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