BioMedMCP MCP server
BioMedMCP provides AI agents with cited access to biomedical sources including PubMed, UniProt, ClinicalTrials.gov, ChEMBL, Open Targets, and GTEx. It allows users to build evidence notebooks, inspect tissue expression, find genetic studies, and retrieve specific records like gene data or literature with verifiable source links.
Endpoint and access
No sign-in to connect and list tools. Individual tools may still need a vendor account, credentials, or permissions; check the documented prerequisites.
sign in when promptedinstall the Python distributionSome sources need a key or installed datasetKeep credentials in environment variables or client secret storage
MCP endpoint (Streamable HTTP)
https://biomedmcp.unibiointelligence.com/mcpWhat its tools do
13 tools, grouped by the hints the server advertises. Hints are self-declared, not verified behavior.
Checks and signals
Each line is separate evidence, not a trust score.
- Passed Endpoint answered the live check ·
- Availability 1 of 1 checks passed in 30 days
What you can do with it
- Build an evidence notebook on LDL-receptor biology
- Inspect tissue expression for a human LDLR target
- Find PCSK9 genetic studies and separate observations
- Get variant evidence for specific alleles
Source and maintenance
Community listingRegistry 0.2.5
- Maintenance checked
Protocol and capabilities
- Server
- BioMed MCP 0.2.1
- MCP protocol negotiated in check
- 2025-11-25
- Tools
- 13 advertised
- Resources
- 3 advertised
- Resource templates
- 2 advertised
- Prompts
- 1 advertised
Server-advertised capabilities
{
"tools": {
"listChanged": true
},
"logging": {},
"prompts": {
"listChanged": true
},
"resources": {
"subscribe": false,
"listChanged": true
}
}Server-provided instructions
Untrusted server output shown for inspection. It is not Koskamo guidance and is excluded from knowledge search.
Tools
13 advertised
search_records — Search biomedical records
Advertised read-onlyOpen-world
Search genes, proteins, drugs, diseases, phenotypes, pathways, variants, pharmacogenomics, GWAS, diagnostics, adverse events, studies, patents or authors by text; returns IDs for get_record (variants: get_variant_evidence). Papers: search_literature. Trials: search_trials. Patent search is chemistry-linked (SureChEMBL); assignee/inventor/CPC search is query_source(source=patents). e.g. {"entity":"gene","query":"BRCA1","filters":{"species":9606}}
search_records input schema
{
"type": "object",
"$defs": {
"RecordFilters": {
"type": "object",
"properties": {
"drug": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"gene": {
"type": [
"string",
"null"
],
"maxLength": 128,
"description": "Gene symbol, e.g. PCSK9."
},
"hgvsp": {
"type": [
"string",
"null"
],
"maxLength": 128,
"description": "Protein change, e.g. p.R46L."
},
"trait": {
"type": [
"string",
"null"
],
"maxLength": 256
},
"region": {
"enum": [
"us",
"eu",
"who",
"all",
null
]
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 64,
"description": "One source ID; omit to query all."
},
"disease": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"p_value": {
"type": [
"number",
"null"
],
"maximum": 1,
"description": "Maximum association p-value.",
"exclusiveMinimum": 0
},
"species": {
"type": "integer",
"default": 9606,
"description": "NCBI taxon ID; 9606 is human.",
"exclusiveMinimum": 0
},
"reviewed": {
"type": [
"boolean",
"null"
],
"description": "Swiss-Prot reviewed entries only."
},
"existence": {
"type": [
"integer",
"null"
],
"maximum": 5,
"minimum": 1,
"description": "UniProt protein existence level."
},
"revel_min": {
"type": [
"number",
"null"
],
"maximum": 1,
"minimum": 0,
"description": "Minimum REVEL score."
},
"cpic_level": {
"type": [
"string",
"null"
],
"maxLength": 32,
"description": "CPIC evidence level, e.g. A."
},
"consequence": {
"type": [
"string",
"null"
],
"maxLength": 64,
"description": "e.g. missense_variant."
},
"manufacturer": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"product_type": {
"enum": [
"finished_pharma",
"api",
"vaccine",
null
]
},
"significance": {
"type": [
"string",
"null"
],
"maxLength": 64,
"description": "ClinVar significance, e.g. pathogenic."
},
"max_frequency": {
"type": [
"number",
"null"
],
"maximum": 1,
"minimum": 0,
"description": "Maximum population allele frequency."
},
"review_status": {
"type": [
"string",
"null"
],
"maxLength": 64
}
},
"additionalProperties": false
}
},
"allOf": [
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "gene"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source",
"species"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "variant"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"consequence",
"gene",
"hgvsp",
"max_frequency",
"revel_min",
"review_status",
"significance",
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "author"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "drug"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"product_type",
"region",
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "disease"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "phenotype"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "protein"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"disease",
"existence",
"reviewed",
"source",
"species"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "pathway"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "pgx"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"cpic_level",
"drug",
"gene",
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "gwas"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"gene",
"p_value",
"source",
"trait"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "diagnostic"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"manufacturer",
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "adverse_event"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "study"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "patent"
}
}
},
"then": {
"properties": {
"filters": {
"propertyNames": {
"enum": [
"source"
]
}
}
}
}
}
],
"required": [
"query",
"entity"
],
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"query": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"description": "next_cursor from the previous page."
},
"entity": {
"enum": [
"gene",
"variant",
"author",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent"
]
},
"output": {
"enum": [
"summary",
"full"
],
"default": "summary",
"description": "summary trims excerpts; full keeps source fields. Omitted evidence stays recoverable."
},
"filters": {
"$ref": "#/$defs/RecordFilters"
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh",
"description": "fresh bypasses the cache."
}
},
"additionalProperties": false
}search_records output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object"
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "search_records"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}search_records annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}get_record — Get record and evidence sections
Advertised read-onlyOpen-world
Fetch one record by ID with optional evidence sections, e.g. gene expression/eqtl/diseases/druggability, drug label/safety, article fulltext, trial eligibility, protein domains/structures. Variants: get_variant_evidence. List an entity's sections with get_capabilities(entity=...). e.g. {"entity":"gene","id":"PCSK9","species":9606}
get_record input schema
{
"type": "object",
"$defs": {
"QTLParameters": {
"type": "object",
"required": [
"tissue_id"
],
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": "string",
"maxLength": 128,
"minLength": 1,
"description": "GTEx tissue, e.g. Liver."
},
"variant_id": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"phenotype_id": {
"type": [
"string",
"null"
],
"maxLength": 128,
"minLength": 1
},
"analysis_mode": {
"enum": [
"gene_associations",
"metasoft",
"dynamic"
],
"default": "gene_associations"
},
"p_value_threshold": {
"type": "number",
"default": 0.05,
"maximum": 1,
"exclusiveMinimum": 0
}
},
"additionalProperties": false
},
"AssetParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 10000,
"minimum": 0
}
},
"additionalProperties": false
},
"CivicParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1,
"description": "CIViC page size; maximum 25."
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1,
"description": "Continuation from a previous CIViC page."
},
"collection": {
"enum": [
"evidenceItems",
"assertions",
null
],
"description": "Required with cursor."
}
},
"additionalProperties": false
},
"RecordParameters": {
"type": "object",
"properties": {
"eqtl": {
"anyOf": [
{
"$ref": "#/$defs/QTLParameters"
},
{
"type": "null"
}
]
},
"sqtl": {
"anyOf": [
{
"$ref": "#/$defs/QTLParameters"
},
{
"type": "null"
}
]
},
"civic": {
"anyOf": [
{
"$ref": "#/$defs/CivicParameters"
},
{
"type": "null"
}
]
},
"exons": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
},
"assets": {
"anyOf": [
{
"$ref": "#/$defs/AssetParameters"
},
{
"type": "null"
}
]
},
"domains": {
"anyOf": [
{
"$ref": "#/$defs/InterProParameters"
},
{
"type": "null"
}
]
},
"fulltext": {
"anyOf": [
{
"$ref": "#/$defs/FulltextParameters"
},
{
"type": "null"
}
]
},
"genetics": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
},
"complexes": {
"anyOf": [
{
"$ref": "#/$defs/InterProParameters"
},
{
"type": "null"
}
]
},
"expression": {
"anyOf": [
{
"$ref": "#/$defs/ExpressionParameters"
},
{
"type": "null"
}
]
},
"transcripts": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
}
},
"additionalProperties": false
},
"FulltextParameters": {
"type": "object",
"properties": {
"end": {
"type": "integer",
"default": 100,
"maximum": 100000,
"minimum": 1
},
"view": {
"enum": [
"outline",
"lines",
"assets"
],
"default": "outline",
"description": "outline lists sections; lines reads start-end; assets lists figures."
},
"start": {
"type": "integer",
"default": 1,
"maximum": 100000,
"minimum": 1
}
},
"description": "One-based inclusive lines, end >= start, up to 100. Defaults: 1–100.",
"additionalProperties": false
},
"InterProParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 25,
"maximum": 25,
"minimum": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1
}
},
"additionalProperties": false
},
"ExpressionParameters": {
"type": "object",
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": [
"string",
"null"
],
"maxLength": 128,
"description": "GTEx tissue, e.g. Liver; required for gene_tissue."
},
"query_type": {
"enum": [
"gene_median",
"gene_tissue"
],
"default": "gene_median"
}
},
"additionalProperties": false
},
"GeneAnnotationParameters": {
"type": "object",
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
}
},
"additionalProperties": false
}
},
"allOf": [
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "gene"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"go",
"pathways",
"protein",
"expression",
"eqtl",
"sqtl",
"transcripts",
"exons",
"target_evidence",
"diseases",
"druggability",
"genetics",
"hpa",
"interactions",
"civic",
"clingen",
"gencc",
"constraint",
"disgenet",
"funding",
"diagnostics"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "article"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"annotations",
"fulltext",
"assets",
"indexing"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "author"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "trial"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"eligibility",
"contacts",
"locations",
"outcomes",
"arms",
"references"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "drug"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"label",
"regulatory",
"safety",
"shortage",
"targets",
"indications",
"interactions",
"civic",
"approvals"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "disease"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"genes",
"phenotypes",
"models",
"variants",
"prevalence",
"survival",
"clinical_features",
"pathways",
"diagnostics",
"funding",
"civic",
"disgenet"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "phenotype"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "protein"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"domains",
"interactions",
"complexes",
"structures"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "pathway"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"genes",
"events"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "pgx"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"interactions",
"recommendations",
"frequencies",
"guidelines"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "gwas"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "diagnostic"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"genes",
"conditions",
"methods",
"regulatory"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "adverse_event"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"reactions",
"outcomes",
"concomitant",
"guidance"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "study"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record"
]
}
}
}
}
},
{
"if": {
"required": [
"entity"
],
"properties": {
"entity": {
"const": "patent"
}
}
},
"then": {
"properties": {
"sections": {
"items": {
"enum": [
"record",
"biblio",
"family",
"claims",
"citations"
]
}
}
}
}
}
],
"required": [
"entity",
"id"
],
"properties": {
"id": {
"type": "string",
"maxLength": 512,
"minLength": 1,
"description": "Exact ID, e.g. PCSK9, PMID:123, NCT04368728, MONDO:0007750, Q8NBP7, R-HSA-109581 or an InChIKey."
},
"entity": {
"enum": [
"gene",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent"
]
},
"sources": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 12,
"description": "Restrict lookups to these source IDs."
},
"species": {
"type": "integer",
"default": 9606,
"description": "NCBI taxon ID; 9606 is human.",
"exclusiveMinimum": 0
},
"sections": {
"type": "array",
"items": {
"enum": [
"annotations",
"approvals",
"arms",
"assets",
"biblio",
"citations",
"civic",
"claims",
"clingen",
"clinical_features",
"complexes",
"concomitant",
"conditions",
"constraint",
"contacts",
"diagnostics",
"diseases",
"disgenet",
"domains",
"druggability",
"eligibility",
"eqtl",
"events",
"exons",
"expression",
"family",
"frequencies",
"fulltext",
"funding",
"gencc",
"genes",
"genetics",
"go",
"guidance",
"guidelines",
"hpa",
"indexing",
"indications",
"interactions",
"label",
"locations",
"methods",
"models",
"outcomes",
"pathways",
"phenotypes",
"prevalence",
"protein",
"reactions",
"recommendations",
"record",
"references",
"regulatory",
"safety",
"shortage",
"sqtl",
"structures",
"survival",
"target_evidence",
"targets",
"transcripts",
"variants"
]
},
"maxItems": 12,
"description": "Empty returns the base record; get_capabilities(entity=...) lists sections."
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh",
"description": "fresh bypasses the cache."
},
"source_versions": {
"type": "object",
"description": "Pin releases as {source: version}.",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"section_parameters": {
"$ref": "#/$defs/RecordParameters",
"description": "Options keyed by requested section."
}
},
"additionalProperties": false
}get_record output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {
"allOf": [
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
},
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "trial"
}
}
},
"then": {
"$ref": "#/$defs/TrialRecord"
}
}
]
},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"TrialRecord": {
"type": "object",
"required": [
"source",
"identities",
"title",
"status",
"phases",
"study_type",
"enrollment",
"has_results",
"results_missingness",
"record_type",
"assertion_type",
"species"
],
"properties": {
"title": {
"type": [
"string",
"null"
]
},
"phases": {
"type": [
"array",
"null"
],
"items": {
"type": "string"
}
},
"source": {
"enum": [
"clinical-trials",
"nci"
]
},
"status": {
"type": [
"string",
"null"
]
},
"species": {
"const": 9606
},
"enrollment": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"count": {
"type": "null"
}
}
},
"else": {
"properties": {
"missingness": {
"const": "reported"
}
}
},
"then": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
}
}
],
"required": [
"count",
"basis",
"missingness",
"role",
"unit"
],
"properties": {
"role": {
"enum": [
"registry_enrollment",
"minimum_target_accrual"
]
},
"unit": {
"const": "participants"
},
"basis": {
"enum": [
"actual",
"estimated",
"minimum_target",
"not_supplied"
]
},
"count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
}
},
"additionalProperties": false
},
"identities": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"namespace": {
"const": "nct"
}
}
},
"else": {
"properties": {
"value": {
"pattern": "^NCI-\\d{4}-\\d{5,}$"
}
}
},
"then": {
"properties": {
"value": {
"not": {
"const": "NCT00000000"
},
"pattern": "^NCT\\d{8}$"
}
}
}
}
],
"required": [
"namespace",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 128,
"minLength": 1
},
"namespace": {
"enum": [
"nct",
"nci"
]
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"study_type": {
"type": [
"string",
"null"
]
},
"has_results": {
"type": [
"boolean",
"null"
]
},
"record_type": {
"const": "trial"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
},
"assertion_type": {
"const": "registry_record"
},
"source_release": {
"type": [
"string",
"null"
]
},
"results_missingness": {
"enum": [
"reported",
"not_supplied",
"not_normalized"
]
}
}
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
},
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "trial"
}
}
},
"then": {
"$ref": "#/$defs/TrialRecord"
}
}
]
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "get_record"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
},
"LiteratureRecord": {
"type": "object",
"required": [
"identities",
"content_scope",
"source_assertions",
"record_type"
],
"properties": {
"doi": {
"type": [
"string",
"null"
]
},
"date": {
"type": [
"string",
"null"
]
},
"pmid": {
"type": [
"string",
"null"
]
},
"pmcid": {
"type": [
"string",
"null"
]
},
"title": {
"type": [
"string",
"null"
]
},
"authors": {
"type": "array",
"items": {
"type": [
"string",
"null"
]
}
},
"abstract": {
"type": [
"string",
"null"
]
},
"identities": {
"type": "array",
"items": {
"type": "object",
"required": [
"namespace",
"source",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"namespace": {
"enum": [
"pmid",
"pmcid",
"doi",
"europepmc",
"openalex"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"record_type": {
"const": "literature"
},
"is_retracted": {
"type": [
"boolean",
"null"
]
},
"content_scope": {
"enum": [
"bibliographic",
"provider_excerpt",
"sentence_excerpt"
]
},
"citation_count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"is_open_access": {
"type": [
"boolean",
"null"
]
},
"source_assertions": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"kind": {
"const": "citation_count"
}
}
},
"else": {
"properties": {
"unit": {
"const": "flag"
},
"value": {
"type": [
"boolean",
"null"
]
}
}
},
"then": {
"properties": {
"unit": {
"const": "citations"
},
"value": {
"type": [
"integer",
"null"
],
"minimum": 0
}
}
}
},
{
"if": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
},
"else": {
"properties": {
"value": {
"not": {
"type": "null"
}
}
}
},
"then": {
"properties": {
"value": {
"type": "null"
}
}
}
}
],
"required": [
"kind",
"source",
"value",
"missingness",
"unit"
],
"properties": {
"kind": {
"enum": [
"retraction",
"open_access",
"citation_count"
]
},
"unit": {
"enum": [
"flag",
"citations"
]
},
"value": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "integer"
},
{
"type": "null"
}
]
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
}
},
"author_completeness": {
"enum": [
"complete",
"source_limited"
]
}
}
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}get_record annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}search_literature — Search literature
Advertised read-onlyOpen-world
Search papers across PubMed, Europe PMC, PubTator and LitSense with date, author, journal, article-type and open-access filters. Deduplicates across sources and reports each source's outcome. Read abstracts or full text with get_record(entity=article). e.g. {"query":"PCSK9 LDL cholesterol"}
search_literature input schema
{
"type": "object",
"$defs": {
"LiteratureFilters": {
"type": "object",
"properties": {
"drug": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"gene": {
"type": [
"string",
"null"
],
"maxLength": 128,
"description": "Gene symbol, e.g. PCSK9."
},
"sort": {
"enum": [
"relevance",
"date",
"citations",
null
]
},
"author": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 64,
"description": "One source ID; omit to query all."
},
"date_to": {
"type": [
"string",
"null"
],
"format": "date",
"description": "YYYY-MM-DD."
},
"disease": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"journal": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"date_from": {
"type": [
"string",
"null"
],
"format": "date",
"description": "YYYY-MM-DD."
},
"open_access": {
"type": [
"boolean",
"null"
]
},
"article_type": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"no_preprints": {
"type": [
"boolean",
"null"
]
},
"ranking_mode": {
"enum": [
"lexical",
"provider",
"hybrid",
null
]
}
},
"additionalProperties": false
}
},
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"query": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"description": "next_cursor from the previous page."
},
"output": {
"enum": [
"summary",
"full"
],
"default": "summary",
"description": "summary trims excerpts; full keeps source fields. Omitted evidence stays recoverable."
},
"filters": {
"$ref": "#/$defs/LiteratureFilters"
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh",
"description": "fresh bypasses the cache."
}
},
"additionalProperties": false
}search_literature output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
}
]
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "search_literature"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
},
"LiteratureRecord": {
"type": "object",
"required": [
"identities",
"content_scope",
"source_assertions",
"record_type"
],
"properties": {
"doi": {
"type": [
"string",
"null"
]
},
"date": {
"type": [
"string",
"null"
]
},
"pmid": {
"type": [
"string",
"null"
]
},
"pmcid": {
"type": [
"string",
"null"
]
},
"title": {
"type": [
"string",
"null"
]
},
"authors": {
"type": "array",
"items": {
"type": [
"string",
"null"
]
}
},
"abstract": {
"type": [
"string",
"null"
]
},
"identities": {
"type": "array",
"items": {
"type": "object",
"required": [
"namespace",
"source",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"namespace": {
"enum": [
"pmid",
"pmcid",
"doi",
"europepmc",
"openalex"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"record_type": {
"const": "literature"
},
"is_retracted": {
"type": [
"boolean",
"null"
]
},
"content_scope": {
"enum": [
"bibliographic",
"provider_excerpt",
"sentence_excerpt"
]
},
"citation_count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"is_open_access": {
"type": [
"boolean",
"null"
]
},
"source_assertions": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"kind": {
"const": "citation_count"
}
}
},
"else": {
"properties": {
"unit": {
"const": "flag"
},
"value": {
"type": [
"boolean",
"null"
]
}
}
},
"then": {
"properties": {
"unit": {
"const": "citations"
},
"value": {
"type": [
"integer",
"null"
],
"minimum": 0
}
}
}
},
{
"if": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
},
"else": {
"properties": {
"value": {
"not": {
"type": "null"
}
}
}
},
"then": {
"properties": {
"value": {
"type": "null"
}
}
}
}
],
"required": [
"kind",
"source",
"value",
"missingness",
"unit"
],
"properties": {
"kind": {
"enum": [
"retraction",
"open_access",
"citation_count"
]
},
"unit": {
"enum": [
"flag",
"citations"
]
},
"value": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "integer"
},
{
"type": "null"
}
]
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
}
},
"author_completeness": {
"enum": [
"complete",
"source_limited"
]
}
}
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}search_literature annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}search_trials — Search clinical trials
Advertised read-onlyOpen-world
Search clinical trials (ClinicalTrials.gov, NCI) by condition, intervention, phase and recruitment status. Read arms, eligibility or outcomes with get_record(entity=trial). Does not assess an individual's eligibility. e.g. {"query":"familial hypercholesterolemia","filters":{"status":"RECRUITING"}}
search_trials input schema
{
"type": "object",
"$defs": {
"TrialFilters": {
"type": "object",
"properties": {
"drug": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"gene": {
"type": [
"string",
"null"
],
"maxLength": 128,
"description": "Gene symbol, e.g. PCSK9."
},
"phase": {
"type": [
"string",
"null"
],
"maxLength": 32,
"description": "e.g. PHASE2, PHASE3."
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 64,
"description": "One source ID; omit to query all."
},
"status": {
"type": [
"string",
"null"
],
"maxLength": 64,
"description": "e.g. RECRUITING, COMPLETED."
},
"disease": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
}
},
"additionalProperties": false
}
},
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"query": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"description": "next_cursor from the previous page."
},
"output": {
"enum": [
"summary",
"full"
],
"default": "summary",
"description": "summary trims excerpts; full keeps source fields. Omitted evidence stays recoverable."
},
"filters": {
"$ref": "#/$defs/TrialFilters"
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh",
"description": "fresh bypasses the cache."
}
},
"additionalProperties": false
}search_trials output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {
"allOf": [
{},
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "trial"
}
}
},
"then": {
"$ref": "#/$defs/TrialRecord"
}
}
]
},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"TrialRecord": {
"type": "object",
"required": [
"source",
"identities",
"title",
"status",
"phases",
"study_type",
"enrollment",
"has_results",
"results_missingness",
"record_type",
"assertion_type",
"species"
],
"properties": {
"title": {
"type": [
"string",
"null"
]
},
"phases": {
"type": [
"array",
"null"
],
"items": {
"type": "string"
}
},
"source": {
"enum": [
"clinical-trials",
"nci"
]
},
"status": {
"type": [
"string",
"null"
]
},
"species": {
"const": 9606
},
"enrollment": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"count": {
"type": "null"
}
}
},
"else": {
"properties": {
"missingness": {
"const": "reported"
}
}
},
"then": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
}
}
],
"required": [
"count",
"basis",
"missingness",
"role",
"unit"
],
"properties": {
"role": {
"enum": [
"registry_enrollment",
"minimum_target_accrual"
]
},
"unit": {
"const": "participants"
},
"basis": {
"enum": [
"actual",
"estimated",
"minimum_target",
"not_supplied"
]
},
"count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
}
},
"additionalProperties": false
},
"identities": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"namespace": {
"const": "nct"
}
}
},
"else": {
"properties": {
"value": {
"pattern": "^NCI-\\d{4}-\\d{5,}$"
}
}
},
"then": {
"properties": {
"value": {
"not": {
"const": "NCT00000000"
},
"pattern": "^NCT\\d{8}$"
}
}
}
}
],
"required": [
"namespace",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 128,
"minLength": 1
},
"namespace": {
"enum": [
"nct",
"nci"
]
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"study_type": {
"type": [
"string",
"null"
]
},
"has_results": {
"type": [
"boolean",
"null"
]
},
"record_type": {
"const": "trial"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
},
"assertion_type": {
"const": "registry_record"
},
"source_release": {
"type": [
"string",
"null"
]
},
"results_missingness": {
"enum": [
"reported",
"not_supplied",
"not_normalized"
]
}
}
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"trial"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "trial"
}
}
},
"then": {
"$ref": "#/$defs/TrialRecord"
}
}
]
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "search_trials"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}search_trials annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}get_variant_evidence — Get variant evidence
Advertised read-onlyOpen-world
Get evidence for one variant (rsID, gene + protein change, HGVS or chr:pos:ref:alt). Defaults: ClinVar, gnomAD population, CIViC; add predictions (AlphaMissense), eve, cosmic, oncokb, hotspots, gwas or cbioportal. Ambiguous assembly or transcript is reported, not guessed; predictions keep source and uncertainty. e.g. {"id":"PCSK9 R46L"}
get_variant_evidence input schema
{
"type": "object",
"$defs": {
"CivicParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1,
"description": "CIViC page size; maximum 25."
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1,
"description": "Continuation from a previous CIViC page."
},
"collection": {
"enum": [
"evidenceItems",
"assertions",
null
],
"description": "Required with cursor."
}
},
"additionalProperties": false
},
"CohortReference": {
"type": "object",
"required": [
"molecular_profile_id",
"sample_list_id"
],
"properties": {
"sample_list_id": {
"type": "string",
"maxLength": 200,
"minLength": 1,
"description": "cBioPortal sample list ID."
},
"molecular_profile_id": {
"type": "string",
"maxLength": 200,
"minLength": 1,
"description": "cBioPortal molecular profile ID."
}
},
"additionalProperties": false
},
"VariantParameters": {
"type": "object",
"properties": {
"gwas": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
},
"civic": {
"anyOf": [
{
"$ref": "#/$defs/CivicParameters"
},
{
"type": "null"
}
]
},
"cbioportal": {
"anyOf": [
{
"$ref": "#/$defs/CohortReference"
},
{
"type": "null"
}
]
}
},
"additionalProperties": false
},
"GeneAnnotationParameters": {
"type": "object",
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
}
},
"additionalProperties": false
}
},
"required": [
"id"
],
"properties": {
"id": {
"type": "string",
"maxLength": 512,
"minLength": 1,
"description": "rsID, gene + protein change (PCSK9 R46L), HGVS or chr:pos:ref:alt."
},
"sources": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 12,
"description": "Restrict lookups to these source IDs."
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
],
"description": "Genome build for coordinate IDs."
},
"sections": {
"type": "array",
"items": {
"enum": [
"record",
"conservation",
"cosmic",
"cgi",
"predictions",
"eve",
"clinvar",
"population",
"civic",
"cbioportal",
"gwas",
"oncokb",
"hotspots"
]
},
"maxItems": 12
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh",
"description": "fresh bypasses the cache."
},
"section_parameters": {
"$ref": "#/$defs/VariantParameters",
"description": "Options keyed by requested section."
}
},
"additionalProperties": false
}get_variant_evidence output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"variant"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object"
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "get_variant_evidence"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}get_variant_evidence annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}analyze_study — Analyze genomics study
Advertised read-onlyOpen-world
Analyze an installed public cancer genomics study: gene_profile, mutation_cohort, survival, compare, co_occurrence, filter_cohort, top_mutated. List installed studies with get_capabilities(source=study); ubi_synthetic is invented demo data. Report sample denominators and exclusions. Private data analysis uses the Ubi platform. e.g. {"analysis":"gene_profile","study":"ubi_synthetic","gene":"TP53"}
analyze_study input schema
{
"type": "object",
"$defs": {
"StudyQuery": {
"type": "object",
"required": [
"gene",
"study",
"analysis"
],
"properties": {
"gene": {
"type": "string",
"pattern": "^[A-Za-z0-9_.-]+$",
"maxLength": 40,
"minLength": 1
},
"type": {
"enum": [
"mutations",
"cna",
"expression",
"sv"
],
"default": "mutations"
},
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"analysis": {
"const": "gene_profile"
}
},
"additionalProperties": false
},
"StudyCohort": {
"type": "object",
"required": [
"gene",
"study",
"analysis"
],
"properties": {
"gene": {
"type": "string",
"pattern": "^[A-Za-z0-9_.-]+$",
"maxLength": 40,
"minLength": 1
},
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"analysis": {
"const": "mutation_cohort"
}
},
"additionalProperties": false
},
"StudyFilter": {
"type": "object",
"required": [
"study",
"analysis"
],
"properties": {
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"deleted": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 10
},
"mutated": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 10
},
"analysis": {
"const": "filter_cohort"
},
"amplified": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 10
},
"cancer_type": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 5
},
"expression_above": {
"type": "object",
"maxProperties": 10,
"additionalProperties": {
"type": "number"
}
},
"expression_below": {
"type": "object",
"maxProperties": 10,
"additionalProperties": {
"type": "number"
}
}
},
"additionalProperties": false
},
"StudyCompare": {
"type": "object",
"required": [
"gene",
"study",
"target",
"analysis"
],
"properties": {
"gene": {
"type": "string",
"pattern": "^[A-Za-z0-9_.-]+$",
"maxLength": 40,
"minLength": 1
},
"type": {
"enum": [
"expression",
"mutations"
],
"default": "mutations"
},
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"target": {
"type": "string",
"pattern": "^[A-Za-z0-9_.-]+$",
"maxLength": 40,
"minLength": 1
},
"analysis": {
"const": "compare"
}
},
"additionalProperties": false
},
"StudySurvival": {
"type": "object",
"required": [
"gene",
"study",
"analysis"
],
"properties": {
"gene": {
"type": "string",
"pattern": "^[A-Za-z0-9_.-]+$",
"maxLength": 40,
"minLength": 1
},
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"analysis": {
"const": "survival"
},
"endpoint": {
"enum": [
"os",
"dfs",
"pfs",
"dss"
],
"default": "os"
}
},
"additionalProperties": false
},
"StudyTopMutated": {
"type": "object",
"required": [
"study",
"analysis"
],
"properties": {
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"analysis": {
"const": "top_mutated"
}
},
"additionalProperties": false
},
"StudyCoOccurrence": {
"type": "object",
"required": [
"genes",
"study",
"analysis"
],
"properties": {
"chart": {
"type": "boolean",
"default": false,
"description": "Add a declarative chart of the returned values."
},
"genes": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 10,
"minItems": 2
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$",
"description": "Installed study ID, e.g. ubi_synthetic."
},
"analysis": {
"const": "co_occurrence"
}
},
"additionalProperties": false
}
},
"oneOf": [
{
"$ref": "#/$defs/StudyQuery"
},
{
"$ref": "#/$defs/StudyCohort"
},
{
"$ref": "#/$defs/StudySurvival"
},
{
"$ref": "#/$defs/StudyCompare"
},
{
"$ref": "#/$defs/StudyCoOccurrence"
},
{
"$ref": "#/$defs/StudyTopMutated"
},
{
"$ref": "#/$defs/StudyFilter"
}
],
"discriminator": {
"mapping": {
"compare": "#/$defs/StudyCompare",
"survival": "#/$defs/StudySurvival",
"top_mutated": "#/$defs/StudyTopMutated",
"gene_profile": "#/$defs/StudyQuery",
"co_occurrence": "#/$defs/StudyCoOccurrence",
"filter_cohort": "#/$defs/StudyFilter",
"mutation_cohort": "#/$defs/StudyCohort"
},
"propertyName": "analysis"
}
}analyze_study output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object"
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "analyze_study"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}analyze_study annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}resolve_entity — Resolve identifiers
Advertised read-onlyOpen-world
Map a name, alias or ambiguous identifier to exact species-qualified IDs before joining evidence. Returns candidates when ambiguous; a provider match score alone is not identity. Skip when you already hold an exact ID. e.g. {"entity":"gene","query":"LDL receptor","species":9606}
resolve_entity input schema
{
"type": "object",
"$defs": {
"Entity": {
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
}
},
"required": [
"query"
],
"properties": {
"query": {
"type": "string",
"maxLength": 512,
"minLength": 1,
"description": "Name, alias, symbol or identifier."
},
"entity": {
"anyOf": [
{
"$ref": "#/$defs/Entity"
},
{
"type": "null"
}
]
},
"species": {
"type": "integer",
"default": 9606,
"description": "NCBI taxon ID; 9606 is human.",
"exclusiveMinimum": 0
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
],
"description": "Genome build for coordinate IDs."
}
},
"additionalProperties": false
}resolve_entity output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object"
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "resolve_entity"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}resolve_entity annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}find_related — Find related records
Advertised read-onlyOpen-world
List records linked to one record. gene/drug/disease: articles, trials. variant: articles, structure. article: citations, references, recommendations, authors, entities. author: articles. Record attributes are get_record sections, not relations. e.g. {"entity":"article","id":"PMID:123","relation":"references"}
find_related input schema
{
"type": "object",
"$defs": {
"Entity": {
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
}
},
"required": [
"entity",
"id",
"relation"
],
"properties": {
"id": {
"type": "string",
"maxLength": 512,
"minLength": 1,
"description": "Record ID, e.g. PCSK9, PMID:123 or openalex:A123."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"entity": {
"$ref": "#/$defs/Entity"
},
"species": {
"type": "integer",
"default": 9606,
"description": "NCBI taxon ID; 9606 is human.",
"exclusiveMinimum": 0
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
],
"description": "Genome build for coordinate IDs."
},
"relation": {
"type": "string",
"maxLength": 64,
"minLength": 1
}
},
"additionalProperties": false
}find_related output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"TrialRecord": {
"type": "object",
"required": [
"source",
"identities",
"title",
"status",
"phases",
"study_type",
"enrollment",
"has_results",
"results_missingness",
"record_type",
"assertion_type",
"species"
],
"properties": {
"title": {
"type": [
"string",
"null"
]
},
"phases": {
"type": [
"array",
"null"
],
"items": {
"type": "string"
}
},
"source": {
"enum": [
"clinical-trials",
"nci"
]
},
"status": {
"type": [
"string",
"null"
]
},
"species": {
"const": 9606
},
"enrollment": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"count": {
"type": "null"
}
}
},
"else": {
"properties": {
"missingness": {
"const": "reported"
}
}
},
"then": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
}
}
],
"required": [
"count",
"basis",
"missingness",
"role",
"unit"
],
"properties": {
"role": {
"enum": [
"registry_enrollment",
"minimum_target_accrual"
]
},
"unit": {
"const": "participants"
},
"basis": {
"enum": [
"actual",
"estimated",
"minimum_target",
"not_supplied"
]
},
"count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
}
},
"additionalProperties": false
},
"identities": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"namespace": {
"const": "nct"
}
}
},
"else": {
"properties": {
"value": {
"pattern": "^NCI-\\d{4}-\\d{5,}$"
}
}
},
"then": {
"properties": {
"value": {
"not": {
"const": "NCT00000000"
},
"pattern": "^NCT\\d{8}$"
}
}
}
}
],
"required": [
"namespace",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 128,
"minLength": 1
},
"namespace": {
"enum": [
"nct",
"nci"
]
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"study_type": {
"type": [
"string",
"null"
]
},
"has_results": {
"type": [
"boolean",
"null"
]
},
"record_type": {
"const": "trial"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
},
"assertion_type": {
"const": "registry_record"
},
"source_release": {
"type": [
"string",
"null"
]
},
"results_missingness": {
"enum": [
"reported",
"not_supplied",
"not_normalized"
]
}
}
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
},
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "trial"
}
}
},
"then": {
"$ref": "#/$defs/TrialRecord"
}
}
]
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "find_related"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
},
"LiteratureRecord": {
"type": "object",
"required": [
"identities",
"content_scope",
"source_assertions",
"record_type"
],
"properties": {
"doi": {
"type": [
"string",
"null"
]
},
"date": {
"type": [
"string",
"null"
]
},
"pmid": {
"type": [
"string",
"null"
]
},
"pmcid": {
"type": [
"string",
"null"
]
},
"title": {
"type": [
"string",
"null"
]
},
"authors": {
"type": "array",
"items": {
"type": [
"string",
"null"
]
}
},
"abstract": {
"type": [
"string",
"null"
]
},
"identities": {
"type": "array",
"items": {
"type": "object",
"required": [
"namespace",
"source",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"namespace": {
"enum": [
"pmid",
"pmcid",
"doi",
"europepmc",
"openalex"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"record_type": {
"const": "literature"
},
"is_retracted": {
"type": [
"boolean",
"null"
]
},
"content_scope": {
"enum": [
"bibliographic",
"provider_excerpt",
"sentence_excerpt"
]
},
"citation_count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"is_open_access": {
"type": [
"boolean",
"null"
]
},
"source_assertions": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"kind": {
"const": "citation_count"
}
}
},
"else": {
"properties": {
"unit": {
"const": "flag"
},
"value": {
"type": [
"boolean",
"null"
]
}
}
},
"then": {
"properties": {
"unit": {
"const": "citations"
},
"value": {
"type": [
"integer",
"null"
],
"minimum": 0
}
}
}
},
{
"if": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
},
"else": {
"properties": {
"value": {
"not": {
"type": "null"
}
}
}
},
"then": {
"properties": {
"value": {
"type": "null"
}
}
}
}
],
"required": [
"kind",
"source",
"value",
"missingness",
"unit"
],
"properties": {
"kind": {
"enum": [
"retraction",
"open_access",
"citation_count"
]
},
"unit": {
"enum": [
"flag",
"citations"
]
},
"value": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "integer"
},
{
"type": "null"
}
]
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
}
},
"author_completeness": {
"enum": [
"complete",
"source_limited"
]
}
}
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}find_related annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}build_dossier — Build research dossier
Advertised read-onlyOpen-world
Build a multi-section dossier in one call: verified identity, default record sections and top related papers, with citations and per-source outcomes. Workflows: target_dossier, model_input_bundle (gene), drug_review, disease_landscape, pathway_review, variant_dossier, negative_evidence (bounded literature check; never proves absence). Add sections with get_record. e.g. {"workflow":"target_dossier","focus":"LDLR","species":9606}
build_dossier input schema
{
"type": "object",
"$defs": {
"QTLParameters": {
"type": "object",
"required": [
"tissue_id"
],
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": "string",
"maxLength": 128,
"minLength": 1,
"description": "GTEx tissue, e.g. Liver."
},
"variant_id": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"phenotype_id": {
"type": [
"string",
"null"
],
"maxLength": 128,
"minLength": 1
},
"analysis_mode": {
"enum": [
"gene_associations",
"metasoft",
"dynamic"
],
"default": "gene_associations"
},
"p_value_threshold": {
"type": "number",
"default": 0.05,
"maximum": 1,
"exclusiveMinimum": 0
}
},
"additionalProperties": false
},
"AssetParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 10000,
"minimum": 0
}
},
"additionalProperties": false
},
"CivicParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1,
"description": "CIViC page size; maximum 25."
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1,
"description": "Continuation from a previous CIViC page."
},
"collection": {
"enum": [
"evidenceItems",
"assertions",
null
],
"description": "Required with cursor."
}
},
"additionalProperties": false
},
"CohortReference": {
"type": "object",
"required": [
"molecular_profile_id",
"sample_list_id"
],
"properties": {
"sample_list_id": {
"type": "string",
"maxLength": 200,
"minLength": 1,
"description": "cBioPortal sample list ID."
},
"molecular_profile_id": {
"type": "string",
"maxLength": 200,
"minLength": 1,
"description": "cBioPortal molecular profile ID."
}
},
"additionalProperties": false
},
"DossierParameters": {
"type": "object",
"properties": {
"eqtl": {
"anyOf": [
{
"$ref": "#/$defs/QTLParameters"
},
{
"type": "null"
}
]
},
"sqtl": {
"anyOf": [
{
"$ref": "#/$defs/QTLParameters"
},
{
"type": "null"
}
]
},
"civic": {
"anyOf": [
{
"$ref": "#/$defs/CivicParameters"
},
{
"type": "null"
}
]
},
"exons": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
},
"assets": {
"anyOf": [
{
"$ref": "#/$defs/AssetParameters"
},
{
"type": "null"
}
]
},
"domains": {
"anyOf": [
{
"$ref": "#/$defs/InterProParameters"
},
{
"type": "null"
}
]
},
"fulltext": {
"anyOf": [
{
"$ref": "#/$defs/FulltextParameters"
},
{
"type": "null"
}
]
},
"genetics": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
},
"complexes": {
"anyOf": [
{
"$ref": "#/$defs/InterProParameters"
},
{
"type": "null"
}
]
},
"cbioportal": {
"anyOf": [
{
"$ref": "#/$defs/CohortReference"
},
{
"type": "null"
}
]
},
"expression": {
"anyOf": [
{
"$ref": "#/$defs/ExpressionParameters"
},
{
"type": "null"
}
]
},
"transcripts": {
"anyOf": [
{
"$ref": "#/$defs/GeneAnnotationParameters"
},
{
"type": "null"
}
]
}
},
"additionalProperties": false
},
"FulltextParameters": {
"type": "object",
"properties": {
"end": {
"type": "integer",
"default": 100,
"maximum": 100000,
"minimum": 1
},
"view": {
"enum": [
"outline",
"lines",
"assets"
],
"default": "outline",
"description": "outline lists sections; lines reads start-end; assets lists figures."
},
"start": {
"type": "integer",
"default": 1,
"maximum": 100000,
"minimum": 1
}
},
"description": "One-based inclusive lines, end >= start, up to 100. Defaults: 1–100.",
"additionalProperties": false
},
"InterProParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 25,
"maximum": 25,
"minimum": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1
}
},
"additionalProperties": false
},
"ExpressionParameters": {
"type": "object",
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": [
"string",
"null"
],
"maxLength": 128,
"description": "GTEx tissue, e.g. Liver; required for gene_tissue."
},
"query_type": {
"enum": [
"gene_median",
"gene_tissue"
],
"default": "gene_median"
}
},
"additionalProperties": false
},
"GeneAnnotationParameters": {
"type": "object",
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0,
"description": "Zero-based page."
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
}
},
"additionalProperties": false
}
},
"required": [
"workflow",
"focus"
],
"properties": {
"focus": {
"type": "string",
"maxLength": 512,
"minLength": 1,
"description": "Gene symbol, drug, disease (MONDO ID or name), pathway (R-HSA ID or exact name), variant, or topic."
},
"species": {
"type": "integer",
"default": 9606,
"description": "NCBI taxon ID; 9606 is human.",
"exclusiveMinimum": 0
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
],
"description": "Genome build for coordinate IDs."
},
"sections": {
"type": [
"array",
"null"
],
"items": {
"enum": [
"annotations",
"approvals",
"assets",
"cbioportal",
"cgi",
"civic",
"clingen",
"clinical_features",
"clinvar",
"conservation",
"constraint",
"cosmic",
"diagnostics",
"diseases",
"disgenet",
"druggability",
"eqtl",
"eve",
"events",
"exons",
"expression",
"fulltext",
"funding",
"gencc",
"genes",
"genetics",
"go",
"gwas",
"hotspots",
"hpa",
"indexing",
"indications",
"interactions",
"label",
"models",
"oncokb",
"pathways",
"phenotypes",
"population",
"predictions",
"prevalence",
"protein",
"record",
"regulatory",
"safety",
"shortage",
"sqtl",
"survival",
"target_evidence",
"targets",
"transcripts",
"variants"
]
},
"maxItems": 12,
"description": "Replace the workflow's default sections."
},
"workflow": {
"enum": [
"target_dossier",
"variant_dossier",
"drug_review",
"disease_landscape",
"pathway_review",
"negative_evidence",
"model_input_bundle"
]
},
"section_parameters": {
"$ref": "#/$defs/DossierParameters",
"description": "Options keyed by requested section."
}
},
"additionalProperties": false
}build_dossier output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"source": {
"const": null
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"type": "object",
"required": [
"record_type"
],
"properties": {
"record_type": {
"const": "literature"
}
}
},
"then": {
"$ref": "#/$defs/LiteratureRecord"
}
}
]
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "build_dossier"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
},
"LiteratureRecord": {
"type": "object",
"required": [
"identities",
"content_scope",
"source_assertions",
"record_type"
],
"properties": {
"doi": {
"type": [
"string",
"null"
]
},
"date": {
"type": [
"string",
"null"
]
},
"pmid": {
"type": [
"string",
"null"
]
},
"pmcid": {
"type": [
"string",
"null"
]
},
"title": {
"type": [
"string",
"null"
]
},
"authors": {
"type": "array",
"items": {
"type": [
"string",
"null"
]
}
},
"abstract": {
"type": [
"string",
"null"
]
},
"identities": {
"type": "array",
"items": {
"type": "object",
"required": [
"namespace",
"source",
"value"
],
"properties": {
"value": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"namespace": {
"enum": [
"pmid",
"pmcid",
"doi",
"europepmc",
"openalex"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"maxItems": 64,
"minItems": 1
},
"record_type": {
"const": "literature"
},
"is_retracted": {
"type": [
"boolean",
"null"
]
},
"content_scope": {
"enum": [
"bibliographic",
"provider_excerpt",
"sentence_excerpt"
]
},
"citation_count": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"is_open_access": {
"type": [
"boolean",
"null"
]
},
"source_assertions": {
"type": "array",
"items": {
"type": "object",
"allOf": [
{
"if": {
"properties": {
"kind": {
"const": "citation_count"
}
}
},
"else": {
"properties": {
"unit": {
"const": "flag"
},
"value": {
"type": [
"boolean",
"null"
]
}
}
},
"then": {
"properties": {
"unit": {
"const": "citations"
},
"value": {
"type": [
"integer",
"null"
],
"minimum": 0
}
}
}
},
{
"if": {
"properties": {
"missingness": {
"const": "not_supplied"
}
}
},
"else": {
"properties": {
"value": {
"not": {
"type": "null"
}
}
}
},
"then": {
"properties": {
"value": {
"type": "null"
}
}
}
}
],
"required": [
"kind",
"source",
"value",
"missingness",
"unit"
],
"properties": {
"kind": {
"enum": [
"retraction",
"open_access",
"citation_count"
]
},
"unit": {
"enum": [
"flag",
"citations"
]
},
"value": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "integer"
},
{
"type": "null"
}
]
},
"source": {
"enum": [
"pubmed",
"europepmc",
"pubtator",
"litsense2",
"openalex"
]
},
"missingness": {
"enum": [
"reported",
"not_supplied"
]
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
}
},
"author_completeness": {
"enum": [
"complete",
"source_limited"
]
}
}
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}build_dossier annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}query_source — Query source directly
Advertised read-onlyOpen-world
Run a source-specific operation that other tools do not cover, e.g. ChEMBL bioactivities, Ensembl coordinates, PDB structure quality, OmniPath interactions, NCBI Datasets genomes, ncbi-records for GenBank/GEO/SRA. Read get_capabilities(source=...) for operations and params first. e.g. {"source":"gtex","operation":"get_metadata","params":{"info_type":"tissues","dataset_id":"gtex_v10"}}
query_source input schema
{
"type": "object",
"required": [
"source",
"operation"
],
"properties": {
"params": {
"type": "object",
"description": "Arguments for that operation's schema.",
"maxProperties": 32
},
"source": {
"enum": [
"gtex",
"uniprot",
"ensembl",
"chembl",
"mychem",
"mygene",
"mydisease",
"clinical-trials",
"dailymed",
"opentargets",
"protein-atlas",
"reactome",
"surechembl",
"pdb",
"omnipath",
"antibody-registry",
"bio-ontology",
"ncbi-records",
"enrichment",
"patents",
"clingen",
"orange-book",
"ncbi",
"openfda"
]
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh",
"description": "fresh bypasses the cache."
},
"operation": {
"type": "string",
"maxLength": 128,
"minLength": 1,
"description": "Operation listed by get_capabilities(source=...)."
}
},
"additionalProperties": false
}query_source output schema
{
"type": "object",
"$defs": {
"Section": {
"type": "object",
"required": [
"outcome"
],
"properties": {
"data": {},
"error": {
"anyOf": [
{
"$ref": "#/$defs/ErrorInfo"
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"recovery": {
"type": "object"
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"evidence_ids": {
"type": "array",
"items": {
"type": "string"
}
}
},
"additionalProperties": false
},
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
},
"ResearchResult": {
"type": "object",
"required": [
"outcome",
"schema_version",
"content_policy",
"receipt"
],
"properties": {
"query": {
"type": "object"
},
"entity": {
"anyOf": [
{
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
},
{
"type": "null"
}
]
},
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"receipt": {
"$ref": "#/$defs/EvidenceReceipt"
},
"records": {
"type": "array",
"items": {
"type": "object"
}
},
"sections": {
"type": "object",
"additionalProperties": {
"$ref": "#/$defs/Section"
}
},
"warnings": {
"type": "array",
"items": {
"type": "string"
}
},
"truncated": {
"type": "boolean"
},
"provenance": {
"type": "array",
"items": {
"type": "object",
"required": [
"evidence_id",
"source",
"content_hash"
],
"properties": {
"url": {
"type": [
"string",
"null"
]
},
"cached": {
"type": "boolean"
},
"source": {
"type": "string"
},
"sources": {
"type": "array",
"items": {
"type": "string"
}
},
"processor": {
"type": [
"string",
"null"
]
},
"record_id": {
"type": [
"string",
"null"
]
},
"evidence_id": {
"type": "string"
},
"content_hash": {
"type": "string"
},
"retrieved_at": {
"type": "string"
},
"source_version": {
"type": [
"string",
"null"
]
}
},
"additionalProperties": false
}
},
"next_cursor": {
"type": [
"string",
"null"
]
},
"next_actions": {
"type": "array",
"items": {
"type": "object"
}
},
"content_policy": {
"const": "data_only"
},
"rejected_links": {
"type": "object",
"additionalProperties": {
"type": "string"
}
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
"EvidenceReceipt": {
"type": "object",
"required": [
"implementation",
"operation",
"request",
"request_sha256",
"result_sha256",
"sources",
"completed_at",
"request_redacted",
"request_omitted",
"time_dependent",
"schema_version",
"reproduction"
],
"properties": {
"request": {
"type": [
"object",
"null"
]
},
"sources": {
"type": "array",
"items": {
"type": "string",
"maxLength": 64,
"minLength": 1
},
"maxItems": 64
},
"operation": {
"const": "query_source"
},
"completed_at": {
"type": "string",
"format": "date-time"
},
"reproduction": {
"const": "not_established"
},
"result_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"implementation": {
"type": "string",
"pattern": "^biomedmcp/\\d+\\.\\d+\\.\\d+$"
},
"request_sha256": {
"type": "string",
"pattern": "^[0-9a-f]{64}$"
},
"schema_version": {
"const": "1.0"
},
"time_dependent": {
"type": "boolean"
},
"request_omitted": {
"type": "boolean"
},
"request_redacted": {
"type": "boolean"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"$ref": "#/$defs/ResearchResult"
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}query_source annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}run_batch — Run batched reads
Advertised read-onlyOpen-world
Run up to ten independent read calls in parallel with one quota reservation; each result keeps its own outcome. build_dossier and utilities are not batchable. e.g. {"calls":[{"operation":"get_record","arguments":{"entity":"gene","id":"PCSK9","species":9606}}]}
run_batch input schema
{
"type": "object",
"$defs": {
"BatchCall": {
"type": "object",
"required": [
"operation",
"arguments"
],
"properties": {
"arguments": {
"type": "object",
"description": "Arguments for that tool.",
"maxProperties": 16
},
"operation": {
"enum": [
"search_records",
"get_record",
"search_literature",
"search_trials",
"get_variant_evidence",
"analyze_study",
"resolve_entity",
"find_related",
"query_source"
]
}
},
"additionalProperties": false
}
},
"required": [
"calls"
],
"properties": {
"calls": {
"type": "array",
"items": {
"$ref": "#/$defs/BatchCall"
},
"maxItems": 10,
"minItems": 1
},
"idempotency_key": {
"type": [
"string",
"null"
],
"maxLength": 128,
"minLength": 1,
"description": "Reuse when retrying so quota is charged once."
}
},
"additionalProperties": false
}run_batch output schema
{
"type": "object",
"$defs": {
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"type": "object",
"required": [
"outcome",
"results",
"schema_version"
],
"properties": {
"outcome": {
"enum": [
"data",
"partial",
"error"
]
},
"results": {
"type": "array",
"items": {
"type": "object",
"required": [
"outcome",
"schema_version"
],
"properties": {
"outcome": {
"enum": [
"data",
"empty",
"partial",
"ambiguous",
"unavailable",
"not_applicable",
"error"
]
},
"schema_version": {
"const": "1.0"
}
}
},
"maxItems": 10,
"minItems": 1
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}run_batch annotations
{
"readOnlyHint": true,
"openWorldHint": true,
"idempotentHint": true,
"destructiveHint": false
}get_capabilities — Inspect get_capabilities
Advertised read-only
List enabled sources, entity sections, dossier workflows and source operations with exact parameter schemas. Narrow with source or entity; diagnose=true probes source health. Examples: biomedmcp://guide. e.g. {}
get_capabilities input schema
{
"type": "object",
"$defs": {
"Entity": {
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse_event",
"study",
"patent",
"sequence"
]
}
},
"properties": {
"entity": {
"anyOf": [
{
"$ref": "#/$defs/Entity"
},
{
"type": "null"
}
]
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 128,
"minLength": 1
},
"diagnose": {
"type": "boolean",
"default": false,
"description": "Probe live source health (slower)."
}
},
"additionalProperties": false
}get_capabilities output schema
{
"type": "object",
"$defs": {
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"type": "object",
"required": [
"routing",
"tools",
"schema_version"
],
"properties": {
"tools": {
"type": "array",
"items": {
"type": "object",
"required": [
"name",
"description"
],
"properties": {
"name": {
"type": "string"
},
"description": {
"type": "string"
}
},
"additionalProperties": false
}
},
"routing": {
"type": "string"
},
"schema_version": {
"const": "1.0"
}
}
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}get_capabilities annotations
{
"readOnlyHint": true,
"openWorldHint": false,
"idempotentHint": true,
"destructiveHint": false
}get_quota — Check quota
Advertised read-only
Show remaining research allowance and reset times; signed-in accounts get higher limits. e.g. {}
get_quota input schema
{
"type": "object",
"properties": {},
"additionalProperties": false
}get_quota output schema
{
"type": "object",
"$defs": {
"ErrorInfo": {
"type": "object",
"required": [
"code",
"message",
"retryable",
"correction"
],
"properties": {
"code": {
"type": "string",
"pattern": "^[a-z][a-z0-9_]{0,79}$"
},
"fields": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"message": {
"type": "string"
},
"retryable": {
"type": "boolean"
},
"correction": {
"type": "string"
}
},
"additionalProperties": false
}
},
"anyOf": [
{
"type": "object",
"required": [
"enabled",
"schema_version"
],
"properties": {
"mode": {
"type": [
"string",
"null"
]
},
"tier": {
"enum": [
"free",
"pro",
"enterprise",
"admin",
null
]
},
"usage": {
"type": [
"integer",
"null"
]
},
"buckets": {
"type": "array",
"items": {
"type": "object",
"required": [
"bucket",
"limit",
"remaining",
"resets_at"
],
"properties": {
"held": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"limit": {
"type": "integer"
},
"bucket": {
"type": "string"
},
"pending": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"consumed": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"remaining": {
"type": "integer"
},
"resets_at": {
"type": "string"
},
"uncertain": {
"type": [
"integer",
"null"
],
"minimum": 0
},
"over_limit": {
"type": [
"integer",
"null"
],
"minimum": 0
}
},
"additionalProperties": false
}
},
"enabled": {
"type": "boolean"
},
"message": {
"type": [
"string",
"null"
]
},
"profile": {
"type": [
"string",
"null"
]
},
"period_start": {
"type": [
"string",
"null"
]
},
"tier_changes": {
"enum": [
"immediate",
null
]
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
},
{
"type": "object",
"required": [
"error",
"schema_version",
"outcome"
],
"properties": {
"error": {
"$ref": "#/$defs/ErrorInfo"
},
"outcome": {
"const": "error"
},
"schema_version": {
"const": "1.0"
}
},
"additionalProperties": false
}
]
}get_quota annotations
{
"readOnlyHint": true,
"openWorldHint": false,
"idempotentHint": true,
"destructiveHint": false
}Prompts
1 advertised
target_research
- gene
- Provide a value matching the following JSON schema: {"type":"string"}. Encode non-string values as JSON. (required)
Resources
3 advertised
guide
guide URI
biomedmcp://guideresult_schema
result_schema URI
biomedmcp://schemas/resultevidence_schema
evidence_schema URI
biomedmcp://schemas/evidencescientific_record_schema
scientific_record_schema URI template
biomedmcp://schemas/records/{family}evidence_range
evidence_range URI template
biomedmcp://evidence/{handle}/{selector}/{start}/{count}30-day availability
Aggregated from read-only remote checks; this is not a tool-execution or security guarantee.
- Successful checks
- 1 of 1 (100%)
- Average latency
- 855 ms
- 95th percentile latency
- 855 ms
Maintenance history
Public check and source-refresh events. Editorial and ownership records remain private.
- · probe · passed · 855 ms · metadata changed · 13 tool(s), 3 resource(s), 2 resource template(s), 1 prompt(s)
Connect from your client
Each snippet registers the same endpoint; pick the client you use.
Claude Code
Claude Code configuration
claude mcp add --transport http biomedmcp-unibiointelligence https://biomedmcp.unibiointelligence.com/mcpCodex
Codex configuration
codex mcp add biomedmcp-unibiointelligence --url https://biomedmcp.unibiointelligence.com/mcpCursor
Cursor configuration
{
"mcpServers": {
"biomedmcp-unibiointelligence": {
"url": "https://biomedmcp.unibiointelligence.com/mcp"
}
}
}Cline
Cline configuration
{
"mcpServers": {
"biomedmcp-unibiointelligence": {
"type": "streamableHttp",
"url": "https://biomedmcp.unibiointelligence.com/mcp",
"disabled": false
}
}
}VS Code
VS Code configuration
{
"servers": {
"biomedmcp-unibiointelligence": {
"type": "http",
"url": "https://biomedmcp.unibiointelligence.com/mcp"
}
}
}Gemini CLI
Gemini CLI configuration
gemini mcp add --transport http biomedmcp-unibiointelligence https://biomedmcp.unibiointelligence.com/mcpClaude Desktop
Claude Desktop configuration
https://biomedmcp.unibiointelligence.com/mcpWindsurf
Windsurf configuration
{
"mcpServers": {
"biomedmcp-unibiointelligence": {
"serverUrl": "https://biomedmcp.unibiointelligence.com/mcp"
}
}
}Let your agent find its tools
Find servers like BioMedMCP from your agent. Add Koskamo once to search the index for endpoints, access requirements, and client setup. Public discovery needs no key.