Integrated public biomedical research with cited, bounded evidence.
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Execute up to ten independent read operations with one atomic quota reservation. e.g. {"calls":[{"operation":"get","arguments":{"entity":"gene","id":"BRAF","species":9606}}]}; biomedmcp://guide
Pick your client. Values in capitals, like YOUR_TOKEN, are yours to fill in.
Run in a terminal
claude mcp add --transport http biomedmcp https://biomedmcp.unibiointelligence.com/mcp
Execute up to ten independent read operations with one atomic quota reservation. e.g. {"calls":[{"operation":"get","arguments":{"entity":"gene","id":"BRAF","species":9606}}]}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| calls* | array | |
| idempotency_key | string | null |
{
"type": "object",
"$defs": {
"BatchCall": {
"type": "object",
"required": [
"operation",
"arguments"
],
"properties": {
"arguments": {
"type": "object",
"maxProperties": 16
},
"operation": {
"enum": [
"search",
"get",
"literature_search",
"trial_search",
"variant_evidence",
"study_analysis",
"resolve",
"relate",
"query_source"
]
}
},
"additionalProperties": false
}
},
"required": [
"calls"
],
"properties": {
"calls": {
"type": "array",
"items": {
"$ref": "#/$defs/BatchCall"
},
"maxItems": 10,
"minItems": 1
},
"idempotency_key": {
"type": [
"string",
"null"
],
"maxLength": 128,
"minLength": 1
}
},
"additionalProperties": false
}Inspect enabled sources, workflows, sections or an advanced operation's exact schema. e.g. {}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| entity | any | |
| source | string | null | |
| diagnose | boolean |
{
"type": "object",
"$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
}
},
"additionalProperties": false
}Read ordinary records/evidence sections; variants use variant_evidence. Sources constrain all lookups and identity dependencies. e.g. {"entity":"gene","id":"BRAF","species":9606}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| id* | string | |
| entity* | any | |
| sources | array | |
| species | integer | |
| sections | array | |
| freshness | any | |
| source_versions | object | |
| section_parameters | any |
{
"type": "object",
"$defs": {
"QTLParameters": {
"type": "object",
"required": [
"tissue_id"
],
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": "string",
"maxLength": 128,
"minLength": 1
},
"variant_id": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"phenotype_id": {
"type": [
"string",
"null"
],
"maxLength": 128,
"minLength": 1
},
"analysis_mode": {
"enum": [
"gene_associations",
"metasoft",
"dynamic"
],
"default": "gene_associations"
},
"p_value_threshold": {
"type": "number",
"default": 0.05,
"maximum": 1,
"exclusiveMinimum": 0
}
},
"additionalProperties": false
},
"AssetParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 10000,
"minimum": 0
}
},
"additionalProperties": false
},
"CivicParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1
},
"collection": {
"enum": [
"evidenceItems",
"assertions",
null
]
}
},
"additionalProperties": false
},
"RecordParameters": {
"type": "object",
"properties": {
"eqtl": {
"anyOf": [
{
"$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"
},
"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
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"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
},
"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
},
"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
},
"species": {
"type": "integer",
"default": 9606,
"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
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh"
},
"source_versions": {
"type": "object",
"maxProperties": 8,
"additionalProperties": {
"type": "string"
}
},
"section_parameters": {
"$ref": "#/$defs/RecordParameters"
}
},
"additionalProperties": false
}Find papers with publication/topic/source filters; deduplicate evidence and retain source outcomes and opaque continuation. e.g. {"query":"KRAS resistance"}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query* | string | |
| cursor | string | null | |
| output | any | Summary bounds record excerpts; full retains source fields within the response budget. Omitted evidence has recovery resources. |
| filters | any | |
| freshness | any |
{
"type": "object",
"$defs": {
"LiteratureFilters": {
"type": "object",
"properties": {
"drug": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"gene": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"sort": {
"enum": [
"relevance",
"date",
"citations",
null
]
},
"author": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"date_to": {
"type": [
"string",
"null"
],
"format": "date"
},
"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"
},
"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
},
"output": {
"enum": [
"summary",
"full"
],
"default": "summary",
"description": "Summary bounds record excerpts; full retains source fields within the response budget. Omitted evidence has recovery resources."
},
"filters": {
"$ref": "#/$defs/LiteratureFilters"
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh"
}
},
"additionalProperties": false
}Run advanced source operations after checking capabilities/schema. Common tasks have dedicated tools. e.g. {"source":"gtex","operation":"get_metadata","params":{"info_type":"tissues","dataset_id":"gtex_v10"}}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| params | object | |
| source* | any | |
| freshness | any | |
| operation* | string |
{
"type": "object",
"required": [
"source",
"operation"
],
"properties": {
"params": {
"type": "object",
"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"
},
"operation": {
"type": "string",
"maxLength": 128,
"minLength": 1
}
},
"additionalProperties": false
}Inspect current research allowance and reset times; sign in for higher limits. e.g. {}; biomedmcp://guide
No arguments.
{
"type": "object",
"properties": {},
"additionalProperties": false
}Traverse an evidence relationship. Relations: gene/drug/disease: articles,trials; variant: articles,structure; article: citations,references,recommendations,authors,entities; author: articles. e.g. {"entity":"article","id":"PMID:123","relation":"references"}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| id* | string | |
| limit | integer | |
| entity* | any | |
| species | integer | |
| assembly | any | |
| relation* | string |
{
"type": "object",
"$defs": {
"Entity": {
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse-event",
"study",
"patent",
"sequence"
]
}
},
"required": [
"entity",
"id",
"relation"
],
"properties": {
"id": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"entity": {
"$ref": "#/$defs/Entity"
},
"species": {
"type": "integer",
"default": 9606,
"exclusiveMinimum": 0
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
]
},
"relation": {
"type": "string",
"maxLength": 64,
"minLength": 1
}
},
"additionalProperties": false
}Dossiers retain citations/outcomes. Inspect capabilities and get further sections for completeness. e.g. {"workflow":"target_dossier","focus":"ERBB2","species":9606}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| focus* | string | |
| species | integer | |
| assembly | any | |
| sections | array | null | |
| workflow* | any | |
| section_parameters | any |
{
"type": "object",
"$defs": {
"QTLParameters": {
"type": "object",
"required": [
"tissue_id"
],
"properties": {
"page": {
"type": "integer",
"default": 0,
"maximum": 100000,
"minimum": 0
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": "string",
"maxLength": 128,
"minLength": 1
},
"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
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1
},
"collection": {
"enum": [
"evidenceItems",
"assertions",
null
]
}
},
"additionalProperties": false
},
"CohortReference": {
"type": "object",
"required": [
"molecular_profile_id",
"sample_list_id"
],
"properties": {
"sample_list_id": {
"type": "string",
"maxLength": 200,
"minLength": 1
},
"molecular_profile_id": {
"type": "string",
"maxLength": 200,
"minLength": 1
}
},
"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"
},
"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
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
},
"tissue_id": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"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
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
}
},
"additionalProperties": false
}
},
"required": [
"workflow",
"focus"
],
"properties": {
"focus": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"species": {
"type": "integer",
"default": 9606,
"exclusiveMinimum": 0
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
]
},
"sections": {
"type": [
"array",
"null"
],
"items": {
"type": "string"
},
"maxItems": 12
},
"workflow": {
"enum": [
"target_dossier",
"drug_review",
"disease_landscape",
"pathway_review",
"negative_evidence",
"model_input_bundle",
"variant_dossier"
]
},
"section_parameters": {
"$ref": "#/$defs/DossierParameters"
}
},
"additionalProperties": false
}Resolve aliases/ambiguity before evidence joins. One exact species-qualified symbol/ID resolves; provider score alone never establishes identity. Retrieve known unambiguous identifiers directly. e.g. {"entity":"gene","query":"HER2","species":9606}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| query* | string | |
| entity | any | |
| species | integer | |
| assembly | any |
{
"type": "object",
"$defs": {
"Entity": {
"enum": [
"gene",
"variant",
"article",
"author",
"trial",
"drug",
"disease",
"phenotype",
"protein",
"pathway",
"pgx",
"gwas",
"diagnostic",
"adverse-event",
"study",
"patent",
"sequence"
]
}
},
"required": [
"query"
],
"properties": {
"query": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"entity": {
"anyOf": [
{
"$ref": "#/$defs/Entity"
},
{
"type": "null"
}
]
},
"species": {
"type": "integer",
"default": 9606,
"exclusiveMinimum": 0
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
]
}
},
"additionalProperties": false
}Find ordinary records with entity filters. Papers use literature_search; trials use trial_search. e.g. {"entity":"gene","query":"BRCA1","filters":{"species":9606}}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query* | string | |
| cursor | string | null | |
| entity* | any | |
| output | any | Summary bounds record excerpts; full retains source fields within the response budget. Omitted evidence has recovery resources. |
| filters | any | |
| freshness | any |
{
"type": "object",
"$defs": {
"RecordFilters": {
"type": "object",
"properties": {
"drug": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"gene": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"hgvsp": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"trait": {
"type": [
"string",
"null"
],
"maxLength": 256
},
"region": {
"enum": [
"us",
"eu",
"who",
"all",
null
]
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"disease": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"p_value": {
"type": [
"number",
"null"
],
"maximum": 1,
"exclusiveMinimum": 0
},
"species": {
"type": "integer",
"default": 9606,
"exclusiveMinimum": 0
},
"reviewed": {
"type": [
"boolean",
"null"
]
},
"existence": {
"type": [
"integer",
"null"
],
"maximum": 5,
"minimum": 1
},
"revel_min": {
"type": [
"number",
"null"
],
"maximum": 1,
"minimum": 0
},
"cpic_level": {
"type": [
"string",
"null"
],
"maxLength": 32
},
"consequence": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"manufacturer": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"product_type": {
"enum": [
"finished_pharma",
"api",
"vaccine",
null
]
},
"significance": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"max_frequency": {
"type": [
"number",
"null"
],
"maximum": 1,
"minimum": 0
},
"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
},
"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 bounds record excerpts; full retains source fields within the response budget. Omitted evidence has recovery resources."
},
"filters": {
"$ref": "#/$defs/RecordFilters"
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh"
}
},
"additionalProperties": false
}Analyze an installed verified public study. Bundled ubi_synthetic is an invented demo; discover installed releases with capabilities(source=study). Report clinical and assayed samples separately, unique mutant samples, events and exclusions. Preserve input hashes and denominators. Private compute uses Ubi platform. e.g. {"analysis":"gene_profile","study":"ubi_synthetic","gene":"TP53"}; biomedmcp://guide
No arguments.
{
"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
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"analysis": {
"const": "gene_profile"
}
},
"additionalProperties": false
},
"StudyCohort": {
"type": "object",
"required": [
"gene",
"study",
"analysis"
],
"properties": {
"gene": {
"type": "string",
"pattern": "^[A-Za-z0-9_.-]+$",
"maxLength": 40,
"minLength": 1
},
"chart": {
"type": "boolean",
"default": false
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"analysis": {
"const": "mutation_cohort"
}
},
"additionalProperties": false
},
"StudyFilter": {
"type": "object",
"required": [
"study",
"analysis"
],
"properties": {
"chart": {
"type": "boolean",
"default": false
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"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_.-]+$",
"maxLength": 40,
"minLength": 1
},
"type": {
"enum": [
"expression",
"mutations"
],
"default": "mutations"
},
"chart": {
"type": "boolean",
"default": false
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"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
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"analysis": {
"const": "survival"
},
"endpoint": {
"enum": [
"os",
"dfs",
"pfs",
"dss"
],
"default": "os"
}
},
"additionalProperties": false
},
"StudyTopMutated": {
"type": "object",
"required": [
"study",
"analysis"
],
"properties": {
"chart": {
"type": "boolean",
"default": false
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"analysis": {
"const": "top_mutated"
}
},
"additionalProperties": false
},
"StudyCoOccurrence": {
"type": "object",
"required": [
"genes",
"study",
"analysis"
],
"properties": {
"chart": {
"type": "boolean",
"default": false
},
"genes": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 10,
"minItems": 2
},
"study": {
"type": "string",
"pattern": "^[a-zA-Z0-9_-]{1,100}$"
},
"analysis": {
"const": "co_occurrence"
}
},
"additionalProperties": false
}
},
"oneOf": [
{
"$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"
}
}Find public clinical trials using disease/intervention and trial-specific filters. Does not determine individual clinical eligibility. e.g. {"query":"melanoma","filters":{"status":"RECRUITING"}}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query* | string | |
| cursor | string | null | |
| output | any | Summary bounds record excerpts; full retains source fields within the response budget. Omitted evidence has recovery resources. |
| filters | any | |
| freshness | any |
{
"type": "object",
"$defs": {
"TrialFilters": {
"type": "object",
"properties": {
"drug": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
},
"gene": {
"type": [
"string",
"null"
],
"maxLength": 128
},
"phase": {
"type": [
"string",
"null"
],
"maxLength": 32
},
"source": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"status": {
"type": [
"string",
"null"
],
"maxLength": 64
},
"disease": {
"type": "array",
"items": {
"type": "string",
"maxLength": 256,
"minLength": 1
},
"maxItems": 5
}
},
"additionalProperties": false
}
},
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"query": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048
},
"output": {
"enum": [
"summary",
"full"
],
"default": "summary",
"description": "Summary bounds record excerpts; full retains source fields within the response budget. Omitted evidence has recovery resources."
},
"filters": {
"$ref": "#/$defs/TrialFilters"
},
"freshness": {
"enum": [
"cached_if_fresh",
"fresh"
],
"default": "cached_if_fresh"
}
},
"additionalProperties": false
}Retrieve variant evidence with assembly/transcript ambiguity preserved. Defaults: ClinVar, population, CIViC. Request predictions for AlphaMissense, or eve for MIT-licensed EVE protein scores; computational predictions retain source and uncertainty. e.g. {"id":"BRAF V600E"}; biomedmcp://guide
| Argument | Type | Description |
|---|---|---|
| id* | string | |
| sources | array | |
| assembly | any | |
| sections | array | |
| freshness | any | |
| section_parameters | any |
{
"type": "object",
"$defs": {
"CivicParameters": {
"type": "object",
"properties": {
"limit": {
"type": "integer",
"default": 10,
"maximum": 25,
"minimum": 1
},
"cursor": {
"type": [
"string",
"null"
],
"maxLength": 2048,
"minLength": 1
},
"collection": {
"enum": [
"evidenceItems",
"assertions",
null
]
}
},
"additionalProperties": false
},
"CohortReference": {
"type": "object",
"required": [
"molecular_profile_id",
"sample_list_id"
],
"properties": {
"sample_list_id": {
"type": "string",
"maxLength": 200,
"minLength": 1
},
"molecular_profile_id": {
"type": "string",
"maxLength": 200,
"minLength": 1
}
},
"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
},
"limit": {
"type": "integer",
"default": 10,
"maximum": 100,
"minimum": 1
}
},
"additionalProperties": false
}
},
"required": [
"id"
],
"properties": {
"id": {
"type": "string",
"maxLength": 512,
"minLength": 1
},
"sources": {
"type": "array",
"items": {
"type": "string"
},
"maxItems": 12
},
"assembly": {
"enum": [
"grch37",
"grch38",
null
]
},
"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"
},
"section_parameters": {
"$ref": "#/$defs/VariantParameters"
}
},
"additionalProperties": false
}We read every tool's name, description and inputs the way the model will, looking for instructions hidden from you. A clean result means no warning signs, not a guarantee. Scanned Nov 5, 2026.