smithery.yaml•6.5 kB
# Smithery configuration file: https://smithery.ai/docs/config#smitheryyaml
startCommand:
type: stdio
configSchema:
# JSON Schema defining the configuration options for the MCP.
type: object
properties: {}
commandFunction:
# A JS function that produces the CLI command based on the given config to start the MCP on stdio.
|-
(config) => ({ command: 'biomcp', args: ['run'], env: {} })
exampleConfig: {}
schemas:
TrialQuery:
type: object
properties:
conditions:
type: array
items:
type: string
description: "List of condition terms."
terms:
type: array
items:
type: string
description: "General search terms that don't fit specific categories."
interventions:
type: array
items:
type: string
description: "Intervention names."
recruiting_status:
type: string
description: "Study recruitment status."
study_type:
type: string
description: "Type of study."
nct_ids:
type: array
items:
type: string
description: "Clinical trial NCT IDs"
lat:
type: number
description: "Latitude for location search"
long:
type: number
description: "Longitude for location search"
distance:
type: integer
description: "Distance from lat/long in miles"
min_date:
type: string
description: "Minimum date for filtering"
max_date:
type: string
description: "Maximum date for filtering"
date_field:
type: string
description: "Date field to filter on"
phase:
type: string
description: "Trial phase filter"
age_group:
type: string
description: "Age group filter"
primary_purpose:
type: string
description: "Primary purpose of the trial"
intervention_type:
type: string
description: "Type of intervention"
sponsor_type:
type: string
description: "Type of sponsor"
study_design:
type: string
description: "Study design"
sort:
type: string
description: "Sort order for results"
next_page_hash:
type: string
description: "Token to retrieve the next page of results"
VariantQuery:
type: object
properties:
gene:
type: string
description: "Gene symbol to search for (e.g. BRAF, TP53)"
hgvsp:
type: string
description: "Protein change notation (e.g., p.V600E, p.Arg557His)"
hgvsc:
type: string
description: "cDNA notation (e.g., c.1799T>A)"
rsid:
type: string
description: "dbSNP rsID (e.g., rs113488022)"
region:
type: string
description: "Genomic region as chr:start-end (e.g. chr1:12345-67890)"
significance:
type: string
description: "ClinVar clinical significance"
max_frequency:
type: number
description: "Maximum population allele frequency threshold"
min_frequency:
type: number
description: "Minimum population allele frequency threshold"
cadd:
type: number
description: "Minimum CADD phred score"
polyphen:
type: string
description: "PolyPhen-2 prediction"
sift:
type: string
description: "SIFT prediction"
sources:
type: array
items:
type: string
description: "Include only specific data sources"
size:
type: integer
description: "Number of results to return"
default: 40
offset:
type: integer
description: "Result offset for pagination"
default: 0
PubmedRequest:
type: object
properties:
chemicals:
type: array
items:
type: string
description: "List of chemicals for filtering results."
diseases:
type: array
items:
type: string
description: "Diseases such as Hypertension, Lung Adenocarcinoma, etc."
genes:
type: array
items:
type: string
description: "List of genes for filtering results."
keywords:
type: array
items:
type: string
description: "List of other keywords for filtering results."
variants:
type: array
items:
type: string
description: "List of variants for filtering results."
tools:
trial_searcher:
input:
schema:
type: object
properties:
query:
$ref: "#/schemas/TrialQuery"
required: ["query"]
variant_searcher:
input:
schema:
type: object
properties:
query:
$ref: "#/schemas/VariantQuery"
required: ["query"]
article_searcher:
input:
schema:
type: object
properties:
query:
$ref: "#/schemas/PubmedRequest"
required: ["query"]
# Simple string parameter functions
trial_protocol:
input:
schema:
type: object
properties:
nct_id:
type: string
description: "A single NCT ID (e.g., NCT04280705)"
required: ["nct_id"]
trial_locations:
input:
schema:
type: object
properties:
nct_id:
type: string
description: "A single NCT ID (e.g., NCT04280705)"
required: ["nct_id"]
trial_outcomes:
input:
schema:
type: object
properties:
nct_id:
type: string
description: "A single NCT ID (e.g., NCT04280705)"
required: ["nct_id"]
trial_references:
input:
schema:
type: object
properties:
nct_id:
type: string
description: "A single NCT ID (e.g., NCT04280705)"
required: ["nct_id"]
article_details:
input:
schema:
type: object
properties:
pmid:
type: string
description: "A single PubMed ID (e.g., 34397683)"
required: ["pmid"]
variant_details:
input:
schema:
type: object
properties:
variant_id:
type: string
description: "A variant identifier (e.g., chr7:g.140453136A>T)"
required: ["variant_id"]