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nickzren

opentargets-mcp

by nickzren

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault
MCP_TRANSPORTNoTransport protocol: stdio, sse, or http.stdio
FASTMCP_SERVER_HOSTNoHost address to bind the server.0.0.0.0
FASTMCP_SERVER_PORTNoPort number for the server.8000
OPEN_TARGETS_API_URLNoBase URL for the Open Targets GraphQL API.https://api.platform.opentargets.org/api/v4/graphql
OPEN_TARGETS_RATE_LIMIT_RPSNoRate limit requests per second.
OPEN_TARGETS_RATE_LIMIT_BURSTNoRate limit burst size.
OPEN_TARGETS_RATE_LIMIT_ENABLEDNoEnable global server-side rate limiting. Can also be set via --rate-limiting.false

Capabilities

Features and capabilities supported by this server

CapabilityDetails
tools
{
  "listChanged": true
}
logging
{}
prompts
{
  "listChanged": false
}
resources
{
  "subscribe": false,
  "listChanged": false
}
extensions
{
  "io.modelcontextprotocol/ui": {}
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
get_target_alternative_genesA

List alternate gene symbols and database cross-references for a target.

get_target_associated_diseasesB

List diseases linked to a target with association scores.

get_target_chemical_probesB

List available chemical probes and their quality metrics.

get_target_classA

Return ChEMBL target class annotations for a gene.

get_target_depmap_essentialityB

Fetch DepMap CRISPR essentiality scores across cell lines.

get_target_expressionA

Return RNA and protein expression profiles for a target across tissues.

get_target_genetic_constraintA

Fetch genetic constraint metrics (gnomAD) for a target.

get_target_hallmarksA

Return cancer hallmark annotations associated with a target.

get_target_homologuesB

Retrieve cross-species homologues for a target gene.

get_target_infoC

Retrieve core identity details for a target gene.

get_target_interactionsA

Retrieve protein interaction partners for a target from curated databases.

get_target_known_drugsC

Return compounds with known activity on the target.

get_target_literature_occurrencesC

Return literature co-occurrence records for a target.

get_target_mouse_phenotypesB

Retrieve mouse knockout phenotypes associated with a target.

get_target_pathways_and_go_termsB

List pathway memberships and Gene Ontology annotations for a target.

get_target_prioritizationB

Return target prioritisation scores compiled across data sources.

get_target_safety_informationA

Retrieve documented safety liabilities for a target.

get_target_subcellular_locationsA

Return subcellular localisation annotations for a target.

get_target_tepB

Fetch Target Enabling Package (TEP) information for a gene.

get_target_tractabilityB

Return tractability assessments across modalities for a target.

get_disease_associated_targetsB

List targets associated with a disease, including evidence scores.

get_disease_infoB

Retrieve core metadata for an Open Targets disease entity.

get_disease_known_drugsA

Retrieve drugs with investigational or approved indications for a disease.

get_disease_literature_occurrencesC

Return literature co-occurrence records mentioning a disease.

get_disease_ontologyA

Retrieve ontology structure for a disease including parents, children, and ancestors.

get_disease_otar_projectsA

List Open Targets Associated Research (OTAR) projects linked to a disease.

get_disease_phenotypesB

Fetch HPO phenotype annotations linked to a disease.

get_disease_similar_entitiesA

Find semantically similar diseases based on PubMed embeddings.

get_drug_adverse_eventsC

Retrieve adverse event signals associated with a drug.

get_drug_cross_referencesB

Retrieve cross-database identifiers related to a drug.

get_drug_infoB

Fetch identity, indication, and mechanism data for a drug.

get_drug_linked_diseasesA

List diseases connected to a drug across indications and mechanisms.

get_drug_linked_targetsA

Return targets linked to a drug via mechanism-of-action data.

get_drug_literature_occurrencesC

Return literature co-occurrence records mentioning a drug.

get_drug_pharmacogenomicsB

Retrieve pharmacogenomics data linking genetic variants to drug response.

get_drug_pharmacovigilanceB

Summarise high-level pharmacovigilance data for a drug.

get_drug_similar_entitiesB

Find semantically similar drugs based on PubMed embeddings.

get_drug_warningsB

Fetch detailed regulatory warnings, including withdrawals and boxed labels.

get_target_disease_biomarkersB

Inspect evidence for biomarker annotations linking a target and disease.

get_target_disease_evidenceB

Retrieve evidence strings linking a target to a disease.

get_similar_targetsA

Identify targets with similar association profiles to the seed target.

search_entitiesA

Search Open Targets entities and resolve synonyms to canonical IDs.

search_facetsB

Return facet counts to help filter search results.

search_suggestionsC

Return autocomplete suggestions for partially typed queries.

get_variant_credible_setsA

List credible sets that include a specific variant.

get_variant_evidencesA

Retrieve evidence strings linking a variant to targets or diseases.

get_variant_infoA

Retrieve core metadata and functional annotations for a variant.

get_variant_intervalsB

Retrieve enhancer-to-gene (E2G) predictions overlapping a variant.

get_variant_pharmacogenomicsC

Retrieve pharmacogenomic annotations for a variant.

get_variant_protein_coordinatesB

Retrieve protein-level consequences for a variant.

get_credible_set_by_idB

Fetch detailed information for a specific study locus credible set.

get_credible_set_colocalisationB

Retrieve colocalisation results for a credible set.

get_credible_setsC

Query credible sets with flexible filtering options.

get_studies_by_diseaseC

List studies linked to one or more diseases.

get_study_credible_setsB

Retrieve fine-mapped credible sets for a study.

get_study_infoB

Retrieve metadata and cohort details for a GWAS study.

get_api_metadataA

Return Open Targets Platform release metadata.

get_association_datasourcesA

List sources contributing target–disease association evidence.

get_diseases_batchC

Retrieve multiple diseases in a single request.

get_drugs_batchA

Retrieve multiple drugs in a single request.

get_gene_ontology_termsA

Resolve Gene Ontology identifiers to human-readable labels.

get_interaction_resourcesA

Enumerate interaction databases integrated into Open Targets.

get_targets_batchB

Retrieve multiple targets in a single request.

map_idsB

Map free-text terms to canonical Open Targets identifiers.

graphql_batch_queryB

Execute one GraphQL query against many variable sets.

graphql_queryA

ADVANCED: Execute a raw GraphQL query against Open Targets.

graphql_schemaA

ADVANCED: Return the GraphQL schema in SDL format.

get_drug_repurposing_candidatesB

Find repurposing candidates by chaining disease, target, and drug evidence.

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

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