opentargets-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| MCP_TRANSPORT | No | Transport protocol: stdio, sse, or http. | stdio |
| FASTMCP_SERVER_HOST | No | Host address to bind the server. | 0.0.0.0 |
| FASTMCP_SERVER_PORT | No | Port number for the server. | 8000 |
| OPEN_TARGETS_API_URL | No | Base URL for the Open Targets GraphQL API. | https://api.platform.opentargets.org/api/v4/graphql |
| OPEN_TARGETS_RATE_LIMIT_RPS | No | Rate limit requests per second. | |
| OPEN_TARGETS_RATE_LIMIT_BURST | No | Rate limit burst size. | |
| OPEN_TARGETS_RATE_LIMIT_ENABLED | No | Enable global server-side rate limiting. Can also be set via --rate-limiting. | false |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| 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
| Name | Description |
|---|---|
| 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
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
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