Opentarget Genetics Tools

Configuration File: opentarget_genetics_tools.json Tool Type: Local Tools Count: 10

This page contains all tools defined in the opentarget_genetics_tools.json configuration file.

Available Tools

OpenTargets_get_credible_set_colocalisation (Type: OpenTarget)

Retrieve GWAS/QTL colocalisation evidence for a credible set (by studyLocusId) from OpenTargets. …

OpenTargets_get_credible_set_colocalisation tool specification

Tool Information:

• Name: OpenTargets_get_credible_set_colocalisation

• Type: OpenTarget

• Description: Retrieve GWAS/QTL colocalisation evidence for a credible set (by studyLocusId) from OpenTargets. Returns the colocalisation count and rows, each with the method (COLOC, COLOC_PIP_ECAVIAR, etc.), the posterior probability h4 of a shared causal variant, the colocalisation posterior probability clpp, numberColocalisingVariants, and the other colocalising study locus (studyLocusId, study type/id). Use to link a GWAS signal to a molecular QTL.

Parameters:

• studyLocusId (string) (required) The credible-set / study-locus ID (e.g., ‘0004aaf4841475f0caf5bcde04432bcf’).

• size (integer) (optional) Maximum number of colocalisation rows to return (1-500).

Example Usage:

query = {
    "name": "OpenTargets_get_credible_set_colocalisation",
    "arguments": {
        "studyLocusId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_credible_set_detail (Type: OpenTarget)

Get detailed information about a specific GWAS credible set (fine-mapped locus) from Open Targets…

OpenTargets_get_credible_set_detail tool specification

Tool Information:

• Name: OpenTargets_get_credible_set_detail

• Type: OpenTarget

• Description: Get detailed information about a specific GWAS credible set (fine-mapped locus) from Open Targets. Returns the lead variant, associated study, fine-mapping method, statistical significance, locus-to-gene (L2G) predictions mapping the signal to likely causal genes, and colocalization evidence with QTLs.

Parameters:

• studyLocusId (string) (required) Credible set identifier (studyLocusId), a 32-character hash (e.g., ‘b758d8fb10924f5338cbad8d27c7dee8’). Obtain from variant credible sets or study credible sets queries.

Example Usage:

query = {
    "name": "OpenTargets_get_credible_set_detail",
    "arguments": {
        "studyLocusId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_gwas_study (Type: OpenTarget)

Get detailed metadata for a GWAS study from Open Targets Platform, including trait information, s…

OpenTargets_get_gwas_study tool specification

Tool Information:

• Name: OpenTargets_get_gwas_study

• Type: OpenTarget

• Description: Get detailed metadata for a GWAS study from Open Targets Platform, including trait information, sample sizes, publication details, disease mappings, cohorts, LD population structure, and availability of summary statistics. Use GCST accession IDs.

Parameters:

• studyId (string) (required) GWAS study accession ID (e.g., ‘GCST000392’ for T1D Barrett et al., ‘GCST90029024’ for T2D Loh et al.)

Example Usage:

query = {
    "name": "OpenTargets_get_gwas_study",
    "arguments": {
        "studyId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_study_credible_sets (Type: OpenTarget)

Get all credible sets (fine-mapped GWAS loci) for a specific GWAS study from Open Targets. Return…

OpenTargets_get_study_credible_sets tool specification

Tool Information:

• Name: OpenTargets_get_study_credible_sets

• Type: OpenTarget

• Description: Get all credible sets (fine-mapped GWAS loci) for a specific GWAS study from Open Targets. Returns the lead variants, fine-mapping details, p-values, effect sizes, and locus-to-gene (L2G) predictions for each locus in the study. Use this to explore all significant loci discovered in a GWAS.

Parameters:

• studyIds (array) (required) GWAS study accession IDs (e.g., [‘GCST000392’])

• size (integer) (optional) Number of credible sets to return (default 20)

• index (integer) (optional) Page index for pagination (0-based, default 0)

Example Usage:

query = {
    "name": "OpenTargets_get_study_credible_sets",
    "arguments": {
        "studyIds": ["item1", "item2"]
    }
}
result = tu.run(query)

OpenTargets_get_variant_credible_sets (Type: OpenTarget)

Get GWAS credible sets (fine-mapped loci) associated with a genetic variant from Open Targets. Re…

OpenTargets_get_variant_credible_sets tool specification

Tool Information:

• Name: OpenTargets_get_variant_credible_sets

• Type: OpenTarget

• Description: Get GWAS credible sets (fine-mapped loci) associated with a genetic variant from Open Targets. Returns studies where this variant appears in a fine-mapped credible set, with locus-to-gene (L2G) predictions, p-values, effect sizes, and the fine-mapping method used. Essential for understanding which GWAS signals a variant is part of and which genes it likely affects.

Parameters:

• variantId (string) (required) Open Targets variant ID in format chr_position_ref_alt (e.g., ‘10_112998590_C_T’ for rs7903146)

• size (integer) (optional) Number of credible sets to return (default 10)

Example Usage:

query = {
    "name": "OpenTargets_get_variant_credible_sets",
    "arguments": {
        "variantId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_variant_effect_predictions (Type: OpenTarget)

Retrieve in-silico functional effect predictions for a variant (chrom_pos_ref_alt) from OpenTarge…

OpenTargets_get_variant_effect_predictions tool specification

Tool Information:

• Name: OpenTargets_get_variant_effect_predictions

• Type: OpenTarget

• Description: Retrieve in-silico functional effect predictions for a variant (chrom_pos_ref_alt) from OpenTargets. Returns one record per prediction method (VEP, SIFT, PolyPhen, AlphaMissense, FoldX, GERP, CADD, etc.), each with an assessment (e.g. ‘missense_variant’, ‘deleterious’, ‘tolerated’) and a numeric score. Use to judge whether a variant is likely damaging.

Parameters:

• variantId (string) (required) Variant ID in chrom_pos_ref_alt format (e.g., ‘19_44908822_C_T’ for the APOE rs7412 variant).

Example Usage:

query = {
    "name": "OpenTargets_get_variant_effect_predictions",
    "arguments": {
        "variantId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_variant_info (Type: OpenTarget)

Get detailed information about a genetic variant from Open Targets Platform, including genomic co…

OpenTargets_get_variant_info tool specification

Tool Information:

• Name: OpenTargets_get_variant_info

• Type: OpenTarget

• Description: Get detailed information about a genetic variant from Open Targets Platform, including genomic coordinates, rsIDs, allele frequencies across populations (gnomAD), functional consequence, transcript consequences, and HGVS notation. Useful for GWAS variant annotation and population genetics.

Parameters:

• variantId (string) (required) Open Targets variant ID in format chr_position_ref_alt (e.g., ‘10_112998590_C_T’ for rs7903146, ‘19_44908684_T_C’ for rs429358). Use the search tool to find variant IDs from rsIDs.

Example Usage:

query = {
    "name": "OpenTargets_get_variant_info",
    "arguments": {
        "variantId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_variant_pharmacogenomics (Type: OpenTarget)

Retrieve variant-level pharmacogenomics (PGx) annotations for a variant (chrom_pos_ref_alt) from …

OpenTargets_get_variant_pharmacogenomics tool specification

Tool Information:

• Name: OpenTargets_get_variant_pharmacogenomics

• Type: OpenTarget

• Description: Retrieve variant-level pharmacogenomics (PGx) annotations for a variant (chrom_pos_ref_alt) from OpenTargets (PharmGKB-derived). Returns one record per PGx association with the drug(s), phenotypeText (clinical effect), evidenceLevel (PharmGKB 1A-4), genotypeAnnotationText, phenotype/PGx category, and source. Use to find drug-response associations for a variant.

Parameters:

• variantId (string) (required) Variant ID in chrom_pos_ref_alt format (e.g., ‘19_44908822_C_T’ for the APOE rs7412 variant).

Example Usage:

query = {
    "name": "OpenTargets_get_variant_pharmacogenomics",
    "arguments": {
        "variantId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_get_variant_transcript_consequences (Type: OpenTarget)

Retrieve per-transcript consequences for a variant (chrom_pos_ref_alt) from OpenTargets. Returns …

OpenTargets_get_variant_transcript_consequences tool specification

Tool Information:

• Name: OpenTargets_get_variant_transcript_consequences

• Type: OpenTarget

• Description: Retrieve per-transcript consequences for a variant (chrom_pos_ref_alt) from OpenTargets. Returns one record per affected transcript with transcriptId, the target gene, aminoAcidChange (when coding), consequenceScore, impact (HIGH/MODERATE/LOW/MODIFIER), and whether it is the canonical/distance transcript. Use to see how a variant affects each transcript/isoform.

Parameters:

• variantId (string) (required) Variant ID in chrom_pos_ref_alt format (e.g., ‘19_44908822_C_T’ for the APOE rs7412 variant).

Example Usage:

query = {
    "name": "OpenTargets_get_variant_transcript_consequences",
    "arguments": {
        "variantId": "example_value"
    }
}
result = tu.run(query)

OpenTargets_search_gwas_studies_by_disease (Type: OpenTarget)

Search for GWAS studies associated with a disease or trait in Open Targets. Takes disease ontolog…

OpenTargets_search_gwas_studies_by_disease tool specification

Tool Information:

• Name: OpenTargets_search_gwas_studies_by_disease

• Type: OpenTarget

• Description: Search for GWAS studies associated with a disease or trait in Open Targets. Takes disease ontology IDs (EFO, MONDO) and returns matching GWAS studies with their metadata including sample sizes, traits, publications, and associated diseases. Use enableIndirect=true to include child disease terms.

Parameters:

• diseaseIds (array) (optional) Disease ontology IDs (e.g., [‘MONDO_0005148’] for type 2 diabetes, [‘MONDO_0004975’] for Alzheimer disease)

• enableIndirect (boolean) (optional) Include studies for child disease terms (default true)

• disease_name (string) (optional) Disease or trait name for auto-resolution (e.g., ‘type 2 diabetes’). Resolved to diseaseIds automatically.

• disease (string) (optional) Alias for disease_name.

• trait (string) (optional) Alias for disease_name.

Example Usage:

query = {
    "name": "OpenTargets_search_gwas_studies_by_disease",
    "arguments": {
    }
}
result = tu.run(query)

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