Forge Tools eqtl_catalogue

eqtl_catalogue read

scidex.forge.eqtl_catalogue

Query the EBI eQTL Catalogue for expression QTL associations across >100 datasets beyond GTEx — including BLUEPRINT, DICE, Alasoo2018, Lepik2017, immune cells, iPSC-derived cells, and disease cohorts. Input: Ensembl gene ID (e.g. ENSG00000141510 for TP53) with optional variant_id, tissue ontology ID, dataset_id, pvalue_threshold (default 1e-5), and limit. Returns eQTL associations with variant, gene, tissue label, beta, SE, p-value, dataset, and study identifiers. Use alongside forge_gtex_eqtl for full eQTL coverage. REST API: https://www.ebi.ac.uk/eqtl/api/v2/ — free, no auth.

HTTP: POST /api/scidex/forge/eqtl_catalogue

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.eqtl_catalogue``.",
  "properties": {
    "gene_id": {
      "description": "Ensembl gene ID to query (e.g. ``ENSG00000141510`` for TP53). The EBI eQTL Catalogue accepts Ensembl IDs directly.",
      "maxLength": 30,
      "title": "Gene Id",
      "type": "string"
    },
    "variant_id": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional variant filter — rsID (e.g. ``rs429358``) or chr_pos_ref_alt (e.g. ``chr17_7571720_C_T``). When supplied, only associations for this variant are returned.",
      "title": "Variant Id"
    },
    "tissue": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional tissue / cell-type ontology ID to restrict results (e.g. ``UBERON:0000178``, ``CL:0000235``). Pass the ontology ID, not a free-text label.",
      "title": "Tissue"
    },
    "dataset_id": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional dataset ID to restrict results to a single study (e.g. ``GTEx_V8_Adipose_Subcutaneous``, ``Alasoo_2018_macrophage_IFNg``). Use ``scidex.forge.eqtl_catalogue`` with no dataset_id to search all.",
      "title": "Dataset Id"
    },
    "pvalue_threshold": {
      "default": 0.00001,
      "description": "Upper p-value threshold. Only associations with pvalue ≤ this value are returned. Default 1e-5 (genome-wide suggestive).",
      "exclusiveMinimum": 0,
      "maximum": 1,
      "title": "Pvalue Threshold",
      "type": "number"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of associations to return (default 20, max 1000).",
      "maximum": 1000,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_id"
  ],
  "title": "ForgeEQTLCatalogueIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "EQTLAssociation": {
      "description": "One eQTL association record from the EBI eQTL Catalogue.",
      "properties": {
        "variant_id": {
          "description": "Variant identifier (rsID or chr_pos_ref_alt).",
          "title": "Variant Id",
          "type": "string"
        },
        "gene_id": {
          "description": "Ensembl gene ID of the target gene.",
          "title": "Gene Id",
          "type": "string"
        },
        "gene_name": {
          "default": "",
          "description": "Gene name / HGNC symbol (when available).",
          "title": "Gene Name",
          "type": "string"
        },
        "beta": {
          "description": "Effect size per copy of the alternative allele.",
          "title": "Beta",
          "type": "number"
        },
        "se": {
          "description": "Standard error of the effect size estimate.",
          "title": "Se",
          "type": "number"
        },
        "pvalue": {
          "description": "Nominal p-value for the eQTL association.",
          "title": "Pvalue",
          "type": "number"
        },
        "tissue_label": {
          "default": "",
          "description": "Human-readable tissue/cell-type label.",
          "title": "Tissue Label",
          "type": "string"
        },
        "tissue_ontology_id": {
          "default": "",
          "description": "Tissue ontology ID (e.g. UBERON:0000178 or CL:0000235).",
          "title": "Tissue Ontology Id",
          "type": "string"
        },
        "dataset_id": {
          "description": "Dataset identifier in the eQTL Catalogue.",
          "title": "Dataset Id",
          "type": "string"
        },
        "study_id": {
          "default": "",
          "description": "Study identifier.",
          "title": "Study Id",
          "type": "string"
        },
        "an": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Allele number (sample size proxy).",
          "title": "An"
        },
        "ac": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Allele count.",
          "title": "Ac"
        }
      },
      "required": [
        "variant_id",
        "gene_id",
        "beta",
        "se",
        "pvalue",
        "dataset_id"
      ],
      "title": "EQTLAssociation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.eqtl_catalogue``.",
  "properties": {
    "gene_id": {
      "description": "The Ensembl gene ID that was queried.",
      "title": "Gene Id",
      "type": "string"
    },
    "results": {
      "description": "eQTL association records matching the query and filters.",
      "items": {
        "$ref": "#/$defs/EQTLAssociation"
      },
      "title": "Results",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Number of associations returned after filtering.",
      "title": "Total Found",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when no associations were found for the gene (gene unknown or no eQTLs).",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "EBI eQTL Catalogue v2",
      "description": "Data source: 'EBI eQTL Catalogue v2'.",
      "title": "Source",
      "type": "string"
    }
  },
  "required": [
    "gene_id"
  ],
  "title": "ForgeEQTLCatalogueOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/eqtl_catalogue' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_id": ""
}'

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