Forge Tools ot_genetics

ot_genetics read

scidex.forge.ot_genetics

Query Open Targets Genetics for variant-to-gene (V2G) fine-mapping, Bayesian credible sets, and Locus2Gene (L2G) scores. Distinct from scidex.forge.opentargets (disease-target platform) and scidex.forge.open_gwas (summary statistics). Three query modes: 'variant' (rsID/positional → ranked genes by V2G score), 'gene' (symbol/ENSG → GWAS loci where gene is top causal candidate by L2G), 'study' (GCST accession → top Manhattan loci with trait metadata). API: https://api.genetics.opentargets.org/graphql — free, no auth required.

HTTP: POST /api/scidex/forge/ot_genetics

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.ot_genetics``.",
  "properties": {
    "query": {
      "description": "Query string. Interpretation depends on ``query_type``:\n- ``'variant'``: rsID (``rs7412``) or positional id (``19_45411941_T_C``).\n- ``'gene'``: gene symbol (``PCSK9``) or Ensembl gene id (``ENSG00000169174``).\n- ``'study'``: GWAS study accession (``GCST90002369``).",
      "maxLength": 200,
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "default": "variant",
      "description": "How to interpret ``query``. One of ``'variant'`` (default), ``'gene'``, or ``'study'``.",
      "enum": [
        "variant",
        "gene",
        "study"
      ],
      "title": "Query Type",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of results to return (default 10, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeOTGeneticsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "OTGeneticsResult": {
      "description": "One V2G / L2G result row from Open Targets Genetics.",
      "properties": {
        "variant_id": {
          "description": "Variant identifier (rsID or chrPos_ref_alt).",
          "title": "Variant Id",
          "type": "string"
        },
        "gene_id": {
          "default": "",
          "description": "Ensembl gene id (e.g. ENSG00000130204).",
          "title": "Gene Id",
          "type": "string"
        },
        "gene_symbol": {
          "default": "",
          "description": "HGNC gene symbol (e.g. APOE).",
          "title": "Gene Symbol",
          "type": "string"
        },
        "v2g_score": {
          "default": 0,
          "description": "V2G or L2G score in [0, 1]. Higher means the gene is more likely causal for the variant/locus.",
          "title": "V2G Score",
          "type": "number"
        },
        "pip": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Posterior Inclusion Probability from Bayesian fine-mapping credible set. None when not available for this query type.",
          "title": "Pip"
        },
        "study_id": {
          "default": "",
          "description": "GWAS study accession (e.g. GCST90002369).",
          "title": "Study Id",
          "type": "string"
        },
        "trait_reported": {
          "default": "",
          "description": "Trait label as reported in the study.",
          "title": "Trait Reported",
          "type": "string"
        }
      },
      "required": [
        "variant_id"
      ],
      "title": "OTGeneticsResult",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.ot_genetics``.",
  "properties": {
    "results": {
      "description": "V2G / L2G result rows, ordered by score descending.",
      "items": {
        "$ref": "#/$defs/OTGeneticsResult"
      },
      "title": "Results",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "``True`` when the query returned no results from OT Genetics.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "title": "ForgeOTGeneticsOut",
  "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/ot_genetics' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.