Forge Tools impc_phenotypes

impc_phenotypes read

scidex.forge.impc_phenotypes

Query the International Mouse Phenotyping Consortium (IMPC) for systematic mouse knockout phenotype data. IMPC has phenotyped 10,000+ gene knockouts using standardised protocols — the most comprehensive source of mammalian gene function data. Returns statistically significant phenotype calls with p-values, effect sizes, zygosity, sex, and IMPC procedure names. Detects lethal/viability phenotypes via the 'lethal' flag. Complements scidex.forge.mgi_mouse_gene (MGI curated data) with systematic screen evidence. API: ebi.ac.uk/mi/impc/solr — public, no auth required.

HTTP: POST /api/scidex/forge/impc_phenotypes

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.impc_phenotypes``.",
  "properties": {
    "gene": {
      "description": "Query value interpreted according to ``query_type``. Default: mouse gene symbol (e.g. 'Trp53').",
      "maxLength": 100,
      "title": "Gene",
      "type": "string"
    },
    "query_type": {
      "default": "gene_symbol",
      "description": "How to interpret ``gene``. ``'gene_symbol'`` — search by marker_symbol; ``'allele_symbol'`` — search by allele_symbol; ``'mp_term_id'`` — search by mp_term_id (e.g. 'MP:0001265'). Default: ``'gene_symbol'``.",
      "title": "Query Type",
      "type": "string"
    },
    "significance_threshold": {
      "default": 0.05,
      "description": "Maximum p-value for a phenotype call to be included. Hits with p_value > threshold are excluded. Default: 0.05.",
      "maximum": 1,
      "minimum": 0,
      "title": "Significance Threshold",
      "type": "number"
    },
    "limit": {
      "default": 30,
      "description": "Maximum number of phenotype hits to return from IMPC.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeImpcPhenotypesIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ImpcPhenotypeHit": {
      "description": "One statistically significant IMPC phenotype call.",
      "properties": {
        "gene_symbol": {
          "description": "Mouse gene symbol (e.g. 'Trp53').",
          "title": "Gene Symbol",
          "type": "string"
        },
        "allele_symbol": {
          "default": "",
          "description": "Allele symbol from the knockout line (e.g. 'Trp53<tm1Tyj>').",
          "title": "Allele Symbol",
          "type": "string"
        },
        "phenotype_name": {
          "description": "MP phenotype term name.",
          "title": "Phenotype Name",
          "type": "string"
        },
        "mp_term_id": {
          "description": "MP ontology term ID (e.g. 'MP:0001265').",
          "title": "Mp Term Id",
          "type": "string"
        },
        "top_level_phenotype": {
          "default": "",
          "description": "Top-level phenotype category (e.g. 'behavior/neurological phenotype').",
          "title": "Top Level Phenotype",
          "type": "string"
        },
        "p_value": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Statistical p-value for the phenotype call.",
          "title": "P Value"
        },
        "effect_size": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Effect size from the IMPC statistical pipeline.",
          "title": "Effect Size"
        },
        "zygosity": {
          "default": "",
          "description": "Zygosity of the knockout: 'homozygote', 'heterozygote', or 'hemizygote'.",
          "title": "Zygosity",
          "type": "string"
        },
        "sex": {
          "default": "not_considered",
          "description": "Sex of the animals: 'male', 'female', or 'not_considered'.",
          "title": "Sex",
          "type": "string"
        },
        "procedure_name": {
          "default": "",
          "description": "IMPC standardised procedure name (e.g. 'Combined SHIRPA and Dysmorphology').",
          "title": "Procedure Name",
          "type": "string"
        }
      },
      "required": [
        "gene_symbol",
        "phenotype_name",
        "mp_term_id"
      ],
      "title": "ImpcPhenotypeHit",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.impc_phenotypes``.",
  "properties": {
    "query": {
      "description": "The input query value, echoed back.",
      "title": "Query",
      "type": "string"
    },
    "query_type": {
      "description": "The input query type, echoed back.",
      "title": "Query Type",
      "type": "string"
    },
    "gene_symbol": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Mouse gene symbol resolved from the query, when available.",
      "title": "Gene Symbol"
    },
    "phenotype_hits": {
      "description": "Statistically significant phenotype calls passing the significance threshold. Sorted by p_value ascending (most significant first).",
      "items": {
        "$ref": "#/$defs/ImpcPhenotypeHit"
      },
      "title": "Phenotype Hits",
      "type": "array"
    },
    "lethal": {
      "default": false,
      "description": "True when ≥1 phenotype hit indicates a viability or lethality phenotype (MP term or top-level phenotype name contains lethal/viability keywords, or MP term ID matches known viability term prefixes).",
      "title": "Lethal",
      "type": "boolean"
    },
    "not_found": {
      "default": false,
      "description": "True when IMPC returned no records for the query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query",
    "query_type"
  ],
  "title": "ForgeImpcPhenotypesOut",
  "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/impc_phenotypes' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.