Forge Tools mgi_mouse_gene

mgi_mouse_gene read

scidex.forge.mgi_mouse_gene

Query Mouse Genome Informatics (MGI) for mouse gene data including KO phenotypes and human disease associations. For each gene symbol, returns the MGI accession ID, mouse symbol, human ortholog, chromosomal location, Mammalian Phenotype (MP) terms from knockout allele experiments (mp_id, term, allele_type), and human disease associations with evidence codes. Human gene symbols (e.g. TP53) are automatically resolved to their mouse ortholog (Trp53) via MGI homology data. Up to 10 symbols per call; up to 5 concurrent gene lookups. Not-found symbols go to the not_found list — not an exception. Complements forge_monarch_initiative (cross-species) with MGI-specific experimental KO evidence. API: api.informatics.jax.org — public, no auth required.

HTTP: POST /api/scidex/forge/mgi_mouse_gene

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.mgi_mouse_gene``.",
  "properties": {
    "gene_symbols": {
      "description": "Mouse gene symbols to look up (e.g. ['Trp53', 'Brca2']). Human gene symbols (all-uppercase, e.g. 'TP53') are auto-resolved to their mouse ortholog via MGI orthology data. Maximum 10 symbols per call.",
      "items": {
        "type": "string"
      },
      "maxItems": 10,
      "minItems": 1,
      "title": "Gene Symbols",
      "type": "array"
    },
    "include_phenotypes": {
      "default": true,
      "description": "If True (default), include MP phenotype terms from KO allele experiments. Set False to reduce response size.",
      "title": "Include Phenotypes",
      "type": "boolean"
    },
    "include_human_diseases": {
      "default": true,
      "description": "If True (default), include human disease associations from MGI. Set False to reduce response size.",
      "title": "Include Human Diseases",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeMGIMouseGeneIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "MGIDiseaseAssoc": {
      "description": "One human disease association for a mouse gene.",
      "properties": {
        "disease_id": {
          "description": "Disease ID (e.g. 'OMIM:151623', 'DOID:162').",
          "title": "Disease Id",
          "type": "string"
        },
        "disease_name": {
          "description": "Human-readable disease name.",
          "title": "Disease Name",
          "type": "string"
        },
        "evidence_codes": {
          "description": "Evidence codes supporting the association (e.g. ['TAS', 'IMP']).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Codes",
          "type": "array"
        }
      },
      "required": [
        "disease_id",
        "disease_name"
      ],
      "title": "MGIDiseaseAssoc",
      "type": "object"
    },
    "MGIGeneResult": {
      "description": "One gene record from MGI.",
      "properties": {
        "mgi_id": {
          "description": "MGI accession ID (e.g. 'MGI:98834').",
          "title": "Mgi Id",
          "type": "string"
        },
        "mouse_symbol": {
          "description": "Mouse gene symbol (e.g. 'Trp53').",
          "title": "Mouse Symbol",
          "type": "string"
        },
        "name": {
          "default": "",
          "description": "Full gene name/description.",
          "title": "Name",
          "type": "string"
        },
        "human_ortholog": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Human gene symbol ortholog (e.g. 'TP53'), if known.",
          "title": "Human Ortholog"
        },
        "chromosome": {
          "default": "",
          "description": "Chromosome (e.g. '11', 'X').",
          "title": "Chromosome",
          "type": "string"
        },
        "strand": {
          "default": "",
          "description": "Genomic strand ('+' or '-').",
          "title": "Strand",
          "type": "string"
        },
        "phenotype_terms": {
          "description": "Mammalian Phenotype (MP) terms from KO allele experiments.",
          "items": {
            "$ref": "#/$defs/MGIPhenotypeTerm"
          },
          "title": "Phenotype Terms",
          "type": "array"
        },
        "human_disease_associations": {
          "description": "Human disease associations curated by MGI.",
          "items": {
            "$ref": "#/$defs/MGIDiseaseAssoc"
          },
          "title": "Human Disease Associations",
          "type": "array"
        }
      },
      "required": [
        "mgi_id",
        "mouse_symbol"
      ],
      "title": "MGIGeneResult",
      "type": "object"
    },
    "MGIPhenotypeTerm": {
      "description": "One Mammalian Phenotype (MP) term from a KO allele experiment.",
      "properties": {
        "mp_id": {
          "description": "MP ontology term ID (e.g. 'MP:0001265').",
          "title": "Mp Id",
          "type": "string"
        },
        "term": {
          "description": "MP term name (e.g. 'decreased body size').",
          "title": "Term",
          "type": "string"
        },
        "allele_type": {
          "default": "",
          "description": "Allele type or genotype class (e.g. 'null/null', 'heterozygous').",
          "title": "Allele Type",
          "type": "string"
        }
      },
      "required": [
        "mp_id",
        "term"
      ],
      "title": "MGIPhenotypeTerm",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.mgi_mouse_gene``.",
  "properties": {
    "genes": {
      "description": "Gene records for found symbols (one per resolved input symbol).",
      "items": {
        "$ref": "#/$defs/MGIGeneResult"
      },
      "title": "Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Input symbols that could not be resolved in MGI.",
      "items": {
        "type": "string"
      },
      "title": "Not Found",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for all upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeMGIMouseGeneOut",
  "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/mgi_mouse_gene' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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