Forge Tools flybase_gene

flybase_gene read

scidex.forge.flybase_gene

Query FlyBase for Drosophila melanogaster gene data including mutant phenotypes and human disease models. For each gene symbol, returns the FlyBase gene ID (FBgn), Drosophila symbol, full name, human ortholog, chromosome, mutant phenotype descriptions from curated allele records (top 10), and human disease models with DOID, evidence codes, and FlyBase URLs. Human gene symbols (e.g. TP53) are automatically resolved to their Drosophila ortholog (Dp53) via FlyBase orthology 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_mgi_mouse_gene (mouse) and forge_monarch_initiative (cross-species). Particularly useful for neurodegeneration, developmental signalling, and aging research. API: flybase.org/api/v1 — public, no auth required.

HTTP: POST /api/scidex/forge/flybase_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.flybase_gene``.",
  "properties": {
    "gene_symbols": {
      "description": "Drosophila gene symbols to look up (e.g. ['Dp53', 'wg', 'Parkin']). Human gene symbols (all-uppercase, e.g. 'TP53') are auto-resolved to their Drosophila ortholog via FlyBase 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 mutant phenotype descriptions. Set False to reduce response size.",
      "title": "Include Phenotypes",
      "type": "boolean"
    },
    "include_human_diseases": {
      "default": true,
      "description": "If True (default), include human disease models from FlyBase. Set False to reduce response size.",
      "title": "Include Human Diseases",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeFlyBaseGeneIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "FlyBaseDiseaseModel": {
      "description": "One human disease model entry from FlyBase.",
      "properties": {
        "doid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Disease Ontology ID (e.g. 'DOID:10652').",
          "title": "Doid"
        },
        "disease_name": {
          "description": "Human-readable disease name.",
          "title": "Disease Name",
          "type": "string"
        },
        "evidence_codes": {
          "description": "Evidence codes supporting this model (e.g. ['IMP', 'TAS']).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Codes",
          "type": "array"
        },
        "flybase_url": {
          "default": "",
          "description": "FlyBase report URL for this disease model record.",
          "title": "Flybase Url",
          "type": "string"
        }
      },
      "required": [
        "disease_name"
      ],
      "title": "FlyBaseDiseaseModel",
      "type": "object"
    },
    "FlyBaseGeneResult": {
      "description": "One gene record from FlyBase.",
      "properties": {
        "fbgn_id": {
          "description": "FlyBase gene ID (e.g. 'FBgn0039044').",
          "title": "Fbgn Id",
          "type": "string"
        },
        "fly_symbol": {
          "description": "Drosophila gene symbol (e.g. 'Dp53').",
          "title": "Fly Symbol",
          "type": "string"
        },
        "full_name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Full gene name.",
          "title": "Full Name"
        },
        "human_ortholog": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Human ortholog gene symbol (e.g. 'TP53'), if known.",
          "title": "Human Ortholog"
        },
        "chromosome": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Chromosome arm (e.g. '2L', '3R', 'X').",
          "title": "Chromosome"
        },
        "phenotype_descriptions": {
          "description": "Top 10 mutant phenotype descriptions from FlyBase allele records.",
          "items": {
            "type": "string"
          },
          "title": "Phenotype Descriptions",
          "type": "array"
        },
        "human_disease_models": {
          "description": "Human disease models curated in FlyBase.",
          "items": {
            "$ref": "#/$defs/FlyBaseDiseaseModel"
          },
          "title": "Human Disease Models",
          "type": "array"
        }
      },
      "required": [
        "fbgn_id",
        "fly_symbol"
      ],
      "title": "FlyBaseGeneResult",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.flybase_gene``.",
  "properties": {
    "genes": {
      "description": "Gene records for found symbols (one per resolved input symbol).",
      "items": {
        "$ref": "#/$defs/FlyBaseGeneResult"
      },
      "title": "Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Input symbols that could not be resolved in FlyBase.",
      "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": "ForgeFlyBaseGeneOut",
  "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/flybase_gene' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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