Forge Tools zfin_gene

zfin_gene read

scidex.forge.zfin_gene

Query the Alliance Genome Resource (ZFIN) for Danio rerio gene data including mutant phenotypes, anatomical expression sites, and human disease associations. For each gene symbol, returns the ZFIN accession ID, zebrafish symbol, full name, human ortholog, chromosome, mutant phenotype annotations (phenotype_term, condition, allele, zygosity), anatomical expression sites with developmental stage, and human disease associations with DOID, evidence codes, and association type. Human gene symbols (e.g. TP53) are automatically resolved to their zebrafish ortholog (tp53) via Alliance 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. Zebrafish is the canonical model for cardiac development, embryogenesis, brain patterning, drug metabolism (CYP enzymes), and tumor biology. Complements forge_mgi_mouse_gene (mouse), forge_flybase_gene (fly), and forge_wormbase_gene (worm) as the vertebrate tier in the model organism suite. API: alliancegenome.org/api — public, no auth required.

HTTP: POST /api/scidex/forge/zfin_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.zfin_gene``.",
  "properties": {
    "gene_symbols": {
      "description": "Zebrafish gene symbols to look up (e.g. ['tp53', 'sox2', 'myod1']). Human gene symbols (all-uppercase, e.g. 'TP53') are auto-resolved to their zebrafish ortholog via Alliance 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 annotations from ZFIN. Set False to reduce response size.",
      "title": "Include Phenotypes",
      "type": "boolean"
    },
    "include_anatomy": {
      "default": true,
      "description": "If True (default), include anatomical expression sites with developmental stage. Set False to reduce response size.",
      "title": "Include Anatomy",
      "type": "boolean"
    },
    "include_human_diseases": {
      "default": true,
      "description": "If True (default), include human disease associations from ZFIN. Set False to reduce response size.",
      "title": "Include Human Diseases",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeZFINGeneIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ZFINAnatomyExpression": {
      "description": "One anatomical expression site for a zebrafish gene.",
      "properties": {
        "anatomy_term": {
          "description": "Anatomical structure name (e.g. 'brain', 'heart', 'somite').",
          "title": "Anatomy Term",
          "type": "string"
        },
        "stage": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Developmental stage name (e.g. 'Pharyngula', 'Segmentation').",
          "title": "Stage"
        }
      },
      "required": [
        "anatomy_term"
      ],
      "title": "ZFINAnatomyExpression",
      "type": "object"
    },
    "ZFINDiseaseAssociation": {
      "description": "One human disease association for a zebrafish gene from ZFIN curation.",
      "properties": {
        "disease_name": {
          "description": "Human-readable disease name.",
          "title": "Disease Name",
          "type": "string"
        },
        "doid": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Disease Ontology ID (e.g. 'DOID:3012').",
          "title": "Doid"
        },
        "evidence_codes": {
          "description": "Evidence codes supporting the association (e.g. ['IMP', 'TAS']).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Codes",
          "type": "array"
        },
        "association_type": {
          "default": "",
          "description": "Association type (e.g. 'is_model_of', 'is_implicated_in').",
          "title": "Association Type",
          "type": "string"
        }
      },
      "required": [
        "disease_name"
      ],
      "title": "ZFINDiseaseAssociation",
      "type": "object"
    },
    "ZFINGeneResult": {
      "description": "One gene record from ZFIN / Alliance Genome Resource.",
      "properties": {
        "zfin_id": {
          "description": "ZFIN accession ID (e.g. 'ZFIN:ZDB-GENE-040426-1711').",
          "title": "Zfin Id",
          "type": "string"
        },
        "zebrafish_symbol": {
          "description": "Zebrafish gene symbol (e.g. 'tp53').",
          "title": "Zebrafish Symbol",
          "type": "string"
        },
        "full_name": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Full gene name/description.",
          "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 (e.g. '5', 'X').",
          "title": "Chromosome"
        },
        "description": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Gene description from ZFIN / Alliance.",
          "title": "Description"
        },
        "phenotypes": {
          "description": "Mutant phenotype annotations from ZFIN allele experiments.",
          "items": {
            "$ref": "#/$defs/ZFINPhenotype"
          },
          "title": "Phenotypes",
          "type": "array"
        },
        "anatomy_expression": {
          "description": "Anatomical expression sites with developmental stage.",
          "items": {
            "$ref": "#/$defs/ZFINAnatomyExpression"
          },
          "title": "Anatomy Expression",
          "type": "array"
        },
        "human_disease_associations": {
          "description": "Human disease associations curated by ZFIN.",
          "items": {
            "$ref": "#/$defs/ZFINDiseaseAssociation"
          },
          "title": "Human Disease Associations",
          "type": "array"
        }
      },
      "required": [
        "zfin_id",
        "zebrafish_symbol"
      ],
      "title": "ZFINGeneResult",
      "type": "object"
    },
    "ZFINPhenotype": {
      "description": "One phenotype annotation from a ZFIN mutant or morphant experiment.",
      "properties": {
        "phenotype_term": {
          "description": "Phenotype statement (e.g. 'body axis, curved').",
          "title": "Phenotype Term",
          "type": "string"
        },
        "condition": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Experimental condition (e.g. 'standard conditions').",
          "title": "Condition"
        },
        "allele": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Allele or morpholino used (e.g. 'tp53^zdf1').",
          "title": "Allele"
        },
        "zygosity": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Genotype zygosity (e.g. 'homozygous', 'heterozygous').",
          "title": "Zygosity"
        }
      },
      "required": [
        "phenotype_term"
      ],
      "title": "ZFINPhenotype",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.zfin_gene``.",
  "properties": {
    "genes": {
      "description": "Gene records for found symbols (one per resolved input symbol).",
      "items": {
        "$ref": "#/$defs/ZFINGeneResult"
      },
      "title": "Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Input symbols that could not be resolved via Alliance/ZFIN.",
      "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": "ForgeZFINGeneOut",
  "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/zfin_gene' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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