Forge Tools wormbase_gene

wormbase_gene read

scidex.forge.wormbase_gene

Query WormBase (wormbase.org) for C. elegans gene data including RNAi/mutant phenotypes and human disease associations. For each gene symbol, returns the WBGene accession ID, worm symbol, sequence name, human ortholog, description, WormBase Phenotype Ontology (WBPhenotype) terms from RNAi/mutant experiments (wbbt_id, term, allele_type), and human disease associations with evidence codes. Human gene symbols (all-uppercase without hyphens, e.g. INSR) are automatically resolved to their C. elegans ortholog (daf-2) via WormBase search. Up to 10 symbols per call; up to 5 concurrent gene lookups. Not-found symbols go to the not_found list — not an exception. C. elegans is the canonical model for neuronal wiring, aging (daf-2/IGF-1), RNAi mechanisms, and apoptosis. API: wormbase.org/rest — public, no auth required.

HTTP: POST /api/scidex/forge/wormbase_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.wormbase_gene``.",
  "properties": {
    "gene_symbols": {
      "description": "C. elegans gene symbols to look up (e.g. ['daf-2', 'unc-22']). Human gene symbols (all-uppercase without hyphens, e.g. 'INSR') are auto-resolved to their C. elegans ortholog via WormBase ortholog 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 WormBase Phenotype Ontology terms from RNAi/mutant 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 WormBase. Set False to reduce response size.",
      "title": "Include Human Diseases",
      "type": "boolean"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeWormBaseGeneIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "WormBaseDiseaseAssoc": {
      "description": "One human disease association for a C. elegans gene.",
      "properties": {
        "omim_id": {
          "description": "Disease ontology ID (e.g. 'OMIM:222100', 'DOID:9352').",
          "title": "Omim Id",
          "type": "string"
        },
        "disease_name": {
          "description": "Human disease name.",
          "title": "Disease Name",
          "type": "string"
        },
        "evidence_codes": {
          "description": "Evidence codes supporting the association (e.g. ['IEA', 'IMP']).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Codes",
          "type": "array"
        }
      },
      "required": [
        "omim_id",
        "disease_name"
      ],
      "title": "WormBaseDiseaseAssoc",
      "type": "object"
    },
    "WormBaseGeneResult": {
      "description": "One gene record from WormBase.",
      "properties": {
        "wbgene_id": {
          "description": "WormBase Gene ID (e.g. 'WBGene00000898').",
          "title": "Wbgene Id",
          "type": "string"
        },
        "worm_symbol": {
          "description": "C. elegans gene symbol (e.g. 'daf-2').",
          "title": "Worm Symbol",
          "type": "string"
        },
        "sequence_name": {
          "default": "",
          "description": "Sequence name or cosmid locus.",
          "title": "Sequence Name",
          "type": "string"
        },
        "human_ortholog": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Human gene symbol ortholog (e.g. 'INSR'), if known.",
          "title": "Human Ortholog"
        },
        "description": {
          "default": "",
          "description": "Concise gene description from WormBase.",
          "title": "Description",
          "type": "string"
        },
        "phenotype_terms": {
          "description": "WormBase Phenotype Ontology terms from RNAi/mutant experiments.",
          "items": {
            "$ref": "#/$defs/WormBasePhenotype"
          },
          "title": "Phenotype Terms",
          "type": "array"
        },
        "human_disease_associations": {
          "description": "Human disease associations curated by WormBase.",
          "items": {
            "$ref": "#/$defs/WormBaseDiseaseAssoc"
          },
          "title": "Human Disease Associations",
          "type": "array"
        }
      },
      "required": [
        "wbgene_id",
        "worm_symbol"
      ],
      "title": "WormBaseGeneResult",
      "type": "object"
    },
    "WormBasePhenotype": {
      "description": "One phenotype term from a WormBase RNAi or mutant allele experiment.",
      "properties": {
        "wbbt_id": {
          "description": "WormBase Phenotype Ontology ID (e.g. 'WBPhenotype:0000589').",
          "title": "Wbbt Id",
          "type": "string"
        },
        "term": {
          "description": "Phenotype term name (e.g. 'dauer formation constitutive').",
          "title": "Term",
          "type": "string"
        },
        "allele_type": {
          "default": "",
          "description": "Allele or evidence class (e.g. 'e1370', 'RNAi').",
          "title": "Allele Type",
          "type": "string"
        }
      },
      "required": [
        "wbbt_id",
        "term"
      ],
      "title": "WormBasePhenotype",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.wormbase_gene``.",
  "properties": {
    "genes": {
      "description": "Gene records for found symbols (one per resolved input symbol).",
      "items": {
        "$ref": "#/$defs/WormBaseGeneResult"
      },
      "title": "Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Input symbols that could not be resolved in WormBase.",
      "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": "ForgeWormBaseGeneOut",
  "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/wormbase_gene' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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