Forge Tools sgd_yeast

sgd_yeast read

scidex.forge.sgd_yeast

Query SGD (Saccharomyces Genome Database) for S. cerevisiae gene data including deletion/overexpression phenotypes, GO annotations, and human ortholog mapping. For each gene symbol, returns the SGD accession ID, systematic name (e.g. YJL145W), standard name (e.g. TOR1), gene description, human ortholog symbol, chromosomal location, phenotype records (experiment_type, mutant_type, phenotype_term, qualifier), and GO annotation records (go_id, go_term, go_aspect, evidence_code). Systematic names (YJL145W) and aliases are also accepted as input. Up to 10 symbols per call; up to 5 concurrent gene lookups. Not-found symbols go to the not_found list — not an exception. Yeast is the primary model for cell cycle (CDC28), DNA repair (RAD52), autophagy (ATG1), and aging/TOR signaling (TOR1). API: www.yeastgenome.org/webservice — public, no auth required.

HTTP: POST /api/scidex/forge/sgd_yeast

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.sgd_yeast``.",
  "properties": {
    "gene_symbols": {
      "description": "Yeast gene symbols to look up (e.g. ['TOR1', 'RAD52', 'ATG1']). Human gene symbols (all-uppercase, e.g. 'MTOR') are auto-resolved to their yeast ortholog via SGD. Systematic names (e.g. 'YJL145W') are also accepted. 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 phenotype records from SGD experiments. Set False to reduce response size.",
      "title": "Include Phenotypes",
      "type": "boolean"
    },
    "include_go_annotations": {
      "default": true,
      "description": "If True (default), include GO annotation records. Set False to reduce response size.",
      "title": "Include Go Annotations",
      "type": "boolean"
    },
    "go_aspects": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Filter GO annotations to specific aspects. Valid values: 'F' (molecular function), 'P' (biological process), 'C' (cellular component). None means include all aspects.",
      "title": "Go Aspects"
    }
  },
  "required": [
    "gene_symbols"
  ],
  "title": "ForgeSGDYeastIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "SGDGOAnnotation": {
      "description": "One Gene Ontology annotation record from SGD.",
      "properties": {
        "go_id": {
          "description": "GO term ID (e.g. 'GO:0004672').",
          "title": "Go Id",
          "type": "string"
        },
        "go_term": {
          "description": "GO term name (e.g. 'protein kinase activity').",
          "title": "Go Term",
          "type": "string"
        },
        "go_aspect": {
          "description": "GO aspect: 'F' (molecular function), 'P' (biological process), 'C' (cellular component).",
          "title": "Go Aspect",
          "type": "string"
        },
        "evidence_code": {
          "description": "Evidence code (e.g. 'IDA', 'IMP', 'IEA').",
          "title": "Evidence Code",
          "type": "string"
        }
      },
      "required": [
        "go_id",
        "go_term",
        "go_aspect",
        "evidence_code"
      ],
      "title": "SGDGOAnnotation",
      "type": "object"
    },
    "SGDPhenotype": {
      "description": "One phenotype record from SGD for a yeast gene.",
      "properties": {
        "experiment_type": {
          "description": "Experiment type (e.g. 'classical genetics').",
          "title": "Experiment Type",
          "type": "string"
        },
        "mutant_type": {
          "description": "Mutant type (e.g. 'null mutation', 'overexpression').",
          "title": "Mutant Type",
          "type": "string"
        },
        "phenotype_term": {
          "description": "Phenotype display name (e.g. 'rapamycin resistant').",
          "title": "Phenotype Term",
          "type": "string"
        },
        "qualifier": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Qualifier, if any (e.g. 'enhanced', 'requires', 'decreased').",
          "title": "Qualifier"
        }
      },
      "required": [
        "experiment_type",
        "mutant_type",
        "phenotype_term"
      ],
      "title": "SGDPhenotype",
      "type": "object"
    },
    "SGDYeastGeneResult": {
      "description": "One gene record from SGD for S. cerevisiae.",
      "properties": {
        "sgd_id": {
          "description": "SGD accession ID (e.g. 'S000006046').",
          "title": "Sgd Id",
          "type": "string"
        },
        "systematic_name": {
          "description": "Systematic name (e.g. 'YJL145W').",
          "title": "Systematic Name",
          "type": "string"
        },
        "standard_name": {
          "default": "",
          "description": "Standard gene name (e.g. 'TOR1').",
          "title": "Standard Name",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "Gene description/function summary.",
          "title": "Description",
          "type": "string"
        },
        "human_ortholog": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Human ortholog gene symbol (e.g. 'MTOR' for TOR1), if known.",
          "title": "Human Ortholog"
        },
        "chromosome": {
          "default": "",
          "description": "Chromosome (e.g. 'X', 'IV').",
          "title": "Chromosome",
          "type": "string"
        },
        "phenotypes": {
          "description": "Phenotype records from SGD experiments.",
          "items": {
            "$ref": "#/$defs/SGDPhenotype"
          },
          "title": "Phenotypes",
          "type": "array"
        },
        "go_annotations": {
          "description": "GO annotation records from SGD.",
          "items": {
            "$ref": "#/$defs/SGDGOAnnotation"
          },
          "title": "Go Annotations",
          "type": "array"
        }
      },
      "required": [
        "sgd_id",
        "systematic_name"
      ],
      "title": "SGDYeastGeneResult",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.sgd_yeast``.",
  "properties": {
    "genes": {
      "description": "Gene records for found symbols (one per resolved input symbol).",
      "items": {
        "$ref": "#/$defs/SGDYeastGeneResult"
      },
      "title": "Genes",
      "type": "array"
    },
    "not_found": {
      "description": "Input symbols that could not be resolved in SGD.",
      "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": "ForgeSGDYeastOut",
  "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/sgd_yeast' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbols": []
}'

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