Forge Tools alliance_genome

alliance_genome read

scidex.forge.alliance_genome

Query the Alliance of Genome Resources for unified cross-species gene data aggregated from HGNC, MGI, ZFIN, FlyBase, WormBase, SGD, and RGD. Given an Alliance gene ID (e.g. HGNC:11998, MGI:97490, ZFIN:ZDB-GENE-990415-8, FB:FBgn0003721, WB:WBGene00000912), returns: gene summary (symbol, name, species, taxon, chromosome, automated synopsis), phenotype annotations (HP/MP/FBbt/WBPhenotype terms), disease associations (Disease Ontology terms with evidence codes), and expression summary (anatomical structures). No authentication required. REST API: https://www.alliancegenome.org/api

HTTP: POST /api/scidex/forge/alliance_genome

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.alliance_genome``.",
  "properties": {
    "gene_id": {
      "description": "Alliance gene ID in curated format, e.g. ``HGNC:11998`` (TP53 human), ``MGI:97490`` (Trp53 mouse), ``ZFIN:ZDB-GENE-990415-8`` (zebrafish tp53), ``FB:FBgn0003721`` (fly p53), ``WB:WBGene00000912`` (worm cep-1), ``SGD:S000001855`` (yeast MEC1), ``RGD:2018`` (rat Trp53).",
      "maxLength": 100,
      "minLength": 3,
      "title": "Gene Id",
      "type": "string"
    },
    "include_phenotypes": {
      "default": true,
      "description": "When True (default), fetch phenotype annotations and include them in ``phenotypes``. Set to False to skip the phenotypes API call.",
      "title": "Include Phenotypes",
      "type": "boolean"
    },
    "include_diseases": {
      "default": true,
      "description": "When True (default), fetch disease associations (DO terms) and include them in ``diseases``. Set to False to skip the diseases API call.",
      "title": "Include Diseases",
      "type": "boolean"
    },
    "include_expression": {
      "default": true,
      "description": "When True (default), fetch expression summary and include it in ``expression``. Set to False to skip the expression API call.",
      "title": "Include Expression",
      "type": "boolean"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of phenotype and disease records to return (each). Expression results are not paginated. Default 50.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_id"
  ],
  "title": "ForgeAllianceGenomeIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "DiseaseAssociation": {
      "description": "One disease association for a gene (Disease Ontology term).",
      "properties": {
        "disease_id": {
          "description": "Disease Ontology ID (e.g. 'DOID:9119').",
          "title": "Disease Id",
          "type": "string"
        },
        "disease_name": {
          "description": "Disease name from the Disease Ontology (e.g. 'acute myeloid leukemia').",
          "title": "Disease Name",
          "type": "string"
        },
        "association_type": {
          "default": "",
          "description": "Type of association, e.g. 'is_implicated_in', 'is_marker_for', 'biomarker_of'.",
          "title": "Association Type",
          "type": "string"
        },
        "evidence_codes": {
          "description": "Evidence codes supporting this association (e.g. ['IMP', 'IEA']).",
          "items": {
            "type": "string"
          },
          "title": "Evidence Codes",
          "type": "array"
        },
        "source_db": {
          "default": "",
          "description": "Curating database that contributed this annotation.",
          "title": "Source Db",
          "type": "string"
        }
      },
      "required": [
        "disease_id",
        "disease_name"
      ],
      "title": "DiseaseAssociation",
      "type": "object"
    },
    "ExpressionTissue": {
      "description": "One anatomical structure where the gene is expressed.",
      "properties": {
        "structure": {
          "description": "Anatomical structure or cell type name.",
          "title": "Structure",
          "type": "string"
        },
        "ontology_id": {
          "default": "",
          "description": "Ontology term ID for the structure (e.g. 'UBERON:0000955').",
          "title": "Ontology Id",
          "type": "string"
        },
        "qualifier": {
          "default": "",
          "description": "Qualifier, e.g. 'expressed', 'not expressed', 'enriched'.",
          "title": "Qualifier",
          "type": "string"
        }
      },
      "required": [
        "structure"
      ],
      "title": "ExpressionTissue",
      "type": "object"
    },
    "PhenotypeAnnotation": {
      "description": "One phenotype annotation for a gene from the Alliance.",
      "properties": {
        "phenotype_id": {
          "default": "",
          "description": "Ontology term ID for the phenotype (e.g. 'HP:0001234', 'MP:0010234').",
          "title": "Phenotype Id",
          "type": "string"
        },
        "phenotype_statement": {
          "description": "Human-readable phenotype statement.",
          "title": "Phenotype Statement",
          "type": "string"
        },
        "source_db": {
          "default": "",
          "description": "Curating database that contributed this annotation (e.g. 'MGI', 'ZFIN').",
          "title": "Source Db",
          "type": "string"
        }
      },
      "required": [
        "phenotype_statement"
      ],
      "title": "PhenotypeAnnotation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.alliance_genome``.",
  "properties": {
    "gene_id": {
      "description": "The queried Alliance gene ID.",
      "title": "Gene Id",
      "type": "string"
    },
    "symbol": {
      "default": "",
      "description": "Gene symbol (e.g. 'TP53', 'Trp53', 'tp53').",
      "title": "Symbol",
      "type": "string"
    },
    "name": {
      "default": "",
      "description": "Full gene name.",
      "title": "Name",
      "type": "string"
    },
    "species": {
      "default": "",
      "description": "Species common name (e.g. 'Homo sapiens', 'Mus musculus').",
      "title": "Species",
      "type": "string"
    },
    "taxon_id": {
      "default": "",
      "description": "NCBI Taxonomy ID prefixed with 'NCBITaxon:' (e.g. 'NCBITaxon:9606').",
      "title": "Taxon Id",
      "type": "string"
    },
    "chromosome": {
      "default": "",
      "description": "Chromosome where the gene is located.",
      "title": "Chromosome",
      "type": "string"
    },
    "summary": {
      "default": "",
      "description": "Automated gene synopsis from the Alliance.",
      "title": "Summary",
      "type": "string"
    },
    "source_db": {
      "default": "",
      "description": "Originating genome database for this gene record (e.g. 'HGNC', 'MGI', 'ZFIN', 'FlyBase', 'WormBase', 'SGD', 'RGD').",
      "title": "Source Db",
      "type": "string"
    },
    "phenotypes": {
      "description": "Phenotype annotations associated with this gene.",
      "items": {
        "$ref": "#/$defs/PhenotypeAnnotation"
      },
      "title": "Phenotypes",
      "type": "array"
    },
    "diseases": {
      "description": "Disease associations (DO terms) for this gene.",
      "items": {
        "$ref": "#/$defs/DiseaseAssociation"
      },
      "title": "Diseases",
      "type": "array"
    },
    "expression": {
      "description": "Anatomical structures where this gene is expressed.",
      "items": {
        "$ref": "#/$defs/ExpressionTissue"
      },
      "title": "Expression",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the Alliance API returned no gene record for this ID.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Alliance of Genome Resources",
      "description": "Data source: 'Alliance of Genome Resources'.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time in milliseconds for all upstream API calls combined.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_id"
  ],
  "title": "ForgeAllianceGenomeOut",
  "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/alliance_genome' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_id": ""
}'

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