ensembl_compara_homology read

{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.ensembl_compara_homology``.",
  "properties": {
    "species": {
      "default": "homo_sapiens",
      "description": "Source species Ensembl slug. Defaults to ``homo_sapiens``. Lowercase ``genus_species`` form.",
      "maxLength": 64,
      "title": "Species",
      "type": "string"
    },
    "gene_symbol": {
      "description": "Gene symbol to look up (e.g. ``BDNF``, ``BRCA1``). Case-insensitive; Ensembl normalises internally.",
      "maxLength": 30,
      "minLength": 1,
      "title": "Gene Symbol",
      "type": "string"
    },
    "homology_type": {
      "default": "all",
      "description": "Type of homology to return: ``orthologues`` (cross-species orthologs only), ``paralogues`` (within-species paralogs only), or ``all`` (both). Defaults to ``all``.",
      "enum": [
        "orthologues",
        "paralogues",
        "all"
      ],
      "title": "Homology Type",
      "type": "string"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "EnsemblComparaHomologyIn",
  "type": "object"
}

{
  "$defs": {
    "HomologyEntry": {
      "description": "One homology record returned by Ensembl Compara.",
      "properties": {
        "species": {
          "description": "Ensembl species slug of the homology target.",
          "title": "Species",
          "type": "string"
        },
        "gene_symbol": {
          "description": "Gene symbol of the homology target.",
          "title": "Gene Symbol",
          "type": "string"
        },
        "ensembl_gene_id": {
          "description": "Ensembl gene ID of the homology target.",
          "title": "Ensembl Gene Id",
          "type": "string"
        },
        "homology_type": {
          "description": "Ensembl homology type: ``ortholog_one2one``, ``ortholog_one2many``, ``ortholog_many2many``, ``within_species_paralog``, or ``other_paralog``.",
          "title": "Homology Type",
          "type": "string"
        },
        "method_link_type": {
          "default": "",
          "description": "Ensembl method link type (e.g. 'ENSEMBL_ORTHOLOGUES').",
          "title": "Method Link Type",
          "type": "string"
        }
      },
      "required": [
        "species",
        "gene_symbol",
        "ensembl_gene_id",
        "homology_type"
      ],
      "title": "HomologyEntry",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.ensembl_compara_homology``.",
  "properties": {
    "gene_symbol": {
      "description": "Echo of the queried gene symbol.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "species": {
      "description": "Echo of the queried source species.",
      "title": "Species",
      "type": "string"
    },
    "homologies": {
      "description": "Homology records returned by Ensembl. Empty when the gene has no homologs of the requested type, or when the gene is not found.",
      "items": {
        "$ref": "#/$defs/HomologyEntry"
      },
      "title": "Homologies",
      "type": "array"
    },
    "returned_homologies": {
      "default": 0,
      "description": "Length of ``homologies``.",
      "title": "Returned Homologies",
      "type": "integer"
    },
    "not_found": {
      "default": false,
      "description": "True when the gene symbol was not found in Ensembl (HTTP 404 or empty homology list).",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "Ensembl Compara",
      "description": "Data source: 'Ensembl Compara'.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time in milliseconds for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "species",
    "took_ms"
  ],
  "title": "EnsemblComparaHomologyOut",
  "type": "object"
}