Forge Tools orthodb_orthologs

orthodb_orthologs read

scidex.forge.orthodb_orthologs

Query OrthoDB for ortholog groups containing a gene or protein. For a gene symbol, Ensembl ID, or UniProt accession, returns OrthoDB ortholog group IDs, descriptions, evolutionary level, organism and gene counts, and representative member records. Optionally restricted to a specific NCBI taxonomic level (e.g. 2759 for Eukaryota). Not-found queries return an empty groups list, not an exception. API: data.orthodb.org — public, no auth required.

HTTP: POST /api/scidex/forge/orthodb_orthologs

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.orthodb_orthologs``.",
  "properties": {
    "query": {
      "description": "Gene symbol, Ensembl ID, UniProt ID, or keyword to search OrthoDB (e.g. 'BRCA1', 'ENSG00000012048', 'P38398').",
      "maxLength": 200,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "level_taxid": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "NCBI taxon ID to restrict the evolutionary level of returned groups (e.g. 2759 for Eukaryota, 33208 for Metazoa, 9606 for Homo sapiens). Omit to return groups at all levels.",
      "title": "Level Taxid"
    },
    "limit": {
      "default": 10,
      "description": "Maximum ortholog groups to return. Maximum 20.",
      "maximum": 20,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeOrthoDBIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "OrthoGroup": {
      "description": "One OrthoDB ortholog group record.",
      "properties": {
        "group_id": {
          "description": "OrthoDB ortholog group ID (e.g. '2510at2759').",
          "title": "Group Id",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "Group functional description.",
          "title": "Description",
          "type": "string"
        },
        "level_taxid": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "NCBI taxon ID of the evolutionary level for this group.",
          "title": "Level Taxid"
        },
        "level_name": {
          "default": "",
          "description": "Name of the evolutionary level (e.g. 'Eukaryota').",
          "title": "Level Name",
          "type": "string"
        },
        "organism_count": {
          "default": 0,
          "description": "Number of organisms with genes in this group.",
          "title": "Organism Count",
          "type": "integer"
        },
        "gene_count": {
          "default": 0,
          "description": "Total number of genes in this group.",
          "title": "Gene Count",
          "type": "integer"
        },
        "members": {
          "description": "Representative member gene records (up to 5 organisms).",
          "items": {
            "$ref": "#/$defs/OrthoGroupMember"
          },
          "title": "Members",
          "type": "array"
        },
        "orthodb_url": {
          "default": "",
          "description": "OrthoDB web URL for this group.",
          "title": "Orthodb Url",
          "type": "string"
        }
      },
      "required": [
        "group_id"
      ],
      "title": "OrthoGroup",
      "type": "object"
    },
    "OrthoGroupMember": {
      "description": "One member gene record within an OrthoDB ortholog group.",
      "properties": {
        "gene_id": {
          "description": "OrthoDB gene ID.",
          "title": "Gene Id",
          "type": "string"
        },
        "organism_name": {
          "default": "",
          "description": "Organism name (e.g. 'Homo sapiens').",
          "title": "Organism Name",
          "type": "string"
        },
        "taxon_id": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "NCBI taxon ID of the organism.",
          "title": "Taxon Id"
        },
        "gene_name": {
          "default": "",
          "description": "Gene symbol or name.",
          "title": "Gene Name",
          "type": "string"
        },
        "uniprot_id": {
          "default": "",
          "description": "UniProt accession, if available.",
          "title": "Uniprot Id",
          "type": "string"
        }
      },
      "required": [
        "gene_id"
      ],
      "title": "OrthoGroupMember",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.orthodb_orthologs``.",
  "properties": {
    "query": {
      "description": "The query string that was searched.",
      "title": "Query",
      "type": "string"
    },
    "groups": {
      "description": "OrthoDB ortholog groups matching the query.",
      "items": {
        "$ref": "#/$defs/OrthoGroup"
      },
      "title": "Groups",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the query returned no OrthoDB ortholog groups.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "orthodb",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeOrthoDBOut",
  "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/orthodb_orthologs' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

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