Forge Tools eggnog_annotations

eggnog_annotations read

scidex.forge.eggnog_annotations

Look up eggNOG 6 orthologous group (OG) membership and functional annotations for a gene or protein query. Returns OG IDs, COG functional categories, descriptions, GO terms, and KEGG orthology links. Supports optional taxonomic scope filtering (e.g. 'Bacteria', 'Eukaryota', or NCBI taxon IDs). Source: eggNOG 6 — https://eggnog6.embl.de — public REST API, no auth required. Not-found queries set not_found=True; no exception raised.

HTTP: POST /api/scidex/forge/eggnog_annotations

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.eggnog_annotations``.",
  "properties": {
    "query": {
      "description": "Gene name, protein name, or identifier to look up in eggNOG 6. Examples: 'BRCA1', 'rplB', 'TP53', 'P04637'.",
      "maxLength": 200,
      "minLength": 1,
      "title": "Query",
      "type": "string"
    },
    "taxonomic_scope": {
      "anyOf": [
        {
          "maxLength": 100,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional taxonomic scope to filter OGs. Accepts level names such as 'Bacteria', 'Eukaryota', 'Archaea', or NCBI taxon IDs like '2' or '2759'. When omitted, all taxonomic levels are returned.",
      "title": "Taxonomic Scope"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeEggNOGAnnotationsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "EggNOGAnnotation": {
      "description": "One eggNOG orthologous group annotation record.",
      "properties": {
        "og_id": {
          "description": "eggNOG OG identifier (e.g. 'COG0001@1|root').",
          "title": "Og Id",
          "type": "string"
        },
        "level": {
          "default": "",
          "description": "Taxonomic level name (e.g. 'root', 'Bacteria').",
          "title": "Level",
          "type": "string"
        },
        "tax_id": {
          "default": "",
          "description": "NCBI taxon ID for the OG level.",
          "title": "Tax Id",
          "type": "string"
        },
        "preferred_name": {
          "default": "",
          "description": "Preferred gene/protein name for this OG (e.g. 'rplB').",
          "title": "Preferred Name",
          "type": "string"
        },
        "description": {
          "default": "",
          "description": "Functional description of the OG.",
          "title": "Description",
          "type": "string"
        },
        "cog_categories": {
          "default": "",
          "description": "COG functional category codes (e.g. 'J' = Translation, 'K' = Transcription, 'M' = Cell wall/membrane).",
          "title": "Cog Categories",
          "type": "string"
        },
        "go_terms": {
          "description": "GO term IDs associated with this OG (e.g. ['GO:0003735']).",
          "items": {
            "type": "string"
          },
          "title": "Go Terms",
          "type": "array"
        },
        "kegg_ko": {
          "description": "KEGG orthology IDs (e.g. ['K02886']).",
          "items": {
            "type": "string"
          },
          "title": "Kegg Ko",
          "type": "array"
        },
        "eggnog_url": {
          "default": "",
          "description": "eggNOG URL for this OG.",
          "title": "Eggnog Url",
          "type": "string"
        }
      },
      "required": [
        "og_id"
      ],
      "title": "EggNOGAnnotation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.eggnog_annotations``.",
  "properties": {
    "query": {
      "description": "The input query as submitted.",
      "title": "Query",
      "type": "string"
    },
    "annotations": {
      "description": "eggNOG OG annotation records for the query.",
      "items": {
        "$ref": "#/$defs/EggNOGAnnotation"
      },
      "title": "Annotations",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the query matched no eggNOG OG entries.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "eggnog6",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeEggNOGAnnotationsOut",
  "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/eggnog_annotations' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "query": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.