Forge Tools compartments

compartments read

scidex.forge.compartments

Query the COMPARTMENTS database (compartments.jensenlab.org) for confidence-scored subcellular localization evidence for a protein or gene. COMPARTMENTS integrates five evidence channels: UniProt knowledge annotations, experimental proteomics (HPA, ProteomicsDB), PubMed text-mining, sequence-based prediction, and a combined integrated score. Returns GO Cellular Component (CC) IDs and names with per-channel confidence scores on a 0–5 scale, filterable by minimum score. Distinct from scidex.forge.quickgo_annotations (raw GO CC annotation provenance without integrated confidence scoring) and scidex.forge.human_protein_atlas (HPA antibody images rather than integrated localization confidence). REST API: https://compartments.jensenlab.org/api — free, no auth required.

HTTP: POST /api/scidex/forge/compartments

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.compartments``.",
  "properties": {
    "gene": {
      "description": "HGNC gene symbol (e.g. 'TP53') or UniProt accession (e.g. 'P04637') to query in COMPARTMENTS.",
      "maxLength": 100,
      "minLength": 1,
      "title": "Gene",
      "type": "string"
    },
    "organism": {
      "default": "9606",
      "description": "NCBI taxon ID (as string) for the organism. Default '9606' (Homo sapiens). Other values: '10090' (mouse), '10116' (rat), '4932' (yeast).",
      "title": "Organism",
      "type": "string"
    },
    "min_score": {
      "default": 2,
      "description": "Minimum confidence score threshold (0–5 scale). Only compartments with score ≥ min_score are returned. Default 2.0.",
      "maximum": 5,
      "minimum": 0,
      "title": "Min Score",
      "type": "number"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of compartment entries to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeCompartmentsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "Compartment": {
      "description": "One subcellular compartment localization result from COMPARTMENTS.",
      "properties": {
        "compartment_id": {
          "description": "GO Cellular Component term identifier (e.g. 'GO:0005634').",
          "title": "Compartment Id",
          "type": "string"
        },
        "compartment_name": {
          "description": "Human-readable compartment name (e.g. 'nucleus').",
          "title": "Compartment Name",
          "type": "string"
        },
        "score": {
          "description": "Confidence score on a 0–5 scale; higher is more confident.",
          "title": "Score",
          "type": "number"
        },
        "channel": {
          "description": "Evidence channel: 'knowledge', 'experiments', 'textmining', 'prediction', or 'integrated'.",
          "title": "Channel",
          "type": "string"
        }
      },
      "required": [
        "compartment_id",
        "compartment_name",
        "score",
        "channel"
      ],
      "title": "Compartment",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.compartments``.",
  "properties": {
    "gene": {
      "description": "The queried gene symbol or identifier, as given.",
      "title": "Gene",
      "type": "string"
    },
    "compartments": {
      "description": "Subcellular compartment entries with GO IDs, names, confidence scores, and evidence channel. Sorted descending by score; capped at limit. Only entries with score ≥ min_score are included.",
      "items": {
        "$ref": "#/$defs/Compartment"
      },
      "title": "Compartments",
      "type": "array"
    },
    "not_found": {
      "description": "True when COMPARTMENTS returned no data for this gene/organism combination. False when the gene was found (even if all results were below min_score).",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "gene",
    "not_found"
  ],
  "title": "ForgeCompartmentsOut",
  "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/compartments' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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