Forge Tools quickgo_annotations

quickgo_annotations read

scidex.forge.quickgo_annotations

Fetch structured Gene Ontology (GO) annotations for a single gene symbol or UniProt accession using the EBI QuickGO API (free, no authentication required). Returns annotations across Biological Process (BP), Molecular Function (MF), and Cellular Component (CC) aspects, filterable by GO aspect and evidence code. Unlike ``scidex.forge.go_term_enrichment`` (which accepts a list of gene symbols), this verb exposes annotation provenance fields (reference, qualifier, assigned_by) and an aspects_summary count, making it suitable for per-gene deep dives in hypothesis-grounding and mechanistic bioanalysis workflows.

HTTP: POST /api/scidex/forge/quickgo_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.quickgo_annotations``.",
  "properties": {
    "gene_id": {
      "description": "HGNC gene symbol (e.g. ``BRCA1``) or UniProt accession (e.g. ``P38398``) to look up in QuickGO.",
      "title": "Gene Id",
      "type": "string"
    },
    "go_aspect": {
      "default": "",
      "description": "GO aspect to filter results. Must be one of ``biological_process``, ``molecular_function``, ``cellular_component``. Empty string (default) returns annotations from all three aspects.",
      "title": "Go Aspect",
      "type": "string"
    },
    "evidence_codes": {
      "description": "GO evidence codes to include (e.g. ``['EXP', 'IDA', 'IPI']`` for experimental, ``['IEA']`` for electronic annotation). Empty list (default) returns all evidence codes.",
      "items": {
        "type": "string"
      },
      "title": "Evidence Codes",
      "type": "array"
    },
    "taxon_id": {
      "default": 9606,
      "description": "NCBI taxon ID for filtering. Default 9606 (Homo sapiens).",
      "minimum": 1,
      "title": "Taxon Id",
      "type": "integer"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of annotations to return. Default 50.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_id"
  ],
  "title": "ForgeQuickGOIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "QuickGOAnnotation": {
      "description": "One GO term annotation returned by the QuickGO annotation/search endpoint.",
      "properties": {
        "go_id": {
          "description": "GO term identifier (e.g. ``GO:0006281``).",
          "title": "Go Id",
          "type": "string"
        },
        "go_name": {
          "default": "",
          "description": "Human-readable GO term name.",
          "title": "Go Name",
          "type": "string"
        },
        "go_aspect": {
          "description": "GO aspect abbreviation: BP, MF, or CC.",
          "title": "Go Aspect",
          "type": "string"
        },
        "evidence_code": {
          "description": "GO evidence code (e.g. ``IDA``, ``IEA``).",
          "title": "Evidence Code",
          "type": "string"
        },
        "reference": {
          "default": "",
          "description": "Source reference (e.g. ``PMID:10888872``).",
          "title": "Reference",
          "type": "string"
        },
        "qualifier": {
          "default": "",
          "description": "Annotation qualifier (e.g. ``involved_in``).",
          "title": "Qualifier",
          "type": "string"
        },
        "assigned_by": {
          "default": "",
          "description": "Database that assigned this annotation.",
          "title": "Assigned By",
          "type": "string"
        }
      },
      "required": [
        "go_id",
        "go_aspect",
        "evidence_code"
      ],
      "title": "QuickGOAnnotation",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.quickgo_annotations``.",
  "properties": {
    "gene_id": {
      "description": "The input gene identifier as given.",
      "title": "Gene Id",
      "type": "string"
    },
    "annotations": {
      "description": "GO term annotations for the resolved gene or protein.",
      "items": {
        "$ref": "#/$defs/QuickGOAnnotation"
      },
      "title": "Annotations",
      "type": "array"
    },
    "total_found": {
      "default": 0,
      "description": "Total annotations reported by QuickGO (may exceed ``len(annotations)`` when ``limit`` is smaller than the full result set).",
      "title": "Total Found",
      "type": "integer"
    },
    "aspects_summary": {
      "additionalProperties": {
        "type": "integer"
      },
      "description": "Count of returned annotations per GO aspect (e.g. ``{'BP': 12, 'MF': 4, 'CC': 2}``).",
      "title": "Aspects Summary",
      "type": "object"
    }
  },
  "required": [
    "gene_id"
  ],
  "title": "ForgeQuickGOOut",
  "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/quickgo_annotations' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_id": ""
}'

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