Forge Tools hocomoco_motifs

hocomoco_motifs read

scidex.forge.hocomoco_motifs

Query HOCOMOCO v12 for transcription factor (TF) binding motifs. HOCOMOCO v12 is a curated database of PWM/PCM binding motifs for human and mouse TFs, valued for its strict quality tiers (A–D). Returns motif records with motif_id, species, collection (H12CORE/H12FULL), motif_length, consensus sequence, quality tier, and a HOCOMOCO URL. Input: tf_symbol (gene symbol, e.g. 'TP53'), optional species filter ('HUMAN'/'MOUSE'/'ALL', default 'HUMAN'), optional collection filter ('H12CORE'/'H12FULL'/'ALL', default 'H12CORE'). Not-found TFs return not_found=True with an empty motifs list — no exception. API: hocomoco12.autosome.org — public, no authentication required.

HTTP: POST /api/scidex/forge/hocomoco_motifs

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.hocomoco_motifs``.",
  "properties": {
    "tf_symbol": {
      "description": "Transcription factor gene symbol to look up (e.g. 'TP53', 'CTCF', 'MYC'). Case-insensitive. HOCOMOCO covers hundreds of human and mouse TFs.",
      "maxLength": 64,
      "minLength": 1,
      "title": "Tf Symbol",
      "type": "string"
    },
    "species": {
      "default": "HUMAN",
      "description": "Species filter: 'HUMAN' (default, Homo sapiens) or 'MOUSE' (Mus musculus). Pass 'ALL' to return motifs from both species.",
      "title": "Species",
      "type": "string"
    },
    "collection": {
      "default": "H12CORE",
      "description": "HOCOMOCO collection to query: 'H12CORE' (default, high-confidence curated motifs) or 'H12FULL' (expanded set including lower-confidence motifs). Pass 'ALL' to include both collections.",
      "title": "Collection",
      "type": "string"
    }
  },
  "required": [
    "tf_symbol"
  ],
  "title": "ForgeHocomocoMotifsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "HocomocoMotif": {
      "description": "One HOCOMOCO v12 TF binding motif record.",
      "properties": {
        "motif_id": {
          "description": "HOCOMOCO motif identifier, e.g. 'TP53_HUMAN.H12CORE.0.P.B'. Format: {TF}_{SPECIES}.{COLLECTION}.{version}.{quality}.{experiment}.",
          "title": "Motif Id",
          "type": "string"
        },
        "tf_name": {
          "description": "Transcription factor gene symbol (e.g. 'TP53').",
          "title": "Tf Name",
          "type": "string"
        },
        "species": {
          "description": "Species code: 'HUMAN' or 'MOUSE'.",
          "title": "Species",
          "type": "string"
        },
        "collection": {
          "description": "HOCOMOCO collection: 'H12CORE' (high-confidence) or 'H12FULL'.",
          "title": "Collection",
          "type": "string"
        },
        "motif_length": {
          "description": "Number of positions in the binding motif.",
          "title": "Motif Length",
          "type": "integer"
        },
        "consensus": {
          "default": "",
          "description": "Consensus binding sequence in IUPAC notation (e.g. 'RRRCWWGYYY').",
          "title": "Consensus",
          "type": "string"
        },
        "quality": {
          "default": "",
          "description": "HOCOMOCO quality tier: 'A' (highest confidence) through 'D' (lowest). Tier is encoded in the motif_id.",
          "title": "Quality",
          "type": "string"
        },
        "hocomoco_url": {
          "description": "Direct URL to the HOCOMOCO v12 motif page.",
          "title": "Hocomoco Url",
          "type": "string"
        }
      },
      "required": [
        "motif_id",
        "tf_name",
        "species",
        "collection",
        "motif_length",
        "hocomoco_url"
      ],
      "title": "HocomocoMotif",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.hocomoco_motifs``.",
  "properties": {
    "tf_symbol": {
      "description": "The TF symbol that was queried.",
      "title": "Tf Symbol",
      "type": "string"
    },
    "motifs": {
      "description": "HOCOMOCO v12 motif records for the requested TF. Multiple motifs may be returned when the TF has profiles in both H12CORE and H12FULL collections or in multiple species.",
      "items": {
        "$ref": "#/$defs/HocomocoMotif"
      },
      "title": "Motifs",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no HOCOMOCO v12 motifs were found for the TF symbol.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "hocomoco_v12",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for upstream API call in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "tf_symbol"
  ],
  "title": "ForgeHocomocoMotifsOut",
  "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/hocomoco_motifs' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "tf_symbol": ""
}'

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