Forge Tools elm_motifs

elm_motifs read

scidex.forge.elm_motifs

Look up predicted and annotated short linear motifs (SLiMs) from the Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org/) for a given UniProt protein accession. ELM covers ~300 functional motif classes (CLV_, DEG_, DOC_, LIG_, MOD_, TRG_) involved in cell signaling, protein degradation, domain binding, post-translational modification, and subcellular targeting. Returns motif positions, matched peptide sequences, instance logic (true/false positive), and experimental validation status. API: GET https://elm.eu.org/instances.json?q=<uniprot_acc> — free, no authentication required.

HTTP: POST /api/scidex/forge/elm_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.elm_motifs``.",
  "properties": {
    "uniprot_acc": {
      "description": "UniProt accession for the target protein, e.g. ``P04637`` (TP53).",
      "maxLength": 20,
      "title": "Uniprot Acc",
      "type": "string"
    }
  },
  "required": [
    "uniprot_acc"
  ],
  "title": "ForgeElmMotifsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ElmMotif": {
      "description": "One ELM motif instance on the queried protein.",
      "properties": {
        "elm_identifier": {
          "description": "ELM class identifier, e.g. ``DEG_APCC_DBOX_1`` or ``LIG_SH3_1``.",
          "title": "Elm Identifier",
          "type": "string"
        },
        "elm_name": {
          "default": "",
          "description": "Short display name for the ELM class (may be the same as identifier).",
          "title": "Elm Name",
          "type": "string"
        },
        "start": {
          "description": "Start position of the motif (1-based, inclusive).",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "description": "End position of the motif (1-based, inclusive).",
          "title": "End",
          "type": "integer"
        },
        "motif_sequence": {
          "default": "",
          "description": "Matched peptide sequence for this instance.",
          "title": "Motif Sequence",
          "type": "string"
        },
        "instance_logic": {
          "default": "",
          "description": "ELM instance logic: ``true positive``, ``false positive``, ``true negative``, or ``false negative``.",
          "title": "Instance Logic",
          "type": "string"
        },
        "is_annotated": {
          "default": false,
          "description": "True when the instance is experimentally annotated (curated), False for computational predictions.",
          "title": "Is Annotated",
          "type": "boolean"
        },
        "methods": {
          "description": "Experimental methods used to validate this instance.",
          "items": {
            "type": "string"
          },
          "title": "Methods",
          "type": "array"
        },
        "references": {
          "description": "PubMed IDs or other references supporting this instance.",
          "items": {
            "type": "string"
          },
          "title": "References",
          "type": "array"
        }
      },
      "required": [
        "elm_identifier",
        "start",
        "end"
      ],
      "title": "ElmMotif",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.elm_motifs``.",
  "properties": {
    "uniprot_acc": {
      "description": "The queried UniProt accession.",
      "title": "Uniprot Acc",
      "type": "string"
    },
    "motifs": {
      "description": "ELM motif instances found for this protein.",
      "items": {
        "$ref": "#/$defs/ElmMotif"
      },
      "title": "Motifs",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no ELM instances are found for the accession.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "elm.eu.org",
      "description": "Data source identifier (``elm.eu.org``).",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "uniprot_acc"
  ],
  "title": "ForgeElmMotifsOut",
  "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/elm_motifs' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "uniprot_acc": ""
}'

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