Forge Tools iptmnet_ptm

iptmnet_ptm read

scidex.forge.iptmnet_ptm

Query iPTMnet (research.bioinformatics.udel.edu/iptmnet) for post-translational modifications (PTMs) on a protein. iPTMnet integrates curated PTM data from 10+ sources including PhosphoSitePlus, PhosphoELM, HPRD, SIGNOR, and UniProt. Returns phosphorylation, ubiquitination, acetylation, methylation, and sumoylation sites with residue positions, modifying enzymes, and supporting database references. Also returns enzyme–substrate relationships for kinase activity and regulatory network queries. API: GET https://research.bioinformatics.udel.edu/iptmnet/api/protein/{id}/sites — free, no authentication required.

HTTP: POST /api/scidex/forge/iptmnet_ptm

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.iptmnet_ptm``.",
  "properties": {
    "gene": {
      "description": "Gene symbol (e.g. TP53, EGFR) or UniProt accession (e.g. P04637). Used to identify the protein in iPTMnet.",
      "maxLength": 50,
      "title": "Gene",
      "type": "string"
    },
    "ptm_type": {
      "default": "all",
      "description": "PTM type to return. One of: ``'all'`` (default), ``'phosphorylation'``, ``'ubiquitination'``, ``'acetylation'``, ``'methylation'``, ``'sumoylation'``.",
      "title": "Ptm Type",
      "type": "string"
    },
    "organism": {
      "default": "human",
      "description": "Organism to query. One of: ``'human'`` (default), ``'mouse'``, ``'rat'``, ``'yeast'``, ``'fly'``, ``'worm'``.",
      "title": "Organism",
      "type": "string"
    },
    "limit": {
      "default": 30,
      "description": "Maximum number of PTM sites to return (default 30, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeIptmnetIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "EnzymeSubstrate": {
      "description": "One enzyme–substrate PTM relationship involving the queried protein.",
      "properties": {
        "enzyme_gene": {
          "description": "Gene symbol of the modifying enzyme.",
          "title": "Enzyme Gene",
          "type": "string"
        },
        "substrate_gene": {
          "description": "Gene symbol of the substrate protein.",
          "title": "Substrate Gene",
          "type": "string"
        },
        "substrate_uniprot": {
          "default": "",
          "description": "UniProt accession of the substrate.",
          "title": "Substrate Uniprot",
          "type": "string"
        },
        "ptm_type": {
          "description": "PTM type catalysed (e.g. phosphorylation).",
          "title": "Ptm Type",
          "type": "string"
        },
        "site": {
          "default": "",
          "description": "Site descriptor on the substrate (e.g. S15) when available.",
          "title": "Site",
          "type": "string"
        },
        "sources": {
          "description": "Supporting databases / PMIDs.",
          "items": {
            "type": "string"
          },
          "title": "Sources",
          "type": "array"
        }
      },
      "required": [
        "enzyme_gene",
        "substrate_gene",
        "ptm_type"
      ],
      "title": "EnzymeSubstrate",
      "type": "object"
    },
    "PtmSite": {
      "description": "One PTM site on the queried protein.",
      "properties": {
        "position": {
          "description": "Residue position (1-based) of the modification.",
          "title": "Position",
          "type": "integer"
        },
        "residue": {
          "description": "Single-letter amino acid code at the modified position.",
          "title": "Residue",
          "type": "string"
        },
        "ptm_type": {
          "description": "PTM type (e.g. phosphorylation, ubiquitination).",
          "title": "Ptm Type",
          "type": "string"
        },
        "enzyme": {
          "default": "",
          "description": "Gene symbol of the modifying enzyme (kinase, E3 ligase, etc.). Empty when unknown.",
          "title": "Enzyme",
          "type": "string"
        },
        "score": {
          "default": 0,
          "description": "Confidence score for this site (0–1 scale when provided by source; else 0).",
          "title": "Score",
          "type": "number"
        },
        "sources": {
          "description": "Databases / publications supporting this site (e.g. PhosphoSitePlus, HPRD).",
          "items": {
            "type": "string"
          },
          "title": "Sources",
          "type": "array"
        }
      },
      "required": [
        "position",
        "residue",
        "ptm_type"
      ],
      "title": "PtmSite",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.iptmnet_ptm``.",
  "properties": {
    "ptm_sites": {
      "description": "PTM sites found on the queried protein.",
      "items": {
        "$ref": "#/$defs/PtmSite"
      },
      "title": "Ptm Sites",
      "type": "array"
    },
    "enzyme_substrates": {
      "description": "Enzyme–substrate relationships involving the queried protein.",
      "items": {
        "$ref": "#/$defs/EnzymeSubstrate"
      },
      "title": "Enzyme Substrates",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the protein was not found in iPTMnet.",
      "title": "Not Found",
      "type": "boolean"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for upstream API calls in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "title": "ForgeIptmnetOut",
  "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/iptmnet_ptm' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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