Forge Tools phosphositeplus

phosphositeplus read

scidex.forge.phosphositeplus

Query PhosphoSitePlus (phosphosite.org) for post-translational modification (PTM) sites, kinase-substrate relationships, and regulatory site data for a given protein. PhosphoSitePlus is the primary curated repository for PTMs, covering phosphorylation, acetylation, ubiquitination, methylation, and sumoylation with residue-level annotations and literature support. Input: protein UniProt accession or gene symbol, organism (default human), modification type (phospho/acetyl/ubiq/methyl/sumo/all). Returns residue position, modification type, kinases, regulatory function, and PMIDs. API: GET https://api.phosphosite.org/ptmcatalog/protein — free, no auth required.

HTTP: POST /api/scidex/forge/phosphositeplus

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.phosphositeplus``.",
  "properties": {
    "protein_id": {
      "description": "UniProt accession (e.g. ``'P04637'``) or gene symbol (e.g. ``'TP53'``) identifying the protein to query in PhosphoSitePlus.",
      "maxLength": 100,
      "title": "Protein Id",
      "type": "string"
    },
    "organism": {
      "default": "human",
      "description": "Organism. One of: ``'human'`` (default), ``'mouse'``, ``'rat'``, ``'yeast'``, ``'fly'``, ``'worm'``.",
      "title": "Organism",
      "type": "string"
    },
    "modification_type": {
      "default": "all",
      "description": "PTM class to return. One of: ``'all'`` (default), ``'phospho'`` (phosphorylation), ``'acetyl'`` (acetylation), ``'ubiq'`` (ubiquitination), ``'methyl'`` (methylation), ``'sumo'`` (sumoylation).",
      "title": "Modification Type",
      "type": "string"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of PTM site records to return (default 50, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "protein_id"
  ],
  "title": "ForgePspIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PspPtmSite": {
      "description": "One PTM site record from PhosphoSitePlus.",
      "properties": {
        "residue": {
          "description": "Single-letter amino acid code at the modified position.",
          "title": "Residue",
          "type": "string"
        },
        "position": {
          "description": "Residue position (1-based) of the modification.",
          "title": "Position",
          "type": "integer"
        },
        "modification_type": {
          "description": "Type of modification (e.g. Phosphorylation, Acetylation, Ubiquitination).",
          "title": "Modification Type",
          "type": "string"
        },
        "kinases": {
          "description": "Gene symbols of kinases or enzymes known to catalyse this modification.",
          "items": {
            "type": "string"
          },
          "title": "Kinases",
          "type": "array"
        },
        "regulatory_function": {
          "default": "",
          "description": "Regulatory role of this PTM site (e.g. 'activating', 'inhibitory', 'binding', or empty when uncharacterised).",
          "title": "Regulatory Function",
          "type": "string"
        },
        "pmids": {
          "description": "PubMed IDs of publications supporting this PTM record.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        }
      },
      "required": [
        "residue",
        "position",
        "modification_type"
      ],
      "title": "PspPtmSite",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.phosphositeplus``.",
  "properties": {
    "ptm_sites": {
      "description": "PTM site records from PhosphoSitePlus for the queried protein.",
      "items": {
        "$ref": "#/$defs/PspPtmSite"
      },
      "title": "Ptm Sites",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the protein was not found in PhosphoSitePlus.",
      "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": "ForgePspOut",
  "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/phosphositeplus' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "protein_id": ""
}'

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