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Panacea

Service responsible for the UI and PML analysis. The UI is a web app available at localhost:4000. Panacea depends on both Asclepius and Chiron to provide DDI analysis, these must be running for Panacea to work.

Api Endpoints

All API endpoints require a valid authorization token to be provided. The token can be sent in the Authorization header or as the authorization_token query parameter.

Tokens can be generated using: Panacea.AccessToken.generate()

/api/pml
Description Validate a PML file and find the drugs it contains
Methods POST
Parameters An object containing the file to be analysed
Returns Response detailed below, or an error object

Example

Response Body
{
  "drugs": [
    {
      "label": "paracetamol",
      "line": 12
    },
    {
      "label": "cocaine",
      "line": 2
    }
  ],
  "unnamed": [
    {
      "type": "task",
      "line": 3
    },
    {
      "type": "sequence",
      "line": 6
    }
  ],
  "clashes": [
    {
      "name": "some_action",
      "occurrences": [
        {"line": 9, "type": "action"},
        {"line": 3, "type": "action"}
      ]
    }
  ],
  "ast": "AST representation of the provided PML file - base64 encoded"
}

/api/uris
Description For a given list of drug labels, find their DINTO URI
Methods POST
Request Body An object containing a list of drug labels, named labels
Returns Response detailed below or and error object

Example

Request Body
{"labels": [ "paracetamol", "flat seven up", "cocaine"]}
Response Body
{
  "uris": {
    "found": [
      {
        "label": "cocaine",
        "uri": "http://purl.obolibrary.org/obo/CHEBI_27958"
      },
      {
        "label": "paracetamol",
        "uri": "http://purl.obolibrary.org/obo/CHEBI_46195"
      }
    ],
    "not_found": [
      "flat seven up"
    ]
  }
}

/api/ddis
Description Find all drug-drug interactions (DDI) in the DINTO ontology which involve only the given drugs, in the context of the given AST
Methods POST
Request Body An object containing a list of drugs and an AST
Returns Response detailed below, or an error object

Example

Request Body
{
  "drugs": [
    {
      "uri": "http://purl.obolibrary.org/obo/DINTO_DB00214",
      "label": "torasemide"
    },
    {
      "uri": "http://purl.obolibrary.org/obo/DINTO_DB00519",
      "label": "trandolapril"
    }
  ],
  "ast": "encoded AST returned from /api/pml"
}
Response Body
{
  "ddis": [
    {
      "drug_a": {
        "uri": "http://purl.obolibrary.org/obo/DINTO_DB00214",
        "label": "torasemide",
        "line": 3
      },
      "drug_b": {
        "uri": "http://purl.obolibrary.org/obo/DINTO_DB00519",
        "label": "trandolapril",
        "line": 6
      },
      "label": "torasemide/trandolapril DDI",
      "uri": "http://purl.obolibrary.org/obo/DINTO_11031",
      "harmful": true,
      "spacing": 2,
      "unit": "yr",
      "agonism": true,
      "category": "sequential",
      "enclosing_constructs": [
        {
          "type": "sequence",
          "line": 6
        }
      ]
    }
  ]
}

/api/ast
Description Convert an PML AST into a PML Document
Methods POST
Parameters An object containing the pml ast to be converted
Returns The PML document as an attachment named pml-tx.pml, or an error object

Error Objects

All error responses take have the following format:

{
  "error": {
    "status_code": "http status code",
    "title": "string summarising the error",
    "detail": "string explaining the specific error",
    "meta": "object containing error specific metadata"
  }
}