Skip to content

Latest commit

 

History

History
164 lines (136 loc) · 6.41 KB

README.md

File metadata and controls

164 lines (136 loc) · 6.41 KB
Raw

Asclepius ⚕

Flask endpoint for querying DINTO. Supports querying for all drugs listed, as well as finding all, or specific drug-drug interactions.

This application acts as an adaptor to Chiron - an instance of Apache Fuseki, Chiron must be running before any queries can be served.

CSV File Exporting

When run as a program, the enrich module will export DDIs, along with mock timing and agonism/harmfulness information.

Run as python3 enrich.py <harmful|agonism> > outfile.csv to export to a CSV file.

HTTP Endpoints

/all_drugs
Description Find all drugs in the DINTO ontology
Methods GET
Parameters None
Returns A list containing pairs of the canonical URI for a drug, as well as its English Label

Example

Response Body (Truncated)
[
  {
    "label": "carbapenem MM22383",
    "uri": "http://purl.obolibrary.org/obo/CHEBI_58998"
  },
  {
    "label": "adenosine-5'-ditungstate",
    "uri": "http://purl.obolibrary.org/obo/DINTO_DB02183"
  },
  {
    "label": "(5z)-13-chloro-14,16-dihydroxy-3,4,7,8,9,10-hexahydro-1h-2-benzoxacyclotetradecine-1,11(12h)-dione",
    "uri": "http://purl.obolibrary.org/obo/DINTO_DB08346"
  },
  {
    "label": "etoposide",
    "uri": "http://purl.obolibrary.org/obo/CHEBI_4911"
  }
]

/all_ddis
Description Find all drug-drug interactions (DDIs) in the DINTO ontology
Methods GET
Parameters None
Returns A list containing pairs of the canonical URI for a drug-drug interaction, as well as its English label and the labels of the drugs involved

Example

Response Body (Truncated)
[
  {
    "label": "torasemide/trandolapril DDI",
    "uri": "http://purl.obolibrary.org/obo/DINTO_11031",
    "drug_a": "torasemide",
    "drug_b": "trandolapril"
  },
  {
    "label": "cimetidine/heroin DDI",
    "uri": "http://purl.obolibrary.org/obo/DINTO_02733",
    "drug_a": "cimetidine",
    "drug_b": "heroin"
  },
  {
    "label": "methylergonovine/telithromycin DDI",
    "uri": "http://purl.obolibrary.org/obo/DINTO_10154",
    "drug_a": "methylergonovine",
    "drug_b": "telithromycin"
  }
]

/ddis
Description Find all drug-drug interactions (DDI) in the DINTO ontology which involve only the given drugs
Methods POST
Request Body An object containing a list of DINTO URIs
Returns A list of DDI objects; its label, its URI, the identifiers of the two drugs involved, the spacing between dosages required to avoid the DDI as well as whether or not it is a harmful interaction and an agonism/antagonism

Example

Request Body
{
  "drugs": [
    "http://purl.obolibrary.org/obo/DINTO_DB00214",
    "http://purl.obolibrary.org/obo/DINTO_DB00519"
  ]
}
Response Body
[
  {
    "drug_a": "http://purl.obolibrary.org/obo/DINTO_DB00214",
    "drug_b": "http://purl.obolibrary.org/obo/DINTO_DB00519",
    "label": "torasemide/trandolapril DDI",
    "uri": "http://purl.obolibrary.org/obo/DINTO_11031",
    "harmful": true,
    "spacing": 2,
    "unit": "yr",
    "agonism": true
  }
]

/uris
Description For a given list of drug labels, find their DINTO URIs (to be used when calling /ddis)
Methods POST
Request Body An object containing a list of drug labels, named labels
Returns See below

Example

Request Body
{"labels": [ "paracetamol", "flat seven up", "cocaine"]}
Response Body
{
  "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"
  ]
}