PubCaseFinder API



OVERVIEW

PubCaseFinder is a diagnostic assistance system that enables clinicians to match structured phenotype profiles - and associated genes - against previously published case reports and receive a ranked list of possible disease diagnosis.

HTTP POST to remote server:
https://pubcasefinder.dbcls.jp/mme/match

SEARCH REQUEST

HTTP POST request to https://pubcasefinder.dbcls.jp/mme/match, with an application/json body with the following format:
https://github.com/ga4gh/mme-apis/blob/master/search-api.md


SEARCH RESULTS RESPONSE

A synchronous application/json response, of the following form:

  • Example:


{
"results": [
    {
      "patient": {
        "contact": {
          "href": "https://pubcasefinder.dbcls.jp/disease_casereport/disease:ORDO:2573/phenotype:HP:0001009,HP:0001249,HP:0001250,HP:0002072,HP:0002315/gene:/page:1/size:20", 
          "name": "PubCaseFinder"
        }, 
        "features": [
          {
            "id": "HP:0002072"
          }, 
          {
            "id": "HP:0001249"
          }, 
          {
            "id": "HP:0002076"
          }, 
          {
            "id": "HP:0001250"
          }, 
          {
            "id": "HP:0001009"
          }
        ], 
        "genomicFeatures": [
          {
            "gene": {
              "id": "ENSG00000107796", 
              "label": "ACTA2"
            }
          }
        ], 
        "id": "ORDO:2573", 
        "label": "Moyamoya disease"
      }, 
      "score": {
        "patient": 1.0
      }
    },
    …
  ]
}
	    

  • Results:

    • Is a list of matches, where each match has a patient object which means a candidate disease diagnosis, and a score object with information about how well the candidate disease diagnosis object matched.

  • Patient:

    • A patient object means a candidate disease diagnosis.

  • Contact:

    • The contact information includes the URL for PubCaseFinder that shows a ranked list of previously published case reports
      • href : The URL for PubCaseFinder
      • name : “PubCaseFinder”

  • Features:

    • Is a list of features described by:
      • id: an HPO term identifier of the form: HP:#######

  • GenomicFeatures:

    • Is a list of candidate causal genes described by:
      • gene:
        • id: Ensembl gene ID
        • label: a human-readable description of the effect.

  • ID:

    • An identifier for a candidate disease diagnosis in Orphanet.

  • Label:

    • A name of a candidate disease diagnosis in Orphanet.

  • Score:

    • Information about how well this result of a candidate disease diagnosis matched the query patient.
    • Currently, this has a single field, patient, with a numerical value corresponding to the overall score of the match. This score must be in the range [0, 1], where 0.0 is a poor match and 1.0 is a perfect match.