JSON Export

JSON Export

ver 1.3

This is a draft. Please report any issues or send your comments to support@phenotips.org and include "JSON Export Documentation" in the subject line.

For earlier versions of PhenoTips JSON Export please refer to: ver 1.2

The patient records stored in PhenoTips can be exported in a JSON format, which is a format commonly used for automatic parsing by computers. Exporting in JSON format is most suited when an external piece of software or a script needs patient information.

The patient records can be exported either individually or in bulk. There are two ways to export an individual record:
- via RESTfulAPI,
- by opening a patient record and hovering over "More actions", and then click "Export JSON". 

To perform a bulk export, navigate to the "Browse all data" page, click "Export database as JSON", and follow the instructions.

The following is an explanation of the name/value pairs of an individual patient record in JSON format based on an example. Each line of the name/value pair of the example patient record is presented on the left, with its explanation on the right. Not all of the name/value pairs will necessarily be present. 

{
  "id": "P0000036",The internal identifier of the patient record generated by PhenoTips. The format is "P" followed by a unique 7 digit combination.
  "external_id": "UDP_1234",The identifier given to the patient record by the user. This is usually an identifier generated by another tool, such as an EMR, and entered into PhenoTips to link back to help identify the patient.
  "reporter":"JohnDoe",The user ID of the creator of the patient record. This user may no longer be responsible for or even have access to this patient record.
  "date":"2016-05-18",
  "last_modified_by":"JohnDoe",
  "last_modification_date":"2016-05-18",
  "report_id":"P0000036",
  "exam_date":"2001-08-24",
  "meta": {Versions of tools/standards used at the time when the patient data was entered.
    "chebi_version": "137",Currently not is use. Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
    "hgnc_version": "2016-03-30",The version of HUGO Gene Nomenclature Committee (HGNC) used to specify genotype information of the patient. The HGNC is the only worldwide authority that assigns standardised nomenclature to human genes.
    "omim_version": "2015-10-07",The version of Online Mendelian Inheritance in Man (OMIM) used to specify disorder(s) of the patient. OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.
    "hpo_version": "releases/2016-01-13",The version of the Human Phenotype Ontology (HPO) used to specify phenotypes of the patient. The HPO aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease.
    "phenotips_version": "1.3-milestone-1r2"
  },
  "contact":{The contact information of the clinician responsible for a patient.
    "user_id":"JohnDoe",The PhenoTips user ID of the clinician.
    "name":"John Doe",
    "email":"support@phenotips.org",
    "institution":"http://phenotips.org/"
  },
  "patient_name":{
    "first_name":"John",
    "last_name":"Hopfield"
  },
  "sex":"M",F for female, M for male, O for other and U for unknown.
  "date_of_birth":"1933-07-15",May be a full or partial date (eg. yyyy, yyyy-MM, or yyyy-MM-dd).
  "life_status":"deceased",
  "date_of_death":"2014-04-02",May be a full or partial date (eg. yyyy, yyyy-MM, or yyyy-MM-dd).
  "ethnicity":{The ethnicities of the patient's parents presented as a list.
    "maternal_ethnicity":["Polish"],
    "paternal_ethnicity":["Japanese"]
  },
  "family_history":{Information about the patient's family.
    "consanguinity":false,true if consanguineous marriages are present in patient's family, false otherwise. Not present if unknown.
    "miscarriages":true,true if patients family has a history of miscarriages, false otherwise. Not present if unknown.
    "affectedRelatives":truetrue if other members of patient's family are affected with the same disorder, false otherwise. Not present if unknown.
  },
  "global_mode_of_inheritance":[{Marks the mode of inheritance of the majority of the patient’s disorders and is used in complement with the suspected_mode_of_inheritance qualifier that can be optionally associated to each phenotypic feature, and the mode_of_inheritance qualifier that can be optionally associated to each disorder.
    "id":"HP:0001475"",The Human Phenotype Ontology ID of the global mode of inheritance.
    "label":"Male-limited autosomal dominant"The description of the Human Phenotype Ontology (HPO) term, as provided by the current HPO version.
    },{
    "id": "HP:0001426",
    "label": "Multifactorial inheritance"
    }],
  "global_age_of_onset":[{Marks the time when the majority of symptoms were first observed and is used in complement with the age_of_onset qualifier that can be optionally associated to each feature or disorder.
    "id":"HP:0003593",The Human Phenotype Ontology ID of the global age of onset.
    "label":"Infantile onset"The description of the Human Phenotype Ontology (HPO) term, as provided by the current HPO version.
    }],
  "measurements":[{
    “date":"2001-08-24",May be a full or partial date (eg. yyyy, yyyy-MM, or yyyy-MM-dd).
    "side":"l",l for left, r for right, otherwise blank 
    "unit":"cm",
    "type":"wieght",height, weight, sitting, armspan, ear, hand, palm, foot,
bmi
for body mass index, philtrum,
hc  for head circumference,
ocd for outer canthal distance,
icd for inner canthal distance,
pfl for palpebral fissure length,
ipd for interpupilary distance ,
    "value":5,
    "age":"68y 1m"Age of patient at the time the measurement was taken.
    }],
  "prenatal_perinatal_history":{Information relating to the prenatal and perinatal development stages.
    "multipleGestation":true,
    "twinNumber":"A",If multiple gestation A,B,Other. Not present is unknown.
    "maternal_age":24,Integer value. The age of the mother given in years at the time of delivery. Not present if unknown.
    "paternal_age":30,Integer value. The age of the father given in years at the time of delivery. Not present if unknown.
    "gestation":36,Integer value representing gestation given in weeks. Not present if unknown.
    "assistedReproduction_fertilityMeds":true,true if fertility medication was used to conceive the patient, false otherwise. Not present if unknown.
    "assistedReproduction_iui":false,true if intrauterine insemination (IUI) was used to conceive the patient, false otherwise. Not present if unknown.
    "ivf":false,true if In Vitro Fertilization was performed, false otherwise. Not present if unknown.
    "icsi":false,true if Intra-cytoplasmic sperm injection was performed, false otherwise. Not present if unknown.
    "assistedReproduction_surrogacy":false,true if the patient is a surrogate child, false otherwise. Not present if unknown.
    "assistedReproduction_donoregg":false,
    "assistedReproduction_donorsperm":false,
    "obstetric-history":{Information relating to the care and treatment of woman in childbirth and during the period before and after delivery. Not present if unknown.
      "para":2Parity, the number of births that a woman has had after 20 weeks gestation. If a woman gives birth to more than one baby from a pregnancy, the pregnancy and birth are only counted once. 
      "tab":0,The total number of therapeutic abortion a woman had.
      "sab":0,The total number of spontaneous abortions (miscarriages) a woman had.
      "preterm":0,The total number of preterm pregnancies (20-37 wks or (>500 gms & <2500gms)) a woman had.
      "term":2,The total number of full term pregnancies((> 37 wks & < 42 wks) or >2500 gms) a woman had.
      "births":2,The total number of live births a woman had.
      "gravida":2The total number of confirmed pregnancies that a woman has had, regardless of the outcome
    }
  },
  "apgar":{The APGAR scores at 1 and 5 minutes. If the score is unknown, the field will not be present.
    "apgar1":6,
    "apgar5":7
  },
  "prenatal_perinatal_phenotype":{
    "prenatal_phenotype":[{The list of prenatal and perinatal phenotypic features which are marked as present and list of features manualy entered by user that are not contained within HPO
        "id":"HP:0001622",
        "label":"Premature birth"
      },{
        "label":"Custom perinatal complications"
     }],
    "negative_prenatal_phenotype":[{The list of prenatal and perinatal phenotypic features that are marked as absent.
        "id":"HP:0001561",
        "label":"Polyhydramnios"
      }]
  },
  "genes":[{The list of candidate, negative and confirmed casual genes. Each element in the list having a gene name, status, strategy and a comment attached.
      "gene":"SP3",
      "status":"candidate",
      "strategy":["common_mutations"],
      "comments":"We have low confidence in this choice"
    },{
      "gene":"GJB6",
      "strategy":[
         "sequencing",
         "familial_mutation"
       ],
      "status":"solved"
    }] 
  "variants":[{The list of variants. Each element in the list represents a single variant for a given gene, mapped to a gene by the genesymbol key.
     "genesymbol":"GJB6",
     "transcript":"NM_0000_1",
     "sanger":"positive",
     "zygosity":"heterozygous",
     "evidence":[
       "rare",
       "predicted",
       "reported"
      ],
     "interpretation": "likely_pathogenic",
     "protein":"p.Gly2873Pro",
     "effect":"missense",
     "dbsnp":"rs274842",
     "inheritance":"paternal",
     "cdna":"c1094C>T",
     "segregation":"segregates"
    }],
  "clinicalStatus":{The clinical status of the patient which can be either affected or unaffected.
    "clinicalStatus":"affected"
  },
  "features":[{The list of all phenotypes marked in the patient record.
      "id":"HP:0000152",
       "label":"Abnormality of head or neck",
       "type":"phenotype",
       "observed":"yes"
     },{
      "id":"HP:0001596",
      "label":"Alopecia",
      "type":"phenotype",
      "observed":"no"
    },{
    "id":"HP:0000982",
    "label":"Palmoplantar keratoderma",
    "type":"phenotype",
    "observed":"yes"
     },{
    "id":"HP:0001622",
    "label":"Premature birth",
    "type":"prenatal_phenotype",
    "observed":"yes"
     },{
    "id":"HP:0001561",
    "label":"Polyhydramnios",
    "type":"prenatal_phenotype",
    "observed":"no"
    }] 
  "nonstandard_features":[{List of features that are not contained within the Human Phenotype Ontology, and were entered manually by the user.
      "label":"Custom craniofacial term",
      "type":"phenotype",
      "observed":"yes"
    },{
     "label":"Custom perinatal complications",
     "type":"prenatal_phenotype",
    "observed":"yes"
    }],
  "disorders":[{List of all disorders the patient has.
      "id":"MIM:129500",Online Mendelian Inheritance in Man Ontology ID of the disorder.
      "label":"#129500 CLOUSTON SYNDROME"
    }],
  "allergies":[List of all environmental, food and  medication allergies the patient has.
      "NKDA", No known drug allergies
      "Peanuts"
  ],
  "notes":{All the note fields in the patient report are united under this section. Generally the name of the field indicates which section the notes are from.
    "indication_for_referral":"Keratoderma of the palms and soles.",
    "family_history":"Autosomal dominant hidrotic ectodermal dysplasia in 15 members in 5 generations.",
    "prenatal_development":"There are no abnormalities during the prenatal stage of development.",
    "medical_history":"Keratoderma of the palms and soles notable since birth.",
    "diagnosis_notes":"Clouston Syndrome"
  },
  "specificity":{Specificity is a measure of how detailed a phenotypic description is and is affected by two main factors: by the ontology level of phenotypes in the description (eg. abnormal eye physiology vs. glaucoma) and the frequency of occurrence of those phenotypes in the general population. 
    "score":0.40192283333333334,The score in the range of 0 to 1 roughly representing the quality of the phenotypic description of the patient.
    "date":"2016-05-19",
    "server":"monarchinitiative.org"
  },
  "solved":{Case resolution
    "pubmed_id":"PMID: 12345678",The unique identifier number used in PubMed
    "notes":"Enter resolution notes...",
    "status":"solved"If the molecular diagnosis for the patient is known.
  }
}