Example (JSON)
pyrophen outputs the codeset in XML or JSON format. See Example (XML) for XML.
The test class HpoFhirTerminologyApplicationTests writes a temporary file with the CodeSystem created for a small excerpt of the HPO located
in src/test/resources/hp_head.obo.
This is the JSON file that is produced.
{
"resourceType": "CodeSystem",
"id": "hpo",
"url": "http://purl.obolibrary.org/obo/hp.fhir",
"version": "http://purl.obolibrary.org/obo/hp/releases/2017-04-13/hp.owl",
"name": "HPO",
"title": "Human Phenotype Ontology Coding",
"status": "active",
"experimental": false,
"date": "2021-05-03T08:04:39-04:00",
"publisher": "The Human Phenotype Ontology",
"contact": [ {
"name": "Peter N. Robinson"
} ],
"description": "A FHIR code system representation of the Human Phenotype Ontology.",
"purpose": "To provide a standardized vocabulary of human phenotypes encountered in human disease in a FHIR context.",
"copyright": "https://hpo.jax.org/app/license",
"concept": [ {
"code": "HP:0000001",
"display": "All"
}, {
"code": "HP:0040282",
"display": "Frequent",
"definition": "Present in 30% to 79% of the cases.",
"property": [ {
"code": "parent",
"valueCode": "HP:0040279"
} ]
}, {
"code": "HP:0040281",
"display": "Very frequent",
"definition": "Present in 80% to 99% of the cases.",
"property": [ {
"code": "parent",
"valueCode": "HP:0040279"
} ]
}, {
"code": "HP:0040284",
"display": "Very rare",
"definition": "Present in 1% to 4% of the cases.",
"property": [ {
"code": "parent",
"valueCode": "HP:0040279"
} ]
}, {
"code": "HP:0040280",
"display": "Obligate",
"definition": "Always present, i.e. in 100% of the cases.",
"property": [ {
"code": "parent",
"valueCode": "HP:0040279"
} ]
}, {
"code": "HP:0100886",
"display": "Abnormality of globe location",
"definition": "An abnormality in the placement of the ocular globe (eyeball).",
"property": [ {
"code": "parent",
"valueCode": "HP:0012374"
} ]
}, {
"code": "HP:0012374",
"display": "Abnormal globe morphology",
"definition": "An anomaly of the eyeball.",
"property": [ {
"code": "parent",
"valueCode": "HP:0012372"
} ]
}, {
"code": "HP:0040279",
"display": "Frequency",
"definition": "Class to represent frequency of phenotypic abnormalities within a patient cohort.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000001"
} ]
}, {
"code": "HP:0100887",
"display": "Abnormality of globe size",
"definition": "An abnormality in the size of the ocular globe (eyeball).",
"property": [ {
"code": "parent",
"valueCode": "HP:0012374"
} ]
}, {
"code": "HP:0000528",
"display": "Anophthalmia",
"definition": "Absence of the globe or eyeball.",
"property": [ {
"code": "parent",
"valueCode": "HP:0100887"
} ]
}, {
"code": "HP:0040285",
"display": "Excluded",
"definition": "Present in 0% of the cases.",
"property": [ {
"code": "parent",
"valueCode": "HP:0040279"
} ]
}, {
"code": "HP:0012372",
"display": "Abnormal eye morphology",
"definition": "A structural anomaly of the eye.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000478"
} ]
}, {
"code": "HP:0012373",
"display": "Abnormal eye physiology",
"definition": "A functional anomaly of the eye.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000478"
} ]
}, {
"code": "HP:0000118",
"display": "Phenotypic abnormality",
"definition": "A phenotypic abnormality.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000001"
} ]
}, {
"code": "HP:0000007",
"display": "Autosomal recessive inheritance",
"definition": "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).",
"property": [ {
"code": "parent",
"valueCode": "HP:0000005"
} ]
}, {
"code": "HP:0000568",
"display": "Microphthalmia",
"definition": "A developmental anomaly characterized by abnormal smallness of one or both eyes.",
"property": [ {
"code": "parent",
"valueCode": "HP:0100887"
} ]
}, {
"code": "HP:0007686",
"display": "Abnormal pupillary function",
"definition": "A functional abnormality of the pupil.",
"property": [ {
"code": "parent",
"valueCode": "HP:0012373"
} ]
}, {
"code": "HP:0000006",
"display": "Autosomal dominant inheritance",
"definition": "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000005"
} ]
}, {
"code": "HP:0000478",
"display": "Abnormality of the eye",
"definition": "Any abnormality of the eye, including location, spacing, and intraocular abnormalities.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000118"
} ]
}, {
"code": "HP:0000632",
"display": "Lacrimation abnormality",
"definition": "Abnormality of tear production.",
"property": [ {
"code": "parent",
"valueCode": "HP:0012373"
} ]
}, {
"code": "HP:0000005",
"display": "Mode of inheritance",
"definition": "The pattern in which a particular genetic trait or disorder is passed from one generation to the next.",
"property": [ {
"code": "parent",
"valueCode": "HP:0000001"
} ]
} ]
}