Example (XML)
pyrophen outputs the codeset in XML or JSON format. See Example (JSON) for JSON.
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 XML file that is produced.
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="hpo"></id>
<url value="http://purl.obolibrary.org/obo/hp.fhir"></url>
<version value="http://purl.obolibrary.org/obo/hp/releases/2017-04-13/hp.owl"></version>
<name value="HPO"></name>
<title value="Human Phenotype Ontology Coding"></title>
<status value="active"></status>
<experimental value="false"></experimental>
<date value="2021-04-18T14:30:10-04:00"></date>
<publisher value="The Human Phenotype Ontology"></publisher>
<contact>
<name value="Peter N. Robinson"></name>
</contact>
<description value="A FHIR code system representation of the Human Phenotype Ontology."></description>
<purpose value="To provide a standardized vocabulary of human phenotypes encountered in human disease in a FHIR context."></purpose>
<copyright value="https://hpo.jax.org/app/license"></copyright>
<concept>
<code value="HP:0000001"></code>
<display value="All"></display>
</concept>
<concept>
<code value="HP:0040282"></code>
<display value="Frequent"></display>
<definition value="Present in 30% to 79% of the cases."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0040279"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0040281"></code>
<display value="Very frequent"></display>
<definition value="Present in 80% to 99% of the cases."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0040279"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0040284"></code>
<display value="Very rare"></display>
<definition value="Present in 1% to 4% of the cases."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0040279"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0040283"></code>
<display value="Occasional"></display>
<definition value="Present in 5% to 29% of the cases."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0040279"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0040280"></code>
<display value="Obligate"></display>
<definition value="Always present, i.e. in 100% of the cases."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0040279"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0100886"></code>
<display value="Abnormality of globe location"></display>
<definition value="An abnormality in the placement of the ocular globe (eyeball)."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0012374"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0012374"></code>
<display value="Abnormal globe morphology"></display>
<definition value="An anomaly of the eyeball."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0012372"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0040279"></code>
<display value="Frequency"></display>
<definition value="Class to represent frequency of phenotypic abnormalities within a patient cohort."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000001"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0100887"></code>
<display value="Abnormality of globe size"></display>
<definition value="An abnormality in the size of the ocular globe (eyeball)."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0012374"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000528"></code>
<display value="Anophthalmia"></display>
<definition value="Absence of the globe or eyeball."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0100887"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0040285"></code>
<display value="Excluded"></display>
<definition value="Present in 0% of the cases."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0040279"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0012372"></code>
<display value="Abnormal eye morphology"></display>
<definition value="A structural anomaly of the eye."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000478"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0012373"></code>
<display value="Abnormal eye physiology"></display>
<definition value="A functional anomaly of the eye."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000478"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000118"></code>
<display value="Phenotypic abnormality"></display>
<definition value="A phenotypic abnormality."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000001"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000007"></code>
<display value="Autosomal recessive inheritance"></display>
<definition value="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)."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000005"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000568"></code>
<display value="Microphthalmia"></display>
<definition value="A developmental anomaly characterized by abnormal smallness of one or both eyes."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0100887"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0007686"></code>
<display value="Abnormal pupillary function"></display>
<definition value="A functional abnormality of the pupil."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0012373"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000006"></code>
<display value="Autosomal dominant inheritance"></display>
<definition value="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."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000005"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000478"></code>
<display value="Abnormality of the eye"></display>
<definition value="Any abnormality of the eye, including location, spacing, and intraocular abnormalities."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000118"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000632"></code>
<display value="Lacrimation abnormality"></display>
<definition value="Abnormality of tear production."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0012373"></valueCode>
</property>
</concept>
<concept>
<code value="HP:0000005"></code>
<display value="Mode of inheritance"></display>
<definition value="The pattern in which a particular genetic trait or disorder is passed from one generation to the next."></definition>
<property>
<code value="parent"></code>
<valueCode value="HP:0000001"></valueCode>
</property>
</concept>
</CodeSystem>