├── .gitattributes ├── .github └── workflows │ ├── maven.yml │ └── python.yml ├── .gitignore ├── .gitmodules ├── .mvn └── wrapper │ ├── maven-wrapper.jar │ └── maven-wrapper.properties ├── .readthedocs.yaml ├── .travis.yml ├── CHANGELOG.rst ├── CONTRIBUTING.rst ├── DISCLAIMER.rst ├── LICENSE ├── MAINTAINERS.rst ├── README.rst ├── deploy-python.sh ├── docs ├── Makefile ├── _static │ ├── custom.css │ └── style.css ├── _templates │ └── layout.html ├── age.rst ├── apiversion.rst ├── basics.rst ├── biosample.rst ├── building-blocks.rst ├── cancer-example-java.rst ├── cancer-example.rst ├── cohort.rst ├── complex-value.rst ├── conf.py ├── covid19-example.rst ├── cpp.rst ├── disease.rst ├── dose-interval.rst ├── drug-type.rst ├── evidence.rst ├── examples.rst ├── exposure.rst ├── externalreference.rst ├── family.rst ├── fhir.rst ├── file.rst ├── gene.rst ├── genomic-interpretation.rst ├── gestational-age.rst ├── graph │ ├── phenopacket-schema-v1-original.gv │ ├── phenopacket-schema-v1-original.svg │ ├── phenopacket-schema-v1-overview.gv │ ├── phenopacket-schema-v1-overview.svg │ ├── phenopacket-schema-v1.gv │ ├── phenopacket-schema-v1.svg │ ├── phenopacket-schema-v2-overview.gv │ ├── phenopacket-schema-v2-overview.svg │ ├── phenopacket-schema-v2.gv │ └── phenopacket-schema-v2.svg ├── images │ └── GA-logo.png ├── index.rst ├── individual.rst ├── interpretation.rst ├── interval.rst ├── introduction.rst ├── java-build.rst ├── java-duration.rst ├── java-evidence.rst ├── java-export.rst ├── java-timestamp.rst ├── java.rst ├── karyotypicsex.rst ├── measurement.rst ├── medical-action.rst ├── metadata.rst ├── ontologies.rst ├── ontologyclass.rst ├── pedigree.rst ├── pharmaceutical-treatment.rst ├── phenopacket.rst ├── phenotype.rst ├── procedure.rst ├── protobuf.rst ├── python.rst ├── quantity.rst ├── radiotherapy.rst ├── rd-example-java.rst ├── rd-example.rst ├── recommended-ontologies.rst ├── reference-range.rst ├── requirements.in ├── requirements.rst ├── requirements.txt ├── resource.rst ├── schema.rst ├── sex.rst ├── stop-reason.rst ├── therapeutic-regimen.rst ├── time-element.rst ├── time-interval.rst ├── timestamp.rst ├── toplevel.rst ├── treatment.rst ├── update.rst ├── value.rst ├── variant-interpretation.rst ├── variant.rst ├── version2.rst ├── vital-status.rst └── working.rst ├── mvnw ├── mvnw.cmd ├── pom.xml ├── python ├── LICENSE ├── README.md ├── README.rst ├── data │ ├── v1 │ │ ├── README.md │ │ ├── cohort.json │ │ ├── cohort.pb │ │ ├── family.json │ │ ├── family.pb │ │ ├── phenopacket.json │ │ └── phenopacket.pb │ └── v2 │ │ ├── cohort.json │ │ ├── cohort.pb │ │ ├── family.json │ │ ├── family.pb │ │ ├── phenopacket.json │ │ └── phenopacket.pb ├── pyproject.toml ├── src │ └── phenopackets │ │ ├── __init__.py │ │ └── schema │ │ └── v2 │ │ └── __init__.py └── tests │ ├── conftest.py │ ├── covid19.json │ ├── mcahs1.json │ ├── test_imports.py │ ├── test_io.py │ └── test_phenopackets.py └── src ├── main ├── java │ └── module-info.java └── proto │ └── phenopackets │ ├── schema │ ├── v1 │ │ ├── base.proto │ │ ├── interpretation.proto │ │ └── phenopackets.proto │ └── v2 │ │ ├── core │ │ ├── base.proto │ │ ├── biosample.proto │ │ ├── disease.proto │ │ ├── genome.proto │ │ ├── individual.proto │ │ ├── interpretation.proto │ │ ├── measurement.proto │ │ ├── medical_action.proto │ │ ├── meta_data.proto │ │ ├── pedigree.proto │ │ └── phenotypic_feature.proto │ │ └── phenopackets.proto │ ├── vrs │ └── v1 │ │ └── vrs.proto │ └── vrsatile │ └── v1 │ └── vrsatile.proto └── test ├── java └── org │ ├── matchmakerexchange │ └── api │ │ └── v1 │ │ └── MmeNodeTest.java │ └── phenopackets │ └── schema │ ├── v1 │ ├── FamilyTest.java │ ├── FhirTest.java │ ├── InterpretationTest.java │ ├── PhenoPacketTestUtil.java │ ├── PhenopacketTest.java │ ├── examples │ │ ├── BethlemMyopathyExample.java │ │ ├── BiosamplesPhenopacketExample.java │ │ ├── CancerFhirExample.java │ │ ├── CancerPhenopacketExample.java │ │ ├── RareDiseaseFamilyExample.java │ │ ├── RareDiseaseFhirExample.java │ │ ├── ResourceOntologyClassExample.java │ │ ├── TestExamples.java │ │ └── UrothelialCarcinomaExample.java │ └── io │ │ ├── FormatMapper.java │ │ ├── PhenopacketFormat.java │ │ └── PhenopacketFormatTest.java │ └── v2 │ ├── FamilyTest.java │ ├── FhirTest.java │ ├── InterpretationTest.java │ ├── PhenoPacketTestUtil.java │ ├── PhenopacketTest.java │ ├── SchemaVersion.java │ ├── doc │ ├── PhenopacketUtil.java │ ├── TestBase.java │ └── YamlGenerationTest.java │ ├── examples │ ├── BethlemMyopathyExample.java │ ├── BiosamplesPhenopacketExample.java │ ├── CancerFhirExample.java │ ├── CancerPhenopacketExample.java │ ├── CovidExample.java │ ├── RareDiseaseFamilyExample.java │ ├── RareDiseaseFhirExample.java │ ├── ResourceOntologyClassExample.java │ ├── TestExamples.java │ └── UrothelialCarcinomaExample.java │ └── io │ ├── FormatMapper.java │ ├── PhenopacketFormat.java │ └── PhenopacketFormatTest.java ├── proto ├── README.md └── 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