Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build International flag

Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions

Table of Contents

.. 0 Table of Contents
... 1 Home
... 2 GA4GH
... 3 Genomic Diagnostics
... 4 Deep phenotyping
... 5 Modeling phenotypic data
... 6 Human Phenotype Ontology
... 7 Examples
... 8 Artifacts Summary
.... 8.1 service-request-supporting-info
.... 8.2 Biosample
.... 8.3 Disease profile
.... 8.4 Individual
.... 8.5 Measurement
.... 8.6 Phenopacket profile
.... 8.7 Phenopackets Genomic Interpretation
.... 8.8 Phenopackets Variant
.... 8.9 Phenotypic Feature
.... 8.10 Treatment
.... 8.11 ACMG Pathogenicity Classification
.... 8.12 Additional Variant Identifier
.... 8.13 Coded Onset
.... 8.14 Diagnostic Marker
.... 8.15 Filter Status
.... 8.16 Histological Diagnosis
.... 8.17 Interpretation Status
.... 8.18 Karyotypic Sex
.... 8.19 Material Sample
.... 8.20 Measurement (Biosample)
.... 8.21 Molecule Context
.... 8.22 Onset
.... 8.23 Pathological TNM Finding
.... 8.24 Pathological Tumor Stage
.... 8.25 Phenotypic Feature (Biosample)
.... 8.26 Phred Quality Score
.... 8.27 Related Concept ID
.... 8.28 Taxonomy
.... 8.29 Therapeutic Actionability
.... 8.30 Tumor Grade
.... 8.31 Tumor Progression
.... 8.32 VCF Info
.... 8.33 VRS Object
.... 8.34 ACMG Pathogenicity Classification Value Set
.... 8.35 Diagnostic Marker
.... 8.36 GENO Ontology Allelic State Value Set
.... 8.37 HistologicalDiagnosis
.... 8.38 Hpo Severity Value Set
.... 8.39 Interpretation Status Value Set
.... 8.40 Karyotypic sex value set
.... 8.41 Molecule Context Value Set
.... 8.42 Observation categories
.... 8.43 Observation Codes for status of a PhenotypicFeature
.... 8.44 Onset ValueSet
.... 8.45 Phenotypic abnormality ValueSet
.... 8.46 Phenotypic component ValueSet
.... 8.47 Phenotypic modifier ValueSet
.... 8.48 Sequence Ontology Structural Variant Value Set
.... 8.49 Taxonomy
.... 8.50 Therapeutic Actionability Value Set
.... 8.51 Tumor Grade
.... 8.52 Tumor Progression
.... 8.53 Tumor Stage
.... 8.54 Categories
.... 8.55 Categories
.... 8.56 HTS Format
.... 8.57 Karyotypic sex code system
.... 8.58 Section Type
.... 8.59 A VALID karyotypic sex Observation instance.
.... 8.60 A valid phenotypic abnormality Observation example.
.... 8.61 amyotrophy
.... 8.62 An INVALID karyotypic sex Observation instance.
.... 8.63 An INVALID phenotypic abnormality Observation example.
.... 8.64 arachnodactyly
.... 8.65 bladderCarcinoma
.... 8.66 CHF-stageIII
.... 8.67 CHF-with-severity
.... 8.68 example-patient
.... 8.69 excluded-disease
.... 8.70 fiberSizeVariability
.... 8.71 globalDevelopmentalDelay
.... 8.72 hypotonia
.... 8.73 intellectualDisabilityDisease
.... 8.74 longPhiltrum
.... 8.75 losartan
.... 8.76 lowSetEars
.... 8.77 lvdysfunction-excluded
.... 8.78 microphthalmia
.... 8.79 muscleBiopsy
.... 8.80 muscleWeakness
.... 8.81 MVP-with-onset
.... 8.82 PeterGeneticist
.... 8.83 Phenopacket (static snapshot of clinical findings to support differential diagnosis of a child with developmental delay).
.... 8.84 phenopacket Patient Example01
.... 8.85 phenopacket Practitioner Example01
.... 8.86 phenopacket Specimen Example01
.... 8.87 Phenopackets Genomic Interpretation Example-1
.... 8.88 Phenopackets Genomic Interpretation Example-2
.... 8.89 Phenopackets Variant Example-1
.... 8.90 PhenopacketsBundleExample01
.... 8.91 Polydactyly-with-modifier
.... 8.92 Proband1
.... 8.93 reducedVisualAcuity
.... 8.94 retinalDetachment
.... 8.95 tga
.... 8.96 This is an example of a composition resource that represents some of the Phenopackets data elements
.... 8.97 thrombocytopenia
.... 8.98 vitreoretinochoroidopathy