Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
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
Generated Narrative: Composition
ResourceComposition "PhenopacketCompositionExample01"
Profile: Phenopacket profile
identifier: Uniform Resource Identifier (URI)/urn:uuid:1111-1111-1111-1112
status: PRELIMINARY
type: Medical records (LOINC#11503-0)
date: 2022-02-02
author: See on this page: Practitioner/PhenopacketPractitionerExample01: John T. Practitioner
title: This is an example of a composition resource that represents some of the Phenopackets data elements
2. http://phenopackets.org/fhir/Patient/example-patient (Patient/example-patient)
Anonymous Patient Male, DoB: 2001-01-20 ( Medical Record Number: m123 (use: usual))
3. http://phenopackets.org/fhir/Practitioner/PhenopacketPractitionerExample01 (Practitioner/PhenopacketPractitionerExample01)
This is an incomplete example that used as a placeholder for a curated Practitioner example
4. http://phenopackets.org/fhir/Observation/CHF-with-severity (Observation/CHF-with-severity)
Generated Narrative: Observation
ResourceObservation "CHF-with-severity"
Profile: Phenotypic Feature
status: FINAL
code: Low-output congestive heart failure (Human Phenotype Ontology#HP:0009805)
subject: See on this page: Patient/example-patient
effective: 2018-03-06
value: Present (LOINC#LA9633-4)
Components
Code Value[x] Severity (Human Phenotype Ontology#HP:0012824) Severe (Human Phenotype Ontology#HP:0012828)
5. http://phenopackets.org/fhir/Observation/thrombocytopenia (Observation/thrombocytopenia)
Generated Narrative: Observation
ResourceObservation "thrombocytopenia"
Profile: Measurement
status: FINAL
code: Platelets [#/volume] in Blood (LOINC#26515-7)
effective: 2018-03-06
value: 20 10^12/L
ReferenceRanges
Low High 150000 10^12/L 450000 10^12/L
6. http://phenopackets.org/fhir/Condition/CHF-stageIII (Condition/CHF-stageIII)
Generated Narrative: Condition
ResourceCondition "CHF-stageIII"
Profile: Disease profile
clinicalStatus: Active (Condition Clinical Status Codes#active)
code: congestive heart failure (Mondo Disease Ontology#MONDO_0005009)
subject: See on this page: Patient/example-patient
Stages
Summary Type moderate heart failure (efo#EFO:0003148) Clinical staging (SNOMED CT#260998006)
7. http://phenopackets.org/fhir/Specimen/bladderCarcinoma (Specimen/bladderCarcinoma)
ResourceSpecimen "bladderCarcinoma"
Profile: Biosample
Histological Diagnosis: Infiltrating Urothelial Carcinoma (NCI Thesaurus#NCIT_C39853)
Tumor Progression: Primary Malignant Neoplasm (NCI Thesaurus#NCIT_C84509)
Tumor Grade: Grade 2 Lesion (NCI Thesaurus#NCIT_C36136)
Pathological Tumor Stage: Stage II (NCI Thesaurus#NCIT_C28054)
Pathological TNM Finding: M0 Stage Finding (NCI Thesaurus#NCIT_C48699)
Material Sample: abnormal sample (efo#EFO_0009655)
identifier: arbitrary identifier
type: primary tumor sample (efo#EFO_0010942)
subject: See on this page: Patient/example-patient
Collections
Collected[x] BodySite 2021-01-20 wall of urinary bladder (uberon#UBERON_0001256) processing
8. http://phenopackets.org/fhir/DiagnosticReport/PhenopacketsGenomicInterpretationExample02 (DiagnosticReport/PhenopacketsGenomicInterpretationExample02)
some loinc code (Genetics)
Subject John Doe Unknown, DoB Unknown ( 04 (use: temp)) Identifier: 02 Report Details
Code Value Genetic variant assessment A rare genetic form of obesity characterized by morbid obesity, hypertension, type 2 diabetes mellitus and dyslipidemia leading to early coronary disease, myocardial infarction and congestive heart failure. Intellectual disability and decreased sperm counts or azoospermia have also been reported.
Coded Conclusions:
- Obesity due to centrosomal protein 19 deficiency (disorder)
9. http://phenopackets.org/fhir/Observation/PhenopacketsVariantExample01 (Observation/PhenopacketsVariantExample01)
Generated Narrative: Observation
ResourceObservation "PhenopacketsVariantExample01"
Profile: Phenopackets Variant
status: FINAL
category: Laboratory (Observation Category Codes#laboratory)
code: Genetic variant assessment (LOINC#69548-6)
IG © 2021+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.uv.phenomics-exchange#0.1.0 based on FHIR 4.0.1. Generated 2024-06-18
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