Search ServiceRequest by supporting resource parameters

A unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted.

This profile stipulates that a FHIR Condition must have a codeable concept that represents the disease. The concepts can be taken from various ontologies, but for rare-disease concepts, we recommend MONDO.

The subject of the Phenopacket is represented by an Individual element. This element intends to represent an individual human or other organism.

This profile defines the GA4GH Measurement element in terms of the FHIR Observation

This is the main element that represents the Phenopacket in FHIR.

A profile of Genomics Reporting Genomics Report profile that represents relevant phenopackets building blocks.

A profile of Genomics Reporting Variant profile that represents relevant phenopackets building blocks.

This profile defines the GA4GH PhenotypicFeature element in terms of the FHIR Observation

This profile defines the GA4GH Treatment element in terms of the FHIR MedicationAdministration

One of the five ACMG pathogenicity categories, default is UNCERTAIN_SIGNIFICANCE.

Used to list of unique identifiers where available. If this is a dbSNP variant, component[dbSNP-id] should be used instead.

The onset of a disease using an ontology class.

Clinically relevant biomarkers. Most of the assays such as immunohistochemistry (IHC) are covered by the NCIT under the sub-hierarchy NCIT:C36292 (Laboratory Test Result), e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive).

Filter status: PASS if this position has passed all filters.

This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis (which could be reported in the Phenopacket that contains this Biosample). Normal samples would be tagged with the term “NCIT:C38757”, “Negative Finding”.

Describes the conclusion made about the genomic interpretation.

Karyotypic sex of an individual (also known as chromosomal sex).

Type of sample (diseases, control, etc.)

Term representing a measurement made on a Biosample

The molecular context of the vrs variation.

Describes the age at which a phenotypic feature was first noticed or diagnosed.

Pathological TNM findings, if applicable. Corresponds to pathological_tnm_finding (GA4GH)

This element can be used if the phenopacket describes cancer. Tumor staging describes the extent of growth of cancer, including the tumor and, if applicable, affected lymph nodes and distant metastases. This element should not be confused with clinical stage.

Term representing phenotypic features of a Biosample

Used to include Phred-scaled quality score for the assertion made in ALT.

Used to provide identifiers to alternative resources representing related, but not equivalent concepts, for example gene ortholog ids

Corresponds to taxonomy (GA4GH). For resources where there may be more than one organism being studied it is advisable to indicate the taxonomic identifier of that organism, to its most specific level.

one of the five ACMG pathogenicity categories, or NOT_PROVIDED. The default is NOT_PROVIDED.

List of terms representing the tumor grade.

This field can be used to indicate if a specimen is from the primary tumor, a metastasis or a recurrence. There are multiple ways of representing this using ontology terms, and the terms chosen should have a specific meaning that is application specific.

Additional information: Semicolon-separated series of additional information fields from VCF info field.

The VRS Variation object (Link: https://vrs.ga4gh.org/en/stable/)

Describes the ACMG five-tier pathogenicity classification system (Richards et al., 2015, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544753/).

Codes to indicate clinically relevant bio markers.

Descendent terms of GENO_0000875

Histological diagnosis codes from NCIT.

The HPO codes for phenotypic feature severity

Describes the conclusion made about the genomic interpretation.

The karyotypic (chromosomal) sex of an individual

Describes The molecular context of the variant. Default is unspecified_molecule_context.

The LOINC codes for present if a feature is observed and absent if a feature was excluded.

ValueSet description here

Set of HPO codes that denote the onset of a disease or phenotypic feature. The codes are descendants of Onset (HP:0003674) or from SNOMED_CT (282032007).

ValueSet description here

ValueSet description here

Human Phenotype Ontology (HPO) Clinical Modifier terms

Descendent terms of SO:0001537.

Taxonomic identifiers of an organism.

Describes the therapeutic actionability of the variant.

Codes to indicate the grade of a tumor.

Codes to indicate if a specimen is from the primary tumor, a metastasis or a recurrence.

Codes to represent the stage of a tumor.

Various categories or tags

Various categories or tags

An enumeration used to represent different high-throughput sequencing file formats.

karyotypic sex of an individual (also known as chromosomal sex)

Section Type

A VALID karyotypic sex Observation instance.

A valid phenotypic abnormality Observation example.

An INVALID karyotypic sex Observation instance.

An INVALID phenotypic abnormality Observation example.

Congestive heart failure, New York Heart Association stage III

PhenotypicFeature Example for severe Low-output congestive heart failure

PhenotypicFeature Example for mitral value prolapse with onset

Extended example: example practitioner

Example use case for a child with undiagnosed developmental delay

This is an example of phenopackets-variant which is a phenopackets profile of the genomics reporting Genomics Report profile. It represents phenopackets GenomicInterpretation building block, i.e., the interpretation for an individual variant or gene.

This is an example of phenopackets-variant which is a phenopackets profile of the genomics reporting Genomics Report profile. It represents phenopackets GenomicInterpretation building block, i.e., the interpretation for an individual variant or gene.

This is an example of phenopackets-genomic-interpretation which is a phenopackets profile of the genomics reporting Variant profile. It represents phenopackets GeneDescriptor, VariationDescriptor, VcfRecord, and VariantInterpretation building blocks.

Example Phenopacket Bundle instance

Bilateral postaxial Polydactyly, example to demonstrate use of Clinical Modifier

Example child with developmental delay

Example Phenopacket Composition instance

Skeletal muscle atrophy (HP:0003202)

PhenotypicFeature Example for arachnodactyly

Biosample Example for bladder carcinoma

Example of Patient

Phenopacket Example for an excluded disease

Increased variability in muscle fiber diameter (HP:0003557)

Global developmental delay (HP:0001263)

Hypotonia (HP:0001252)

Intellectual disability (disease)

Long philtrum (HP:0000343)

Treatment Example (Losartan))

Low-set ears (HP:0000369)

PhenotypicFeature Example for exclusion of LV dysfunction

Long philtrum (HP:0000568)

Biosample Example – muscle biopsy

Muscle weakness (HP:0001324)

This is an example of a patient resource to be used in the assocaited patient examples. It is not representative of phenopackets patient’s data representation

This is an incomplete example that used as a placeholder for a curated Practitioner example

This is an incomplete example that used as a placeholder for a curated specimen example

Reduced visual acuity (HP:0007663)

Retinal detachment (HP:0000541)

Transposition of the great arteries (HP:0001669)

Measurement Example for thrombocytopenia

Phenopacket Example for autosomal dominant vitreoretinochoroidopathy