| TEMPLATE ID | Phenopacket |
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| Concept | Phenopacket |
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| Description | A Phenopacket is an anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses. |
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| Use | It can be used for multiple use cases. For instance, it can be used to describe the phenotypic findings observed in an individual with a disease that is being studied or for an individual in whom the diagnosis is being sought. The phenopacket can contain information about genetic findings that are causative of the disease, or alternatively it can contain a reference to a VCF file if exome sequencing is being performed as a part of the differential diagnostic process. A Phenopacket can also be used to describe the constitutional phenotypic findings of an individual with cancer (a Biosample should be used to describe the phenotypic abnormalities directly associated with an extirpated or biopsied tumor). |
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| Purpose | A Phenopacket is an anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses. |
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| References | |
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| Authors | date: 2019-09-26; name: Heather Leslie; organisation: Atomica Informatics; email: heather.leslie@atomicainformatics.com |
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| Other Details Language | date: 2019-09-26; name: Heather Leslie; organisation: Atomica Informatics; email: heather.leslie@atomicainformatics.com |
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| Other Details (Language Independent) | - Licence: This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/.
- Custodian Organisation: openEHR Foundation
- Original Namespace: org.openehr
- Original Publisher: openEHR Foundation
- Custodian Namespace: org.openehr
- MD5-CAM-1.0.1: cf3a7401834c08c93c9e7bb1640c83c6
- PARENT:MD5-CAM-1.0.1: 9BE3F8F0DFED663A22D1D73600BA675E
|
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| Language used | en |
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| Citeable Identifier | 1013.26.234 |
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| Root archetype id | openEHR-EHR-CLUSTER.pp_phenopacket_framework.v0 |
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| Phenopacket | Phenopacket: Phenotypic framework |
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| id | id: * |
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| subject | subject: * |
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| Phenotypic feature | Phenotypic feature: Phenotypic feature |
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| description | description: Human-readable verbiage NOT for structured text. |
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| type | type: *
For example: "HP::0000520|Proptosis". |
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| negated | negated: *
Assumed value: false |
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| severity | severity: Description of the severity of the feature described in type representing HP:0012824.
For example: "HP::0012825|Mild". |
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| modifier | modifier: representing one or more terms from HP:0012823 |
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| onset | onset: ??The age group in which disease manifestations appear.
HP:0003674
HP:0011462
For example: "HP::0003577|Congenital onset". |
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| Evidence | Evidence: Phenopacket evidence |
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| evidence_code | evidence_code: An coded value that represents the evidence type.
For example: "ECO::0006017|author statement from published clinical study used in manual assertion|". |
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| External reference | External reference: Phenopacket external reference |
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| id | id: * |
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| description | description: * |
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| Biosample | Biosample: biosample |
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| id | id: Arbitrary identifier.
For example: "sample1". |
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| individual id | individual id: Arbitrary identifier.
For example: "patient1". |
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| description | description: Arbitrary text |
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| sampled_tissue | sampled_tissue: Tissue from which the sample was taken.
To be represented as a code and a text label pair. For example: "UBERON::0001256 | wall of urinary bladder |". |
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| taxonomy | taxonomy: Species of the sampled individual.
To be represented as a code and a text label pair. |
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| individual_age_at_collection | individual_age_at_collection: Age, or age range, of the proband at the time the sample was taken
For example: "P52Y2M".
 Duration Interval of Duration
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| histological diagnosis | histological diagnosis: Disease diagnosis that was inferred from the histological examination.
To be represented as a code and a text label pair. For example: NCIT::C39853|Infiltrating Urothelial Carcinoma|". |
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| tumor_progression | tumor_progression: Indicates primary, metastatic, recurrent.
To be represented as a code and a text label pair. For example: "NCIT::C84509|Primary Malignant Neoplasm|". |
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| tumor_grade | tumor_grade: List of terms representing the tumor grade or stage.
To be represented as a code and a text label pair. For example: "NCIT::C48766|pT2b Stage Finding|" or "NCIT::C48750|pN2 Stage Finding|". |
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| diagnostic_markers | diagnostic_markers: Clinically relevant biomarkers.
To be represented as a code and a text label pair. |
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| Procedure | Procedure: Phenopacket procedure |
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| code | code: clinical procedure performed on a subject
To be represented as a code and a text label pair. For example: "NCIT::C28743|Punch Biopsy". |
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| body_site | body_site: Specific body site if unable to represent this as the code.
To be represented as a code and a text label pair. For example: "UBERON::0003403|skin of forearm". |
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| is_control_sample | is_control_sample: Whether the sample is being used as a normal control.
Assumed value: false |
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| Gene | Gene: Phenopacket gene |
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| gene symbol | gene symbol: * |
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| Variant | Variant: This archetype should be used to describe candidate variants or diagnosed causative variants. There is currently no standard variant nomenclature that can represent all kinds of genetic variation that is relevant to human medicine, science, and model organisms. Therefore, we represent variants using the keyword oneof, which is used in protobuf for an item with many optional fields where at most one field will be set at the same time. Variant messages contain an allele and the zygosity of the allele.
Alleles can be listed using HGVS, VCF, SPDI or ISCN notation. The phenopacket schema will implement the GA4GH Variation Representation Specification once that is mature. The VR-Spec will be the recommended option in some settings.
See: https://vr-spec.readthedocs.io/en/1.0rc/
See: https://github.com/ga4gh-beacon/specification/blob/master/beacon.yaml
The Variant element itself is an optional element of a Phenopacket or Biosample. If it is present, the Phenopacket standard has the following requirements.
Alleles can refer to external sources, for example the ClinGen allele registry, ClinVar, dbSNP, dbVAR etc. using the id field. It is RECOMMENDED to use a CURIE identifier and corresponding Resource.
N.B. phase information for alleles are not represented in this model. |
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| HgvsAllele | HgvsAllele: * |
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| id | id: An arbitrary identifier. |
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| hgvs | hgvs: *
For example: NM_000226.3:c.470T>G. |
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| IscnAllele | IscnAllele: IscnAllele |
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| id | id: An arbitrary identifier.
For example: ""ISCN:12345"" |
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| iscn | iscn: *
For example: "t(8;9;11)(q12;p24;p12)". |
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| SpdiAllele | SpdiAllele: SpdiAllele |
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| id | id: An arbitrary identifier.
For example: "clinvar:13294". |
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| seq_id | seq_id: *
For example: "NC_000001.10". |
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| position | position: *
For example: "12346". |
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| deleted_sequence | deleted_sequence: *
For example: "A". |
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| inserted_sequence | inserted_sequence: *
For example: "G". |
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| VcfAllele | |
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| genome_assembly | genome_assembly: *
For example: "GRCh38". |
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| id | id: An arbitrary identifier. |
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| chr | chr: *
For example: "2". |
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| pos | pos: *
For example: "134327882". |
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| re | re: *
For example: "A". |
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| alt | alt: *
For example: "C" or "<DUP>". |
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| info | info: *
For example: "END=43500;SVTYPE=DUP;CHR2=1;SVLEN=29000;". |
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| zygosity | zygosity: *
The zygosity of the variant as determined in all of the samples represented in this Phenopacket is represented using a list of terms taken from the Genotype Ontology (GENO). For instance, if a variant affects one of two alleles at a certain locus, we could record the zygosity using the term heterozygous (GENO:0000135). |
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| Disease | Disease: Phenopacket disease |
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| term | term: An coded term that represents the disease. |
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| onset | onset: *
- Duration>=P0D
Units:  Coded Text- Interval of DurationLower constraint: >=P0D
Units:
Upper constraint: >=P0D
Units:
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| tumor_stage | tumor_stage: * |
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| HtsFile | HtsFile: Phenopacket HtsFile |
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| uri | uri: A valid URI.
For example: "file://data/genomes/germline_wgs.vcf.gz". |
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| description | description: Arbitrary description of the file
For example; "Matched normal germline sample". |
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| hts_format | hts_format: *
For example: "VCF".
- UNKNOWN
- SAM
- BAM
- CRAM
- VCF
- BCF
- GVCF
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| genome_assembly | genome_assembly: *
For example: "GRCh38". |
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| individual_identifier | individual_identifier: The Individual.id component required for mapping between the Individual.id or Biosample.id to the sample identifier in the HTS file.
For example: "patient23456". |
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| sample_identifier | sample_identifier: The Biosample.id component required for mapping between the Individual.id or Biosample.id to the sample identifier in the HTS file.
For example: "NA12345". |
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| MetaData | MetaData: Phenopacket MetaData |
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| created | created: Representation of the time when this object was created.
For example: "2019-04-01T15:10:17.808Z". |
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| created by | created by: Name of person who created the phenopacket.
This is a string that represents an identifier for the contributor/ program. The expected syntax and semantics are application-dependent. |
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| submitted by | submitted by: Name of person who submitted the phenopacket.
This is a string that represents an identifier for the person who submitted the phenopacket (who may not be the person who created the phenopacket). |
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| Resource | Resource: Phenopacket resource |
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| id | id: * |
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| name | name: * |
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| namespace_prefix | namespace_prefix: * |
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| url | url: * |
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| version | version: * |
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| iri-prefix | iri-prefix: * |
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| Update | Update: Phenopacket update |
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| timestamp | timestamp: ISO8601 UTC timestamp at which this record was updated |
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| updated_by | updated_by: Information about the person/organisation/network that has updated the phenopacket. |
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| comment | comment: Textual comment about the changes made to the content and/or reason for the update. |
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| phenopacket_schema_version | phenopacket_schema_version: Schema version of the current phenopacket.
A string representing the version of the phenopacket-schema according to which a phenopacket was made. |
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| External reference | External reference: Phenopacket external reference |
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| id | id: * |
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| description | description: * |
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