TEMPLATE Cohort (Cohort)

Name: Cohort
License: http://creativecommons.org/licenses/by-sa/3.0/

TEMPLATE ID	Cohort
Concept	Cohort
Description	This dataset describes a group of individuals related in some phenotypic or genotypic aspect. For instance, a cohort can consist of individuals all of whom have been diagnosed with a certain disease or have been found to have a certain phenotypic feature.
Purpose	This dataset describes a group of individuals related in some phenotypic or genotypic aspect. For instance, a cohort can consist of individuals all of whom have been diagnosed with a certain disease or have been found to have a certain phenotypic feature.
References
Authors	date: 2019-09-26; name: Heather Leslie; organisation: Atomica Informatics; email: heather.leslie@atomicainformatics.com
Other Details Language	date: 2019-09-26; name: Heather Leslie; organisation: Atomica Informatics; email: heather.leslie@atomicainformatics.com
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: 93b4ff978ac05ffae32a89139be30b3c PARENT:MD5-CAM-1.0.1: F1AE88E842C8441C1505E7DEBF69C395
Language used	en
Citeable Identifier	1013.26.236
Root archetype id	openEHR-EHR-EVALUATION.pp_cohort.v0
Cohort	Cohort: Phenopacket cohort
Data
id	id: *
description	description: *
Phenopacket	Phenopacket: Phenotypic framework
id	id: *
subject	subject: *
Phenotypic feature	Phenotypic feature: Phenotypic feature
description	description: Human-readable verbiage NOT for structured text.
type	type: * For example: "HP::0000520\|Proptosis".
negated	negated: * Assumed value: false
severity	severity: Description of the severity of the feature described in type representing HP:0012824. For example: "HP::0012825\|Mild".
modifier	modifier: representing one or more terms from HP:0012823
onset	onset: ??The age group in which disease manifestations appear. HP:0003674 HP:0011462 For example: "HP::0003577\|Congenital onset".
Evidence	Evidence: Phenopacket evidence
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\|".
External reference	External reference: Phenopacket external reference
id	id: *
description	description: *
Biosample	Biosample: biosample
id	id: Arbitrary identifier. For example: "sample1".
individual id	individual id: Arbitrary identifier. For example: "patient1".
description	description: Arbitrary text
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 \|".
taxonomy	taxonomy: Species of the sampled individual. To be represented as a code and a text label pair.
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
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\|".
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\|".
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\|".
diagnostic_markers	diagnostic_markers: Clinically relevant biomarkers. To be represented as a code and a text label pair.
Procedure	Procedure: Phenopacket procedure
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".
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".
is_control_sample	is_control_sample: Whether the sample is being used as a normal control. Assumed value: false
Gene	Gene: Phenopacket gene
gene symbol	gene symbol: *
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.
HgvsAllele	HgvsAllele: *
id	id: An arbitrary identifier.
hgvs	hgvs: * For example: NM_000226.3:c.470T>G.
IscnAllele	IscnAllele: IscnAllele
id	id: An arbitrary identifier. For example: ""ISCN:12345""
iscn	iscn: * For example: "t(8;9;11)(q12;p24;p12)".
SpdiAllele	SpdiAllele: SpdiAllele
id	id: An arbitrary identifier. For example: "clinvar:13294".
seq_id	seq_id: * For example: "NC_000001.10".
position	position: * For example: "12346".
deleted_sequence	deleted_sequence: * For example: "A".
inserted_sequence	inserted_sequence: * For example: "G".
VcfAllele
genome_assembly	genome_assembly: * For example: "GRCh38".
id	id: An arbitrary identifier.
chr	chr: * For example: "2".
pos	pos: * For example: "134327882".
re	re: * For example: "A".
alt	alt: * For example: "C" or "<DUP>".
info	info: * For example: "END=43500;SVTYPE=DUP;CHR2=1;SVLEN=29000;".
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).
Disease	Disease: Phenopacket disease
term	term: An coded term that represents the disease.
onset	onset: * Duration>=P0D Units: Year Month Day Coded Text Interval of DurationLower constraint: >=P0D Units: Year Month Day Upper constraint: >=P0D Units: Year Month Day
tumor_stage	tumor_stage: *
HtsFile	HtsFile: Phenopacket HtsFile
uri	uri: A valid URI. For example: "file://data/genomes/germline_wgs.vcf.gz".
description	description: Arbitrary description of the file For example; "Matched normal germline sample".
hts_format	hts_format: * For example: "VCF". UNKNOWN SAM BAM CRAM VCF BCF GVCF
genome_assembly	genome_assembly: * For example: "GRCh38".
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".
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".
MetaData	MetaData: Phenopacket MetaData
created	created: Representation of the time when this object was created. For example: "2019-04-01T15:10:17.808Z".
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.
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).
Resource	Resource: Phenopacket resource
id	id: *
name	name: *
namespace_prefix	namespace_prefix: *
url	url: *
version	version: *
iri-prefix	iri-prefix: *
Update	Update: Phenopacket update
timestamp	timestamp: ISO8601 UTC timestamp at which this record was updated
updated_by	updated_by: Information about the person/organisation/network that has updated the phenopacket.
comment	comment: Textual comment about the changes made to the content and/or reason for the update.
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.
External reference	External reference: Phenopacket external reference
id	id: *
description	description: *