| ARCHETYPE ID | openEHR-EHR-CLUSTER.pp_biosample.v0 |
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| Concept | Phenopacket biosample |
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| Description | biosample |
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| Purpose | |
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| References | |
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| Copyright | © openEHR Foundation |
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| Authors | Author name: Heather Leslie
Organisation: Atomica Informatics
Email: heather.leslie@atomicainformatics.com
Date originally authored: 2019-09-25
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| Other Details Language | Author name: Heather Leslie
Organisation: Atomica Informatics
Email: heather.leslie@atomicainformatics.com
Date originally authored: 2019-09-25
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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: DAF8772578930B5C7EF35C9382FCACDC
- Build Uid: 1fab9318-a552-48f2-a219-b4a00ff3c251
- Revision: 0.0.1-alpha
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| Keywords | |
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| Lifecycle | in_development |
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| UID | 208c36cf-16ec-4981-b4e2-4e79743ac345 |
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| Language used | en |
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| Citeable Identifier | 1013.1.4150 |
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| Revision Number | 0.0.1-alpha |
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| items | |
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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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| phenotypic_features | phenotypic_features: List of phenotypic abnormalities of the sample.
Include:
openEHR-EHR-CLUSTER.pp_phenotypic_feature.v0 |
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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".
Choice of:
 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: The procedure used to extract the biosample.
For example: "NCIT:C5189|Radical Cystoprostatectomy|".
Include:
openEHR-EHR-CLUSTER.pp_procedure.v0 |
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| hts_files | hts_files: list of high-throughput sequencing files derived from the biosample
Include:
openEHR-EHR-CLUSTER.pp_htsfile.v0 |
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| variants | variants: List of variants determined to be present in the biosample.
Include:
openEHR-EHR-CLUSTER.pp_variant.v0 |
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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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| Other contributors | |
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| Translators | |
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