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Hot fix (#62)
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* Fix range for slots in Dataset
* Bump version to 0.7.0
* Add case control status slot to Sample
* Add enum for capturing paired end or single end status
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deepakunni3 authored Apr 29, 2022
1 parent 97e6ec2 commit 4664636
Showing 1 changed file with 36 additions and 5 deletions.
41 changes: 36 additions & 5 deletions src/schema/ghga.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ id: https://w3id.org/GHGA-Metadata-Schema
name: GHGA-Metadata-Schema
description: >-
The metadata schema for the German Human Genome-Phenome Archive (GHGA).
version: 0.6.0
version: 0.7.0

imports:
- linkml:types
Expand Down Expand Up @@ -713,6 +713,7 @@ classes:
- name
- type
- description
- case control status
- vital status at sampling
- isolation
- storage
Expand Down Expand Up @@ -1086,29 +1087,30 @@ classes:
inlined_as_list: true
has experiment:
description: >-
One or more Analysis entities that are referenced by this Dataset.
range: analysis
One or more Experiment entities that are referenced by this Dataset.
range: experiment
multivalued: true
inlined: true
inlined_as_list: true
has sample:
description: >-
One or more Sample entities that are referenced by this Dataset.
range: study
range: sample
multivalued: true
required: true
inlined: true
inlined_as_list: true
has analysis:
description: >-
One or more Analysis entities that are referenced by this Dataset.
range: study
range: analysis
multivalued: true
inlined: true
inlined_as_list: true
has file:
description: >-
One or more File entities that collectively are part of this Dataset.
range: file
required: true
multivalued: true
inlined: true
Expand Down Expand Up @@ -2172,6 +2174,10 @@ slots:
description: >-
Denotes whether a submitted FASTQ file contains forward (R1) or reverse (R2) reads for paired-end sequencing.
The number that identifies each read direction in a paired-end nucleotide sequencing replications.
range: paired or single end enum
in_subset:
- recommended
- public

reference chromosome:
description: >-
Expand Down Expand Up @@ -2267,6 +2273,14 @@ slots:
- recommended
- public

case control status:
description: >-
Whether the sample is to be treated as Case or Control in a Study.
range: case control status enum
in_subset:
- recommended
- public

vital status at sampling:
description: >-
Vital Status of an Individual at the point of sampling (eg:'Alive', 'Deceased').
Expand Down Expand Up @@ -2441,6 +2455,23 @@ enums:
description: >-
Other format.
case control status enum:
description: >-
Enum to capture whether a Sample in a Study is to be considered as Case or Control.
permissible_values:
control:
description: The Sample is to be treated as Control
case:
description: The Sample is to be treated as Case

paired or single end enum:
description: >-
Enum to capture whether a sequencing experiment generates reads that are Paired-end or Single-end.
permissible_values:
paired:
description: The reads are Paired-end
single:
description: The reads are Single-end

submission status enum:
description: >-
Expand Down

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