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Task/enum update #174

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Dec 17, 2024
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Merged

Task/enum update #174

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df57f95
added IDAT to ResearchDataFileFormatEnum
mauerk Dec 17, 2024
d233233
updated FlowCellTypeEnums
mauerk Dec 17, 2024
901d752
updated LibraryPreparationKitRetailNameEnum
mauerk Dec 17, 2024
9f27ba7
generated artifacts
mauerk Dec 17, 2024
666f2a5
addressed comment; updated artifacts
mauerk Dec 17, 2024
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13 changes: 13 additions & 0 deletions docs/schema_markdown/FlowCellTypeEnum.md
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Expand Up @@ -16,8 +16,21 @@ URI: [GHGA:FlowCellTypeEnum](https://w3id.org/GHGA/FlowCellTypeEnum)

| Text | Description | Meaning | Other Information |
| :--- | :---: | :---: | ---: |
| ELEMENT_BIOSCIENCES_AVITI_LOW_OUTPUT | Usage of Element Biosciences Aviti Low Output flow cell. | | |
| ELEMENT_BIOSCIENCES_AVITI_MID_OUTPUT | Usage of Element Biosciences Aviti Mid Output flow cell. | | |
| ELEMENT_BIOSCIENCES_AVITI_HIGH_OUTPUT | Usage of Element Biosciences Aviti High Output flow cell. | | |
| ILLUMINA_NOVA_SEQ_SP | Usage of Illumina NovaSeq SP flow cell. | | |
| ILLUMINA_NOVA_SEQ_S1 | Usage of Illumina NovaSeq S1 flow cell. | | |
| ILLUMINA_NOVA_SEQ_S2 | Usage of Illumina NovaSeq S2 flow cell. | | |
| ILLUMINA_NOVA_SEQ_S4 | Usage of Illumina NovaSeq S4 flow cell. | | |
| ILLUMINA_NOVA_SEQ_XPLUS_1_5B | Usage of Illumina NovaSeq X Plus 1.5B flow cell. | | |
| ILLUMINA_NOVA_SEQ_XPLUS_10B | Usage of Illumina NovaSeq X Plus 10B flow cell. | | |
| ILLUMINA_NOVA_SEQ_XPLUS_25B | Usage of Illumina NovaSeq X Plus 25B flow cell. | | |
| ILLUMINA_MISEQ_MICRO | Usage of Illumina MiSeq Micro flow cell. | | |
| ILLUMINA_MISEQ_NANO | Usage of Illumina MiSeq Nano flow cell. | | |
| ILLUMINA_NEXTSEQ_HIGH_OUTPUT | Usage of Illumina NextSeq High Output flow cell. | | |
| ILLUMINA_NEXTSEQ_MID_OUTPUT | Usage of Illumina NextSeq Mid Output flow cell. | | |
| PACBIO_SEQUELL_II | Usage of PacBio Sequell II flow cell. | | |
| PROMETHION | Usage of PromethION flow cell. | | |
| FLONGLE | Usage of Flongle flow cell. | | |
| MINION | Usage of MinION flow cell. | | |
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7 changes: 7 additions & 0 deletions docs/schema_markdown/LibraryPreparationKitRetailNameEnum.md
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Expand Up @@ -18,6 +18,13 @@ URI: [GHGA:LibraryPreparationKitRetailNameEnum](https://w3id.org/GHGA/LibraryPre
| :--- | :---: | :---: | ---: |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V2 | 10X Genomics Chromium Single Cell 3' v2 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V3 | 10X Genomics Chromium Single Cell 3' v3 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V4 | 10X Genomics Chromium Single Cell 3' v4 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_SINGLE_CELL_5_V3 | 10X Genomics Chromium Single Cell 5' v3 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_ATAC_V2 | 10X Genomics Chromium ATAC v2 Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_MULTIOME_ATAC_RNA | 10X Genomics Chromium Multiome ATAC + RNA Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_VISIUM_FF | 10X Genomics Chromium Visium FF Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_VISIUM_FFPE | 10X Genomics Chromium Visium FFPE Reagent Kit | | |
| 10X_GENOMICS_CHROMIUM_VISIUM_CYTASSIST | 10X Genomics Chromium Visium Cytassist Reagent Kit | | |
| ACCEL_NGS_2_S_PLUS_DNA_LIBRARY_KIT | Accel-NGS 2S Plus DNA Library Kit | | |
| ACCEL_NGS_METHYL_SEQ_DNA | Accel-NGS Methyl-Seq DNA Library Kit | | |
| AGILENT_STRAND_SPECIFIC_RNA | Agilent SureSelect Strand Specific RNA Library Preparation Kit | | |
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1 change: 1 addition & 0 deletions docs/schema_markdown/ResearchDataFileFormatEnum.md
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Expand Up @@ -24,5 +24,6 @@ URI: [GHGA:ResearchDataFileFormatEnum](https://w3id.org/GHGA/ResearchDataFileFor
| D | Raw .d files for mass spectrometry proteomics data. | | |
| MZML | mzML format for mass spectrometry proteomics data. | | |
| MZDATA | mzData for mass spectrometry proteomics data. | | |
| IDAT | IDAT file format for BeadArray data. | | |
| OTHER | A file format not captured by the controlled vocabulary. | | |

Binary file modified spreadsheets/ghga_submission_full.xlsx
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63 changes: 63 additions & 0 deletions src/schema/submission.yaml
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Expand Up @@ -1790,6 +1790,9 @@ enums:
MZDATA:
description: >-
mzData for mass spectrometry proteomics data.
IDAT:
description: >-
IDAT file format for BeadArray data.
OTHER:
description: >-
A file format not captured by the controlled vocabulary.
Expand Down Expand Up @@ -2022,6 +2025,27 @@ enums:
10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V3:
description: >-
10X Genomics Chromium Single Cell 3' v3 Reagent Kit
10X_GENOMICS_CHROMIUM_SINGLE_CELL_3_V4:
description: >-
10X Genomics Chromium Single Cell 3' v4 Reagent Kit
10X_GENOMICS_CHROMIUM_SINGLE_CELL_5_V3:
description: >-
10X Genomics Chromium Single Cell 5' v3 Reagent Kit
10X_GENOMICS_CHROMIUM_ATAC_V2:
description: >-
10X Genomics Chromium ATAC v2 Reagent Kit
10X_GENOMICS_CHROMIUM_MULTIOME_ATAC_RNA:
description: >-
10X Genomics Chromium Multiome ATAC + RNA Reagent Kit
10X_GENOMICS_CHROMIUM_VISIUM_FF:
description: >-
10X Genomics Chromium Visium FF Reagent Kit
10X_GENOMICS_CHROMIUM_VISIUM_FFPE:
description: >-
10X Genomics Chromium Visium FFPE Reagent Kit
10X_GENOMICS_CHROMIUM_VISIUM_CYTASSIST:
description: >-
10X Genomics Chromium Visium Cytassist Reagent Kit
ACCEL_NGS_2_S_PLUS_DNA_LIBRARY_KIT:
description: >-
Accel-NGS 2S Plus DNA Library Kit
Expand Down Expand Up @@ -2771,12 +2795,51 @@ enums:
description: >-
Permitted values for flow cell type.
permissible_values:
ELEMENT_BIOSCIENCES_AVITI_LOW_OUTPUT:
description: >-
Usage of Element Biosciences Aviti Low Output flow cell.
ELEMENT_BIOSCIENCES_AVITI_MID_OUTPUT:
description: >-
Usage of Element Biosciences Aviti Mid Output flow cell.
ELEMENT_BIOSCIENCES_AVITI_HIGH_OUTPUT:
description: >-
Usage of Element Biosciences Aviti High Output flow cell.
ILLUMINA_NOVA_SEQ_SP:
description: >-
Usage of Illumina NovaSeq SP flow cell.
ILLUMINA_NOVA_SEQ_S1:
description: >-
Usage of Illumina NovaSeq S1 flow cell.
ILLUMINA_NOVA_SEQ_S2:
description: >-
Usage of Illumina NovaSeq S2 flow cell.
ILLUMINA_NOVA_SEQ_S4:
description: >-
Usage of Illumina NovaSeq S4 flow cell.
ILLUMINA_NOVA_SEQ_XPLUS_1_5B:
description: >-
Usage of Illumina NovaSeq X Plus 1.5B flow cell.
ILLUMINA_NOVA_SEQ_XPLUS_10B:
description: >-
Usage of Illumina NovaSeq X Plus 10B flow cell.
ILLUMINA_NOVA_SEQ_XPLUS_25B:
description: >-
Usage of Illumina NovaSeq X Plus 25B flow cell.
ILLUMINA_MISEQ_MICRO:
description: >-
Usage of Illumina MiSeq Micro flow cell.
ILLUMINA_MISEQ_NANO:
description: >-
Usage of Illumina MiSeq Nano flow cell.
ILLUMINA_NEXTSEQ_HIGH_OUTPUT:
description: >-
Usage of Illumina NextSeq High Output flow cell.
ILLUMINA_NEXTSEQ_MID_OUTPUT:
description: >-
Usage of Illumina NextSeq Mid Output flow cell.
PACBIO_SEQUELL_II:
description: >-
Usage of PacBio Sequell II flow cell.
PROMETHION:
description: >-
Usage of PromethION flow cell.
Expand Down
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