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Add BioSample Accession column to SDRF-Proteomics format #747

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Copilot Aug 18, 2025
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Add BioSample Accession column to SDRF-Proteomics format
Copilot Aug 18, 2025
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10 changes: 7 additions & 3 deletions sdrf-proteomics/README.adoc
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Expand Up @@ -178,13 +178,17 @@ The Sample metadata has different Categories/Headings to organize all the attrib
- *characteristics[organism part]*: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, (e.g., liver)
- *characteristics[cell type]*: A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.

Additionally, the following OPTIONAL characteristics can be provided to enable better integration with other repositories:

- *characteristics[BioSample Accession]*: The BioSample accession number that identifies the sample in EBI BioSamples database. This enables cross-referencing with other omics datasets and external repositories. Example values include `SAMEA115947232` or `not available` if no BioSample exists.

Example:

|===
| source name | characteristics[organism] | characteristics[organism part] | characteristics[disease] | characteristics[cell type]
| source name | characteristics[organism] | characteristics[organism part] | characteristics[disease] | characteristics[cell type] | characteristics[BioSample Accession]

|sample_treat | homo sapiens | liver | liver cancer | not available
|sample_control | homo sapiens | liver | liver cancer | not available
|sample_treat | homo sapiens | liver | liver cancer | not available | SAMEA115947232
|sample_control | homo sapiens | liver | liver cancer | not available | not available
|===

NOTE: Additional characteristics can be added depending on the type of the experiment and sample. The https://github.com/bigbio/proteomics-metadata-standard/tree/master/templates[SDRF-Proteomics templates] defines a set of templates and checklists of properties that should be provided depending on the proteomics experiment.
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1 change: 1 addition & 0 deletions templates/README.adoc
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Expand Up @@ -27,6 +27,7 @@ NOTE: Each of the templates is a tsv file with the minimum columns to describe t
|characteristics[developmental stage] | |:zero: |:zero: | |:zero: |
|characteristics[sex] | |:white_check_mark: |:zero: | | |
|characteristics[disease] | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: | |:white_check_mark:
|characteristics[BioSample Accession] | :zero: |:zero: |:zero: |:zero: |:zero: |:zero:
|characteristics[organism part] | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
|characteristics[cell type] | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
|characteristics[individual] | |:zero: |:zero: |:zero: |:zero: |:zero:
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2 changes: 1 addition & 1 deletion templates/sdrf-cell-line.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[cell line] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[BioSample Accession] characteristics[cell line] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
2 changes: 1 addition & 1 deletion templates/sdrf-default.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[BioSample Accession] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]

2 changes: 1 addition & 1 deletion templates/sdrf-human.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[ancestry category] characteristics[age] characteristics[sex] characteristics[disease] characteristics[individual] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details]
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[ancestry category] characteristics[age] characteristics[sex] characteristics[disease] characteristics[BioSample Accession] characteristics[individual] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details]
2 changes: 1 addition & 1 deletion templates/sdrf-invertebrates.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[cell type] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details]
source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[BioSample Accession] characteristics[cell type] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details]
2 changes: 1 addition & 1 deletion templates/sdrf-plants.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details]
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[BioSample Accession] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[instrument] comment[cleavage agent details]
2 changes: 1 addition & 1 deletion templates/sdrf-vertebrates.sdrf.tsv
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source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[developmental stage] characteristics[disease] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[developmental stage] characteristics[disease] characteristics[BioSample Accession] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]