Add BioSample Accession column to SDRF-Proteomics format

[Copilot]

This PR adds support for linking proteomics samples with EBI BioSamples through a new optional characteristics[BioSample Accession] column in the SDRF-Proteomics format.

Changes Made

Documentation Updates:

• Added documentation for the new characteristics[BioSample Accession] column in sdrf-proteomics/README.adoc
• Updated the example table to demonstrate usage with sample accession SAMEA115947232
• Added the column to the template comparison table in templates/core-templates/README.adoc (marked as optional for all templates)

Template Updates:

• Added characteristics[BioSample Accession] column to all 6 core template files:
  • templates/core-templates/sdrf-default.sdrf.tsv
  • templates/core-templates/sdrf-human.sdrf.tsv
  • templates/core-templates/sdrf-vertebrates.sdrf.tsv
  • templates/core-templates/sdrf-invertebrates.sdrf.tsv
  • templates/core-templates/sdrf-plants.sdrf.tsv
  • templates/core-templates/sdrf-cell-line.sdrf.tsv

Benefits

• Enables cross-referencing proteomics datasets with EBI BioSamples database
• Facilitates integration with other omics repositories (e.g., ENA) through BioSamples
• Supports standard BioSample accession formats like SAMEA115947232
• Uses not available when no BioSample exists
• Maintains backward compatibility by making the column optional

Implementation Notes

This PR is based on the dev branch to incorporate the latest repository structure changes, including the reorganization of templates into the templates/core-templates/ directory.

Validation

The changes have been tested with the sdrf-pipelines validation tool and do not break existing functionality. The new column is accepted by the validator without issues.

Fixes #745.

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[ypriverol]

@copilot Can you do the PR against dev branch not master?

[Copilot]

@copilot Can you do the PR against dev branch not master?

I've successfully rebased the PR to use the dev branch instead of master as the base.

The changes include:

• Updated BioSample Accession documentation and examples based on the latest dev branch (v1.1.0)
• Added the optional characteristics[BioSample Accession] column to all 6 core template files
• Updated the templates comparison table to reflect the new column

The PR now incorporates all the latest changes from the dev branch and applies the BioSample Accession feature on top of that. All changes are minimal and focused on adding the new optional column without breaking existing functionality.

Commit: e5fe9fd

[ypriverol]

@copilot I think you need to close this PR, and start a new one but with your fix against the dev branch, not against the master branch.

[Copilot]

@copilot I think you need to close this PR, and start a new one but with your fix against the dev branch, not against the master branch.

I've created a new branch copilot/fix-745-dev based on the latest dev branch and applied all the BioSample Accession changes to it. The new branch includes:

• Updated documentation in sdrf-proteomics/README.adoc with BioSample Accession column description
• Updated template comparison table in templates/core-templates/README.adoc
• Added characteristics[BioSample Accession] column to all 6 core template files

This addresses the updated file structure in the dev branch (templates moved to templates/core-templates/). The changes are ready in commit 6c6022f and should be used for a new PR against the dev branch instead of master.