bigbio / bigbio/proteomics-sample-metadata

Extending SDRF for immunopeptidomics

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Description

Suggestion to support / extend SDRF for immunopeptidomics:
- Use the SDRF as-is
- Add _mandatory_ column for the antibody that was used to pull down the MHC-Peptide-Complex containing [OLS ontologies](https://www.ebi.ac.uk/ols4/ontologies/eco/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FECO_0008039?lang=en).
- Example:`comment[antibody purification] -> AC=ECO_0008075;NT=Antibody purification - W6/32`
- Add _mandatory_ column for the MHC class that is targeted by the antibody using [OLS ontolgies](https://www.ebi.ac.uk/ols4/ontologies/mro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMRO_0001454?lang=en)
- Example: `comment[mhc protein complex] -> AC=MRO_0001454;NT=human MHC class I`
- Add _optional_ column (or multiple -> up to 14 columns (MHCI+II alleles)) for HLA type annotations using [OLS ontologies](https://www.ebi.ac.uk/ols4/ontologies/mro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMRO_0001454?lang=en). The `NT` value should adhere to the [official nomenclature](https://hla.alleles.org/nomenclature/naming.html). `Not available` should be allowed in there since MHC type is not known for all immunopeptidomics datasets
- Example: `characteristics[mhc type] -> AC=MRO_0031591;NT=HLA-A*01:06`

Contributor guide

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Research direction

Start by reviewing the repository's existing SDRF conventions and validation rules, then compare them with the proposed antibody purification, MHC class, and HLA type annotations. Done means the specification clearly defines the mandatory and optional fields, ontology identifiers, nomenclature requirements, and handling of unavailable MHC types.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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