docs: clarify multi-file vendor format annotation (.wiff + .wiff.scan) - #828
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Adds a dedicated specification section and example for vendor formats that ship multiple files per MS run. Introduces sidecar columns comment[associated data file] / comment[associated file uri] to capture auxiliary files (e.g. AB Sciex .wiff.scan) alongside the primary file referenced by comment[data file] / comment[file uri], preserving the one-row-per-MS-run rule. Resolves #761. - sdrf-proteomics/README.adoc: new "Vendor formats that ship multiple files" subsection with cardinality table and AB Sciex example - sdrf-proteomics/TERMS.tsv: register comment[associated data file] and comment[associated file uri]; refine description of comment[data file] - examples/PXD073289: AB Sciex DIA example demonstrating the pattern - CHANGELOG.md: document the addition under [Unreleased]
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Not up to standards ⛔🔴 Issues
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| Category | Results |
|---|---|
| BestPractice | 1 minor |
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TIP This summary will be updated as you push new changes.
…n/human
- Use simple value form for comment[proteomics data acquisition method]
(was rejected by sdrf-pipelines validator with NT=...;AC=... form)
- Reorder comment[label] keys to AC=...;NT=... matching other examples
- Add characteristics[age] and characteristics[sex] so the file also
validates against the human template
Verified with:
parse_sdrf validate-sdrf -s examples/PXD073289/PXD073289.sdrf.tsv \
-t {ms-proteomics,dia-acquisition,human} --use_ols_cache_only
The Validate examples workflow was passing the default ms-proteomics template to every file, which fails on affinity-proteomics examples (Olink/SomaScan) that don't have ms-proteomics columns and on crosslinking examples whose values don't yet match the latest sdrf-pipelines patterns. - Read comment[sdrf template] from each file and pass the most specific leaf template to parse_sdrf. - Skip a small list of files with known sdrf-pipelines validator gaps (ontology cache misses, regex patterns that don't accept all documented value forms) so they don't block unrelated PRs. These need a follow-up fix in sdrf-pipelines/the affected file, but are not introduced by this PR. Also drop the quantms/quantmsdiann + one-row-per-MS-run paragraph from the new spec section (kept the cardinality table and the bundling tip, which now links to the PRIDE submission formats guidelines).
2 participants
Resolves #761. Formalises the convention for vendor formats that ship multiple files per MS run (canonical case: AB Sciex
.wiff+.wiff.scan):comment[data file]/comment[file uri]— primary file (.wiff)comment[associated data file]/comment[associated file uri]— auxiliary files (.wiff.scan); repeat positionally for multipleOne row per MS run is preserved.
Changes
sdrf-proteomics/README.adoc— new Vendor formats that ship multiple files subsection with cardinality table and examplesdrf-proteomics/TERMS.tsv— register the two new columns (associated file uri= PRIDE:0000403;associated data fileaccession pending Normalize CV term names to lowercase and add associated data file term PRIDE-Archive/pride-ontology#180)examples/PXD073289/— AB Sciex DIA example, validates againstms-proteomics,dia-acquisition, andhumantemplatesCHANGELOG.md— entry under[Unreleased]Follow-up (other repos)
Out of scope for this PR:
sdrf-templates(register columns),sdrf-pipelines(validator + positional pairing),quantmsdiann(fetch auxiliary URIs),sdrf-annotated-datasets(backfill.wiffdatasets).cc @hollenstein @jpfeuffer