Test pull request

[mbiletska]

Hi,
My name is Maryna, and I created an SDRF annotation for PXD009172.
The file was validated using the SDRF Validator and manually reviewed against the associated publication.
Thanks!

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[coderabbitai]

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[Copilot]

Pull request overview

Adds a new SDRF annotation file for ProteomeXchange dataset PXD009172 under the repository’s datasets/ collection, expanding the set of curated, validator-ready SDRF TSVs for downstream parsing/validation workflows.

Changes:

• Added datasets/PXD009172/PXD009172.sdrf.tsv containing sample- and run-level metadata for PXD009172.
• Populated key MS acquisition, instrument, digestion, tolerance, and modification metadata columns for 21 assays.

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[ypriverol]

Thanks for the PXD009172 annotation, @mbiletska! The SDRF passes parse_sdrf validate-sdrf structurally, the 21 sample rows map cleanly to the actual .raw files in the PRIDE record, and the search parameters (Trypsin, fixed Carbamidomethyl, variable Oxidation, 4.5 ppm precursor / 0.5 Da fragment) match the publication's methods. Nice work anchoring it to the source.

A few issues to address before merge (details inline):

1. .DS_Store committed — a macOS artifact was added at the repo root; please remove it and consider adding it to .gitignore.
2. Instrument — listed as Orbitrap Velos Pro, but the PRIDE record and the paper (PMID: 30510230) say LTQ Orbitrap Velos (a different PSI-MS instrument). Recommend NT=LTQ Orbitrap Velos;AC=MS:1001742, which also matches the NT=...;AC=... format used by every other file in the repo.
3. Missing comment[sdrf version] / comment[sdrf template] — present in 307/308 existing files; please add them for consistency.
4. Minor — the two olfactory-disorder disease labels trigger ontology warnings (not errors); see the inline note.

Items 1–3 are worth fixing; 4 is optional. Happy to help once updated.

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Generated by Claude Code

[ypriverol]

Missing comment[sdrf version] and comment[sdrf template] columns.

307 of the 308 existing dataset files in this repo include these two trailing columns — this PR would be the only file without them. Please add them, e.g.:

• comment[sdrf version] → 1.1
• comment[sdrf template] → default (or human, matching the template you annotated against)

Minor (disease ontology): parse_sdrf validate-sdrf passes, but emits warnings that idiopathic olfactory disorder and post-infectious olfactory disorder in characteristics[disease]/factor value[disease] aren't found in the disease ontologies (mondo;efo;doid;ncit;pato). If a matching ontology term exists, prefer the NT=...;AC=... form; otherwise it's fine to keep the study-defined labels — just flagging since CI surfaces them.

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Generated by Claude Code

[ypriverol]

@nithujohn Can you help here?