SDRF for PXD063467

[liza-d1]

Hello!

My name is Lisa. I have created a SDRF annotation for data from PXD063467 project on PRIDE. I split it into two SDRF (for DDA and DIA analysis), however I still have a problem with PXD063467_dda.sdrf.tsv validation - for some reason, the validator (https://www.ebi.ac.uk/pride/services/sdrf-validator?utm_source=chatgpt.com) won`t accept "data-dependent acquisition" in comment[proteomics data acquisition method] column. I will try to figure it out, but any suggestions will be greatly appreciated. Otherwise, both annotations were validated and checked manually against the publication.

Best regards!

Summary by CodeRabbit

• Chores
  • Added proteomics dataset PXD063467 with experimental metadata for data-dependent and data-independent acquisition methods, including baseline controls and treatment conditions across multiple compounds with technical replicates.

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[coderabbitai]

📝 Walkthrough

Walkthrough

Two new SDRF annotation files are added for dataset PXD063467: one for DDA acquisition and one for DIA acquisition. Each file contains a header row followed by 96 sample rows mapping AC16 and HCM cell-line cohorts—baseline controls and canagliflozin, dapagliflozin, and empagliflozin treatments at low/high doses—to their respective raw .d data files.

Changes

PXD063467 SDRF Annotation Files

Layer / File(s)	Summary
DDA SDRF: header, AC16 and HCM sample rows datasets/PXD063467/PXD063467_dda.sdrf	Adds the SDRF column header and 96 data rows for DDA proteomics: AC16 controls (rows 2–13), AC16 canagliflozin/dapagliflozin/empagliflozin treatments (rows 14–49), HCM controls (rows 50–61), and HCM canagliflozin/dapagliflozin/empagliflozin treatments (rows 62–97). Each row includes cell-line, compound, dose, exposure time, assay settings, and a data file path. Rows 98–195 are blank trailing lines.
DIA SDRF: header, AC16 and HCM sample rows datasets/PXD063467/PXD063467_dia.sdrf	Adds the SDRF column header and 96 data rows for DIA (diaPASEF/timsTOF HT) proteomics: AC16 cohort (rows 2–49) and HCM PromoCell controls plus compound treatments (rows 50–97). One row (PXD063467_43_Empa_high1) carries sdrf version v1.1.1; all others use v1.1.0.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐇 Hoppin' through the data rows,
Each sample tagged where science goes—
AC16, HCM cells aligned,
DDA and DIA combined.
The rabbit stamps them: looks just right,
Proteomics leaps to bright new light! 🧬

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'SDRF for PXD063467' accurately describes the main change—adding SDRF annotation files for the PXD063467 dataset. It is concise and clearly summarizes the primary change.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

Actionable comments posted: 6

🧹 Nitpick comments (1)

datasets/PXD063467/PXD063467_dda.sdrf (1)

98-196: 💤 Low value

Remove excessive trailing blank lines.

The file contains 99 trailing blank lines after the last data row. While these don't break parsing, they unnecessarily increase file size and reduce readability.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dda.sdrf` around lines 98 - 196, The file
contains 99 trailing blank lines after the last data row in the range from line
98 to line 196. Remove all these excessive trailing blank lines to reduce file
size and improve readability. Ensure the file ends immediately after the last
data row without any unnecessary whitespace or blank lines at the end.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@datasets/PXD063467/PXD063467_dda.sdrf`:
- Line 1: The file is named PXD063467_dda.sdrf but the CI validation pipeline
only processes files matching the pattern *.sdrf.tsv. The missing .tsv extension
means this file will be completely skipped during automated validation. Rename
the file from PXD063467_dda.sdrf to PXD063467_dda.sdrf.tsv to ensure it is
properly validated by the validation script and GitHub Actions workflow.
- Line 91: The source name PXD063467_HCM42_Empa_low5 indicates biological
replicate 5, but the characteristics biological replicate field contains 6,
creating an inconsistency. Resolve this by choosing one approach: either rename
the source name to PXD063467_HCM42_Empa_low6 to match the replicate number 6 in
the characteristics field, or change the biological replicate value from 6 to 5
to match the source name suffix. Ensure consistency between the source name and
the biological replicate field value.

In `@datasets/PXD063467/PXD063467_dia.sdrf`:
- Line 1: The file name PXD063467_dia.sdrf is missing the required .tsv
extension that the CI validation scripts and GitHub Actions workflow expect to
match the pattern *.sdrf.tsv. Rename the file from PXD063467_dia.sdrf to
PXD063467_dia.sdrf.tsv so that it will be properly detected and validated by the
automated validation processes.
- Line 66: The data file reference for the PXD063467_HCM17_Cana_low5 sample
contains "DDA" in the filename (HCM17_DDA_GC8_1_4283.d) but the row specifies
"data-independent acquisition" in the proteomics data acquisition method column,
which is inconsistent with the DIA nature of the dataset and all other 95 rows
that correctly reference DIA files. Replace the data file reference from
HCM17_DDA_GC8_1_4283.d to HCM17_DIA_GC8_1_4283.d to align with the declared
acquisition method and match the naming convention used in the rest of the
dataset.
- Line 91: The source name PXD063467_HCM42_Empa_low5 indicates biological
replicate 5, but the biological replicate field contains value 6, creating an
inconsistency. To fix this, either rename the source name from
PXD063467_HCM42_Empa_low5 to PXD063467_HCM42_Empa_low6 to match the replicate
number 6, or change the biological replicate field value from 6 to 5 to match
the source name suffix. Choose one approach and apply the same fix to the
corresponding line in the DDA SDRF file.
- Line 44: The SDRF version is inconsistent across the file. The row for
PXD063467_43_Empa_high1 declares the comment[sdrf version] as v1.1.1 while all
other 95 rows use v1.1.0. Locate the PXD063467_43_Empa_high1 row and change the
SDRF version value from v1.1.1 to v1.1.0 to ensure consistency throughout the
file.

---

Nitpick comments:
In `@datasets/PXD063467/PXD063467_dda.sdrf`:
- Around line 98-196: The file contains 99 trailing blank lines after the last
data row in the range from line 98 to line 196. Remove all these excessive
trailing blank lines to reduce file size and improve readability. Ensure the
file ends immediately after the last data row without any unnecessary whitespace
or blank lines at the end.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 7c5db40b-5b1e-49e3-b0b7-2ee4126ab61b

📥 Commits

Reviewing files that changed from the base of the PR and between 44b4cc9 and ce37d90.

📒 Files selected for processing (2)

• datasets/PXD063467/PXD063467_dda.sdrf
• datasets/PXD063467/PXD063467_dia.sdrf

[coderabbitai]

⚠️ Potential issue | 🔴 Critical | ⚡ Quick win

Critical: File extension must be .sdrf.tsv for CI validation.

The filename PXD063467_dda.sdrf is missing the .tsv extension. Both the validation script and the GitHub Actions workflow only process files matching the pattern *.sdrf.tsv, so this file will be skipped entirely during automated validation.

Rename to: PXD063467_dda.sdrf.tsv

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dda.sdrf` at line 1, The file is named
PXD063467_dda.sdrf but the CI validation pipeline only processes files matching
the pattern *.sdrf.tsv. The missing .tsv extension means this file will be
completely skipped during automated validation. Rename the file from
PXD063467_dda.sdrf to PXD063467_dda.sdrf.tsv to ensure it is properly validated
by the validation script and GitHub Actions workflow.

[coderabbitai]

⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Source name and biological replicate mismatch.

The source name PXD063467_HCM42_Empa_low5 suggests biological replicate 5, but the characteristics[biological replicate] field contains 6. This inconsistency may cause confusion in downstream analysis.

Expected: Either rename to PXD063467_HCM42_Empa_low6 or correct the replicate number to 5.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dda.sdrf` at line 91, The source name
PXD063467_HCM42_Empa_low5 indicates biological replicate 5, but the
characteristics biological replicate field contains 6, creating an
inconsistency. Resolve this by choosing one approach: either rename the source
name to PXD063467_HCM42_Empa_low6 to match the replicate number 6 in the
characteristics field, or change the biological replicate value from 6 to 5 to
match the source name suffix. Ensure consistency between the source name and the
biological replicate field value.

[coderabbitai]

⚠️ Potential issue | 🔴 Critical | ⚡ Quick win

Critical: File extension must be .sdrf.tsv for CI validation.

The filename PXD063467_dia.sdrf is missing the .tsv extension. Both the validation script and the GitHub Actions workflow only process files matching the pattern *.sdrf.tsv, so this file will be skipped entirely during automated validation.

Rename to: PXD063467_dia.sdrf.tsv

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dia.sdrf` at line 1, The file name
PXD063467_dia.sdrf is missing the required .tsv extension that the CI validation
scripts and GitHub Actions workflow expect to match the pattern *.sdrf.tsv.
Rename the file from PXD063467_dia.sdrf to PXD063467_dia.sdrf.tsv so that it
will be properly detected and validated by the automated validation processes.

[coderabbitai]

⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Inconsistent SDRF version across rows.

Row for PXD063467_43_Empa_high1 declares comment[sdrf version] as v1.1.1, while all other 95 rows use v1.1.0. The SDRF version should be consistent throughout a single file.

Please verify the intended version and standardize all rows.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dia.sdrf` at line 44, The SDRF version is
inconsistent across the file. The row for PXD063467_43_Empa_high1 declares the
comment[sdrf version] as v1.1.1 while all other 95 rows use v1.1.0. Locate the
PXD063467_43_Empa_high1 row and change the SDRF version value from v1.1.1 to
v1.1.0 to ensure consistency throughout the file.

[coderabbitai]

⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Source name and biological replicate mismatch.

The source name PXD063467_HCM42_Empa_low5 suggests biological replicate 5, but the characteristics[biological replicate] field contains 6. This inconsistency may cause confusion in downstream analysis.

Expected: Either rename to PXD063467_HCM42_Empa_low6 or correct the replicate number to 5.

Note: This same issue exists in the DDA SDRF file at line 91.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@datasets/PXD063467/PXD063467_dia.sdrf` at line 91, The source name
PXD063467_HCM42_Empa_low5 indicates biological replicate 5, but the biological
replicate field contains value 6, creating an inconsistency. To fix this, either
rename the source name from PXD063467_HCM42_Empa_low5 to
PXD063467_HCM42_Empa_low6 to match the replicate number 6, or change the
biological replicate field value from 6 to 5 to match the source name suffix.
Choose one approach and apply the same fix to the corresponding line in the DDA
SDRF file.

[nithujohn]

@liza-d1 I checked your file with validator to produce the same error you have mentioned but I was not able to reproduce it. Can you please confirm the templates you used for validation? Thanks!

[Copilot]

Pull request overview

This PR adds SDRF annotations for PRIDE dataset PXD063467, split into separate metadata sheets for DDA and DIA analyses, under datasets/PXD063467/.

Changes:

• Added a DIA SDRF containing sample/treatment metadata and DIA-specific method fields.
• Added a DDA SDRF containing sample/treatment metadata and DDA-specific method fields.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 13 comments.

File	Description
datasets/PXD063467/PXD063467_dia.sdrf	New DIA SDRF annotation for PXD063467 samples/runs.
datasets/PXD063467/PXD063467_dda.sdrf	New DDA SDRF annotation for PXD063467 samples/runs (currently includes trailing empty rows).

---

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[nithujohn]

@liza-d1 can you please annotate comment[label] as NT=label free sample;AC=MS:1002038 instead of label free sample.