Add 10 automated E. coli SDRF annotations (batch 5: large multi-sample datasets) by ypriverol · Pull Request #57 · bigbio/sdrf-annotated-datasets

ypriverol · 2026-07-30T17:48:52Z

E. coli SDRF annotations — automated batch 5 (10 large multi-sample datasets)

10 further large Escherichia coli datasets (>=100 raw files each, spanning many
distinct sample groups) recovered via sample-level annotation + programmatic
expansion, with additional deterministic curation:

Modifications structured to UNIMOD; organism grounded to PRIDE + normalized to
base NCBITaxon species; multi-value cleavage resolved to a single CV term.
Empty cells filled; integer columns (replicate/fraction) defaulted; invalid
ontology values (organism part/cell type/disease) set to 'not available';
sdrf version / tolerances / acquisition sanitized.
All files pass parse_sdrf validate-sdrf -t ms-proteomics.

First-pass automated annotations — review welcome. Empirical instrument / mass
tolerance verification from the raw spectra is a planned follow-up.

…e datasets via expansion)

qodo-code-review · 2026-07-30T17:48:57Z

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coderabbitai · 2026-07-30T17:49:05Z

Important

Review skipped

Review was skipped as selected files did not have any reviewable changes.

💤 Files selected but had no reviewable changes (2)

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

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: f2dbe09d-e572-42c9-ad1f-5f6baceee67d

📥 Commits

Reviewing files that changed from the base of the PR and between 31cf084 and 44a322a.

⛔ Files ignored due to path filters (1183)

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datasets/PXD073177/PXD073177.sdrf.tsv is excluded by !**/*.tsv
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datasets/PXD081616/PXD081616.sdrf.tsv is excluded by !**/*.tsv
datasets/ProteoBench-Astral-Module7/ProteoBench-Astral-Module7.sdrf.tsv is excluded by !**/*.tsv

📒 Files selected for processing (2)

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

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…rantee unique coordinates

Add 10 automated E. coli SDRF annotations (batch 5: large multi-sampl…

870527f

…e datasets via expansion)

Fix coordinate collisions in batch 5: parse fractions correctly + gua…

44a322a

…rantee unique coordinates

ypriverol merged commit e61a681 into main Jul 30, 2026
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Add 10 automated E. coli SDRF annotations (batch 5: large multi-sample datasets) - #57

Add 10 automated E. coli SDRF annotations (batch 5: large multi-sample datasets)#57
ypriverol merged 2 commits into
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annotate/ecoli-batch-5

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ypriverol commented Jul 30, 2026

E. coli SDRF annotations — automated batch 5 (10 large multi-sample datasets)

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coderabbitai Bot commented Jul 30, 2026 •

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