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Add affinity proteomics SDRF annotationsFeat/affinity proteomics #17

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b77ccf6
Create .DS_Store
deeptijk May 6, 2026
4d4da2e
Update .DS_Store
deeptijk May 6, 2026
2cd1a64
Add affinity proteomics PRIDE drafts
deeptijk May 12, 2026
9d1178b
Refine affinity drafts from deposited matrices
deeptijk May 18, 2026
1f79fd0
Prune unavailable optional affinity columns
deeptijk May 18, 2026
0a09c3d
Remove repetitive affinity columns
deeptijk May 19, 2026
1fc903c
Update .DS_Store
deeptijk May 20, 2026
bdd5922
Correct affinity sample type values
deeptijk Jun 2, 2026
9d604c8
Promote affinity annotations to datasets
deeptijk Jun 2, 2026
debd46a
Annotate affinity sample type and source names
deeptijk Jun 2, 2026
85de8db
Update validate-sdrf.yml
deeptijk Jun 16, 2026
9f4e569
Merge branch 'main' into feat/affinity-proteomics
deeptijk Jul 13, 2026
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Binary file added .DS_Store
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7 changes: 6 additions & 1 deletion .github/workflows/validate-sdrf.yml
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Expand Up @@ -87,6 +87,11 @@ jobs:
fi
echo "::group::parse_sdrf validate-sdrf --sdrf_file $f"
# Options aligned with current sdrf-pipelines main (see parse_sdrf validate-sdrf -h).
parse_sdrf validate-sdrf --sdrf_file "$f" --use_ols_cache_only
# Files named PAD* are affinity-proteomics SDRFs; validate them with that template.
if [[ "$(basename "$f")" == PAD* ]]; then
parse_sdrf validate-sdrf --sdrf_file "$f" --use_ols_cache_only -t affinity-proteomics
else
parse_sdrf validate-sdrf --sdrf_file "$f" --use_ols_cache_only
fi
echo "::endgroup::"
done
21 changes: 21 additions & 0 deletions datasets/PAD000001/PAD000001.sdrf.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[age] characteristics[sex] characteristics[biological replicate] characteristics[sample type] characteristics[sample matrix] assay name technology type comment[technical replicate] comment[data file] comment[file uri] comment[platform] comment[quantification unit] comment[plate] comment[normalization method] comment[olink panel] comment[olink platform] comment[npx normalization] comment[sdrf version] comment[sdrf annotation tool]
PAD000001-XB6 Homo sapiens not available not available not available not available 1 not applicable blood plasma PAD000001-r00001-XB6 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB65 Homo sapiens not available not available not available not available 2 not applicable blood plasma PAD000001-r00002-XB65 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB68 Homo sapiens not available not available not available not available 3 not applicable blood plasma PAD000001-r00003-XB68 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_5 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB115 Homo sapiens not available not available not available not available 4 not applicable blood plasma PAD000001-r00004-XB115 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB20 Homo sapiens not available not available not available not available 5 not applicable blood plasma PAD000001-r00005-XB20 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB95 Homo sapiens not available not available not available not available 6 not applicable blood plasma PAD000001-r00006-XB95 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_7 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB54 Homo sapiens not available not available not available not available 7 not applicable blood plasma PAD000001-r00007-XB54 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_6 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB22 Homo sapiens not available not available not available not available 8 not applicable blood plasma PAD000001-r00008-XB22 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_9 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB25 Homo sapiens not available not available not available not available 9 not applicable blood plasma PAD000001-r00009-XB25 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_11 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB97 Homo sapiens not available not available not available not available 10 not applicable blood plasma PAD000001-r00010-XB97 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB79 Homo sapiens not available not available not available not available 11 not applicable blood plasma PAD000001-r00011-XB79 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB59 Homo sapiens not available not available not available not available 12 not applicable blood plasma PAD000001-r00012-XB59 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_10 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB114 Homo sapiens not available not available not available not available 13 not applicable blood plasma PAD000001-r00013-XB114 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_12 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB94 Homo sapiens not available not available not available not available 14 not applicable blood plasma PAD000001-r00014-XB94 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_13 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB14 Homo sapiens not available not available not available not available 15 not applicable blood plasma PAD000001-r00015-XB14 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_4 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB100 Homo sapiens not available not available not available not available 16 not applicable blood plasma PAD000001-r00016-XB100 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_2 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB112 Homo sapiens not available not available not available not available 17 not applicable blood plasma PAD000001-r00017-XB112 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_2 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB89 Homo sapiens not available not available not available not available 18 not applicable blood plasma PAD000001-r00018-XB89 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_8 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB107 Homo sapiens not available not available not available not available 19 not applicable blood plasma PAD000001-r00019-XB107 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_3 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
PAD000001-XB21 Homo sapiens not available not available not available not available 20 not applicable blood plasma PAD000001-r00020-XB21 protein expression profiling by antibody array 1 olink_npx.csv ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PAD000001/olink_npx.csv Olink Target 96 NPX sample_manifest_plate_3 Intensity Cardiometabolic; Inflammation; Neurology; Oncology Olink Target 96 intensity normalized v1.1.0 NT=sdrf-skills-autoresearch;VV=v0.0.0
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