Datasets:
Card: metadata v2.2 (tag metadata-v2.2-20261106, corrections from human review)
Browse files
README.md
CHANGED
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@@ -248,15 +248,15 @@ catalog has no per-sample license column. See the
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reuse terms and citation, and cite the original studies with the data you use (`sda-db cite` writes BibTeX for
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a selection).
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## Curated sample metadata v2 (2026-11-
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`metadata/v2/` adds a curated table on top of the same 12,163 samples. No data file changed: the paper release is
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still tag `v1.0.0-20261025`.
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- `samples_metadata_v2.parquet` / `.csv` has one row per sample:
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- organ (43 sites);
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- UBERON tissue term (11,
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- MONDO disease terms (6,
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- sample kind, disease status (normal / disease / perturbation / not stated), life stage and sex;
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- NCBI taxonomy, and the species implied by the gene IDs;
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- corrected platform family and assay name.
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@@ -267,7 +267,7 @@ still tag `v1.0.0-20261025`.
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sample's GEO record, so it could not invent identifiers. Fixed rules handle unambiguous ages.
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- **Quality, estimated on 300 random samples.** An independent model judged each label and every "wrong" verdict
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was read by hand. Estimated wrong rates: organ 0.3%, tissue term 0.7%, sample kind 0.7%, life stage 1.7%,
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disease 3.0%. Labels judged correct were not re-read, so these are estimates.
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- **Known limit.** A study's disease sometimes lands on a control whose own record does not say it is a control
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(about 1.5% of samples). Use `annotation_low_confidence`, `metadata_flags` and the raw fields when this matters.
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- Full description: `metadata/v2/README.md`.
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reuse terms and citation, and cite the original studies with the data you use (`sda-db cite` writes BibTeX for
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a selection).
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| 250 |
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| 251 |
+
## Curated sample metadata v2 (version 2.2, 2026-11-06)
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`metadata/v2/` adds a curated table on top of the same 12,163 samples. No data file changed: the paper release is
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| 254 |
+
still tag `v1.0.0-20261025`; the current metadata is tag `metadata-v2.2-20261106`.
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| 255 |
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- `samples_metadata_v2.parquet` / `.csv` has one row per sample:
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- organ (43 sites);
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| 258 |
+
- UBERON tissue term (11,605 samples);
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| 259 |
+
- MONDO disease terms (6,479);
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- sample kind, disease status (normal / disease / perturbation / not stated), life stage and sex;
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| 261 |
- NCBI taxonomy, and the species implied by the gene IDs;
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| 262 |
- corrected platform family and assay name.
|
|
|
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sample's GEO record, so it could not invent identifiers. Fixed rules handle unambiguous ages.
|
| 268 |
- **Quality, estimated on 300 random samples.** An independent model judged each label and every "wrong" verdict
|
| 269 |
was read by hand. Estimated wrong rates: organ 0.3%, tissue term 0.7%, sample kind 0.7%, life stage 1.7%,
|
| 270 |
+
disease 3.0%. Labels judged correct were not re-read, so these are estimates. A human reader then reviewed 200 samples, and the errors found were corrected in version 2.2.
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- **Known limit.** A study's disease sometimes lands on a control whose own record does not say it is a control
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(about 1.5% of samples). Use `annotation_low_confidence`, `metadata_flags` and the raw fields when this matters.
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- Full description: `metadata/v2/README.md`.
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