Datasets:

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tcga-ov-multiomics-network-derived-results

Error code:   DatasetGenerationError
Exception:    CastError
Message:      Couldn't cast
auc_observed: double
auc_null_mean: double
auc_null_sd: double
p_value_right_tail: double
model: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 881
to
{'path': Value('string'), 'size_bytes': Value('int64'), 'sha256': Value('string')}
because column names don't match
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1914, in _prepare_split_single
                  num_examples, num_bytes = writer.finalize()
                                            ^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 781, in finalize
                  self.write_rows_on_file()
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 663, in write_rows_on_file
                  self._write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 773, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2281, in table_cast
                  return cast_table_to_schema(table, schema)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2227, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              auc_observed: double
              auc_null_mean: double
              auc_null_sd: double
              p_value_right_tail: double
              model: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 881
              to
              {'path': Value('string'), 'size_bytes': Value('int64'), 'sha256': Value('string')}
              because column names don't match
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1347, in compute_config_parquet_and_info_response
                  parquet_operations = convert_to_parquet(builder)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
                  builder.download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 884, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 947, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1739, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1925, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset

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path string	size_bytes int64	sha256 string
data\raw\external_validation\GSE160705\GSE160705_Raw_data_read_counts_and_normalized_read_counts.xlsx	3,870,722	e89fe7291e73954334211273013aaf99affeba34bf055ffbaac7d58a445de213
data\raw\external_validation\car_benchmark\SRR31001810\SRR31001810_1.fastq.gz	1,594,117,031	3c9417c1f2ef8e64066e2587d4614d0840865f23a2c61b9e8bc5a8da54b67329
data\raw\external_validation\car_benchmark\SRR31001810\SRR31001810_2.fastq.gz	1,747,874,203	6b359d9d8ee1e0bd031e24577c9e3c01cef27f5a72eabdd098f858745a9d7dc8

TCGA-OV Multiomics Network Derived Results

This dataset contains derived, publication-ready outputs from a reproducible TCGA-OV multi-omics network analysis pipeline.

Current status

Primary manuscript target: Journal of Biomedical Informatics
Preferred bundle: manuscript/journal_of_biomedical_informatics/
Current JBI main manuscript status:
- required statement-of-significance table included
- main-paper combined tables/figures reduced to a compliant <=8
- sequential in-text callouts and corrected reference-order audit completed

Release notes

Refreshed JBI submission bundle with compliant main manuscript, declarations, title page, cover letter, checklist, supplement, and graphical abstract
Clarified CAR motif benchmark interpretation so heuristic all-zero motif rows are not misread as construct absence
Preserved prior IJCO and BJC bundles for provenance while marking JBI as the active preferred package
Kept the release derived-only: no raw GDC redistribution and no engineered CAR construct FASTA

Preferred manuscript package

manuscript/journal_of_biomedical_informatics/: primary current submission-grade package with main manuscript, cover letter, declarations, supplementary appendix, graphical abstract, and submission metadata
manuscript/ijco/ and manuscript/british_journal_of_cancer/: prior journal-tailored packages retained for provenance

Included

results/models/: MOFA-like factors, DIABLO-like scores
results/tables/: matching summary, feature counts, benchmark metrics with CIs, perturbation deltas, external validation tables, and CAR benchmark audits
results/networks/: multilayer edges and network centrality/stability
results/figures/: manuscript/report figures
results/reports/: external validation, CAR benchmark, and workflow audit reports
references/car_t/: metadata-only scaffold for user-supplied approved CAR reference panels
metadata/manifests/: GDC query/manifests templates
manuscript/journal_of_biomedical_informatics/: JBI-targeted manuscript and submission bundle
public_release/kaggle_kernel/tcga_ov_car_panel_scaffold.ipynb: notebook demonstrating the CAR scaffold workflow
public_release/kaggle_kernel/tcga_ov_host_alignment_car_benchmark.ipynb: notebook demonstrating the host-alignment-only CAR benchmark workflow

Not included

Raw GDC downloads are not redistributed.
No engineered CAR construct FASTA panel is redistributed.

Reproducibility

Use the companion repository workflow and scripts to regenerate these artifacts from public TCGA-OV sources.

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