Add mutation data, reactome ontology, and xmodalix image extension; rebuild base set from full 8-subtype cohort

README.md

@@ -1,25 +1,58 @@
 ---
+license: unknown
+task_categories:
+- tabular-classification
+- feature-extraction
 tags:
+- tcga
 - bulk-rna-seq
 - methylation
+- mutation
 - cancer
 - genomics
-pretty_name: TCGA PanCancer Atlas (trimmed, multi-omics)
+- multi-omics
+pretty_name: TCGA PanCancer Atlas (8-subtype base set + per-architecture extensions)
 ---
 
 # TCGA
 
-A trimmed multi-omics subset of the TCGA PanCancer Atlas (RNA + methylation + clinical), for use with [AUTOENCODIX](https://github.com/jan-forest/autoencodix_package) tutorials (`Ontix.ipynb`, `XModalix.ipynb`, `InputDataTutorials.ipynb`).
+A multi-omics subset of the TCGA PanCancer Atlas (RNA, methylation, mutation, clinical),
+for use with [AUTOENCODIX](https://github.com/jan-forest/autoencodix_package) tutorials.
 
-## Contents
+## Base set (used by `Vanillix`, and by every other architecture)
 
-- **3,246 samples** across 6 cancer types (fully paired RNA ∩ methylation ∩ clinical): BRCA (1,065), KIRC (509), THCA (497), SKCM (438), COAD (437), OV (300).
-- **7,941 genes** — full shared RNA ∩ methylation ∩ chromosome-ontology gene pool.
-- Files:
-  - `rna.parquet` — RNA expression, samples × genes
-  - `methylation.parquet` — methylation, samples × genes
-  - `clinical.parquet` — sample-level clinical/annotation metadata
-  - `chromosome_ont_lvl1_ncbi.txt`, `chromosome_ont_lvl2.txt` — chromosome-level ontology reference files (used by Ontix)
+Covers **8 cancer types**: BRCA, OV, LUAD, UCEC, LUSC, COAD, READ, UCS.
+
+- `rna.parquet` — 3552 samples × 17448 genes (RNA expression)
+- `methylation.parquet` — 3875 samples × 9829 genes (per-gene methylation)
+- `mutation.parquet` — 3461 samples × 20304 genes (combined mutation/CNA score per gene;
+  restricted to samples that belong to the 8 cancer types above — the source file is a
+  pan-cancer TCGA mutation matrix, trimmed here to match this cohort)
+- `clinical.parquet` — 3902 samples × 56 columns (sample-level clinical/annotation
+  metadata, incl. `CANCER_TYPE_ACRONYM`, `SUBTYPE`)
+
+Gene identifiers are NCBI/Entrez gene IDs throughout, consistent with the ontology files
+below.
+
+## `ontology/` — extension for `Ontix` Tutorial
+
+Two ontology hierarchies, each as a 2-level gene-grouping file (gene ID → level-1 group,
+level-1 group → level-2 group):
+
+- `chromosome_ont_lvl1_ncbi.txt`, `chromosome_ont_lvl2.txt` — chromosome/cytoband-based
+  grouping
+- `reactome_ont_lvl1.txt`, `reactome_ont_lvl2.txt` — Reactome pathway-based grouping
+  (level 2 uses human-readable Reactome pathway names)
+
+## `xmodalix/` — extension for `XModalix` Tutorial
+
+Synthetic MNIST-style images paired to TCGA samples, one per sample, for the
+image↔omics translation tutorial:
+
+- `xmodalix/tcga_fake_images.zip` — 3907 grayscale 28×28 PNGs
+- `xmodalix/tcga_image_mappings.txt` — tab-separated `sample_ids`, `img_paths`,
+  `extra_class_labels`, `CANCER_TYPE_ACRONYM`; 3230 of the 3902 base-set clinical
+  samples have a paired image (one image label per cancer type)
 
 ## Loading
 
@@ -29,11 +62,28 @@ import pandas as pd
 
 rna_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="rna.parquet")
 meth_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="methylation.parquet")
+mut_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="mutation.parquet")
 clin_path = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="clinical.parquet")
 
 rna = pd.read_parquet(rna_path)
 ```
 
+Ontix additionally needs, e.g.:
+
+```python
+chr1 = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="ontology/chromosome_ont_lvl1_ncbi.txt")
+rea1 = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="ontology/reactome_ont_lvl1.txt")
+```
+
+XModalix additionally needs:
+
+```python
+images_zip = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="xmodalix/tcga_fake_images.zip")
+mapping = hf_hub_download(repo_id="autoencodix/tcga", repo_type="dataset", filename="xmodalix/tcga_image_mappings.txt")
+```
+
 ## License
 
-**Needs to be finalized.** This data derives from the TCGA PanCancer Atlas, governed by the NIH Genomic Data Sharing Policy rather than a standard copyright license (e.g. CC-BY) (?)
+**Needs to be finalized.** This data derives from the TCGA PanCancer Atlas, governed by
+the NIH Genomic Data Sharing Policy rather than a standard copyright license (e.g.
+CC-BY). The Reactome pathway groupings are separately licensed under CC0 by Reactome.

clinical.parquet

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+size 434111

methylation.parquet

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+size 368426620

mutation.parquet

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+size 171919376

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