Slim down dataset card to stable bits (license + redistribution)

README.md

@@ -21,181 +21,16 @@ configs:
 
 # TCGA Patients (Open Access)
 
-One row per patient. **Open-access** TCGA clinical data from the NCI Genomic
-Data Commons (GDC), pre-joined into a single nested record per case so
-multi-modal oncology models can stream rich patient context in batches without
-doing joins.
+**Open-access** TCGA patient data from the NCI Genomic Data Commons (GDC).
+One HuggingFace subset per TCGA project; one row per patient.
 
 - **Projects included:** `TCGA-CHOL`, `TCGA-DLBC`
-- **Generated:** 2026-05-04 00:06:17 UTC
-- **Source:** NCI GDC `/cases` endpoint with expansions on `demographic`,
-  `diagnoses`, `diagnoses.treatments`, `follow_ups`, `exposures`,
-  `family_histories`, `project`.
-- **Access tier:** open. Redistributable; see the License & redistribution
-  section below.
-- **Subsets:** one HF subset (config) per TCGA project, mirroring the
-  [`wikimedia/wikipedia`](https://huggingface.co/datasets/wikimedia/wikipedia)
-  per-language pattern. Files are laid out as `<TCGA-XXXX>/train.parquet`.
-
-## Loading
-
-```python
-from datasets import load_dataset
-
-# Pick a single project — same pattern as wikimedia/wikipedia per-language subsets:
-ds = load_dataset("<repo_id>", "TCGA-CHOL", split="train")
-for patient in ds:
-    case_id = patient["case_id"]
-    diagnoses = patient["diagnoses"]                # list of dicts
-    treatments = [tx for dx in diagnoses for tx in dx["treatments"]]
-    ...
-
-# Stream a project's patients (no full download):
-stream = load_dataset("<repo_id>", "TCGA-CHOL", split="train", streaming=True)
-
-# Iterate every project — concat across subsets yourself:
-from datasets import get_dataset_config_names, concatenate_datasets
-configs = get_dataset_config_names("<repo_id>")
-all_ds = concatenate_datasets(
-    [load_dataset("<repo_id>", c, split="train") for c in configs]
-)
-```
-
-Or load into pyarrow / polars / pandas directly:
-
-```python
-import pyarrow.parquet as pq
-
-table = pq.read_table(
-    "TCGA-CHOL/train.parquet",
-    columns=["case_id", "project_id", "demographic", "diagnoses"],
-)
-```
-
-## Verification
-
-This dataset's source is the NCI GDC. The same TCGA cases are also browsable on
-[cBioPortal](https://www.cbioportal.org/). cBioPortal hosts **multiple versions**
-of TCGA per disease (Firehose Legacy, PanCancer Atlas, GDC-sourced); the
-`*_tcga_gdc` family shares our upstream source and is the like-for-like
-comparison. Disease prefixes use cBioPortal's own taxonomy, not always the
-TCGA project suffix (e.g. `TCGA-DLBC` → `dlbclnos_tcga_gdc`).
-
-```
-https://www.cbioportal.org/patient/summary?studyId=<study>&caseId=<case_submitter_id>
-```
-
-For example, patient `TCGA-W5-AA39` (project `TCGA-CHOL`) →
-`https://www.cbioportal.org/patient/summary?studyId=chol_tcga_gdc&caseId=TCGA-W5-AA39`.
-
-## Schema
-
-```
-case_id: string
-case_submitter_id: string
-project_id: string
-primary_site: string
-disease_type: string
-demographic: struct<
-  demographic_id: string,
-  submitter_id: string,
-  gender: string,
-  sex_at_birth: string,
-  race: string,
-  ethnicity: string,
-  vital_status: string,
-  age_at_index: int64,
-  days_to_birth: int64,
-  days_to_death: int64,
-  year_of_birth: int64,
-  year_of_death: int64,
-  country_of_residence_at_enrollment: string,
->
-diagnoses: list<struct<
-  diagnosis_id: string,
-  submitter_id: string,
-  primary_diagnosis: string,
-  morphology: string,
-  tissue_or_organ_of_origin: string,
-  site_of_resection_or_biopsy: string,
-  icd_10_code: string,
-  ajcc_pathologic_stage: string,
-  ajcc_pathologic_t: string,
-  ajcc_pathologic_n: string,
-  ajcc_pathologic_m: string,
-  ajcc_staging_system_edition: string,
-  age_at_diagnosis: int64,
-  days_to_diagnosis: double,
-  year_of_diagnosis: int64,
-  prior_malignancy: string,
-  prior_treatment: string,
-  synchronous_malignancy: string,
-  classification_of_tumor: string,
-  last_known_disease_status: string,
-  days_to_last_follow_up: double,
-  days_to_last_known_disease_status: double,
-  days_to_recurrence: double,
-  residual_disease: string,
-  diagnosis_is_primary_disease: bool,
-  treatments: list<struct<
-    treatment_id: string,
-    submitter_id: string,
-    treatment_type: string,
-    treatment_or_therapy: string,
-    treatment_intent_type: string,
-    treatment_outcome: string,
-    therapeutic_agents: string,
-    days_to_treatment_start: double,
-    days_to_treatment_end: double,
-    initial_disease_status: string,
-  >>,
->>
-follow_ups: list<struct<
-  follow_up_id: string,
-  submitter_id: string,
-  timepoint_category: string,
-  disease_response: string,
-  progression_or_recurrence: string,
-  days_to_follow_up: double,
-  days_to_progression: double,
-  days_to_recurrence: double,
-  ecog_performance_status: string,
->>
-exposures: list<struct<
-  exposure_id: string,
-  submitter_id: string,
-  tobacco_smoking_status: string,
-  cigarettes_per_day: double,
-  years_smoked: double,
-  alcohol_history: string,
-  alcohol_intensity: string,
-  bmi: double,
-  weight: double,
-  height: double,
->>
-family_histories: list<struct<
-  family_history_id: string,
-  submitter_id: string,
-  relationship_type: string,
-  relative_with_cancer_history: string,
-  relationship_primary_diagnosis: string,
->>
-```
-
-Notes on the nested layout:
-
-- `demographic` is a single `struct` (1:1 with the patient).
-- `diagnoses`, `follow_ups`, `exposures`, `family_histories` are `list<struct<...>>`
-  (0..N per patient).
-- `treatments` is nested *inside* each diagnosis (`diagnoses[i].treatments`), so
-  the source 1:N relationship between diagnosis and treatment is preserved.
-- All leaf fields are nullable.
+- **Generated:** 2026-05-04 00:20:17 UTC
+- **Source:** NCI GDC `/cases` endpoint, open-access tier only.
 
 ## License & redistribution
 
-This dataset only contains TCGA data fetched from the GDC's **open-access** tier
-(`/cases` endpoint with `access=open`). Per the
-[NCI GDC Data Analysis Policy](https://gdc.cancer.gov/analyze-data/data-analysis-policies):
+Per the [NCI GDC Data Analysis Policy](https://gdc.cancer.gov/analyze-data/data-analysis-policies):
 
 > The GDC itself places no restrictions (other than attempts at reidentification)
 > on analysis or publication of open access data provided through the GDC Data Portal.
@@ -211,13 +46,8 @@ Per the [GDC Data Access Processes and Tools page](https://gdc.cancer.gov/access
 > individually identifiable, as well as most clinical and all biospecimen data
 > elements.
 
-The clinical data here is squarely within that scope.
-
 ## Restrictions on use
 
-The single hard restriction inherited from the GDC policy applies to all
-downstream users:
-
 > Users of any data provided by GDC, whether open or controlled access, agree
 > not to attempt to reidentify any individual participant in any study
 > represented by GDC data, for any purpose whatever.
@@ -225,30 +55,27 @@ downstream users:
 
 ## Required acknowledgement
 
-If you publish or present results derived from this dataset, please include the
+If you publish or present results derived from this dataset, include the
 [NCI-required TCGA acknowledgement](https://www.cancer.gov/ccg/research/genome-sequencing/tcga/using-tcga-data/citing):
 
 > The results <published or shown> here are in whole or part based upon data
 > generated by the TCGA Research Network: https://www.cancer.gov/tcga.
 
-Suggested citations for the GDC and TCGA:
+Suggested citations:
 
 - Grossman, R. L., et al. (2016). Toward a Shared Vision for Cancer Genomic Data.
   *NEJM*, 375(12), 1109-1112.
 - The Cancer Genome Atlas Research Network. https://www.cancer.gov/tcga
 - NCI Genomic Data Commons. https://gdc.cancer.gov
 
-Additional policy references:
-
-- [GDC Policies (umbrella)](https://gdc.cancer.gov/about-gdc/gdc-policies)
-- [GDC Encyclopedia — Controlled Access][controlled] (defines what is *not* in this dataset)
+References:
+[GDC Policies](https://gdc.cancer.gov/about-gdc/gdc-policies),
+[GDC Encyclopedia — Controlled Access][controlled] (defines what is *not* here),
+[NIH Genomic Data Sharing Policy](https://sharing.nih.gov/genomic-data-sharing).
 
 [controlled]: https://docs.gdc.cancer.gov/Encyclopedia/pages/Controlled_Access/
-- [NIH Genomic Data Sharing Policy](https://sharing.nih.gov/genomic-data-sharing)
 
 ## Disclaimer
 
-Prototype dataset for engineering validation. Schemas, projects, and column
-coverage will change as additional modalities (mutations, expression, copy number)
-are added — likely as additional top-level nested columns on the same patient row.
-Re-derive from the GDC for any analysis where freshness matters.
+Prototype dataset. Schema, included projects, and column coverage are still
+evolving. Re-derive from the GDC for any analysis where freshness matters.