Rework #9 into workhorse neoag DB (tested + candidates) + HLA population freqs

- immunogenicity/neoag_tested.tsv.gz: 526k tested patient-derived neoantigens
(immunogenicity 0/1) from TESLA, Neopep, CEDAR, Gfeller, ITSNdb, GBM, VACCIMEL,
Bjerregaard; adds patient_id, cancer_type, validated, affinity_wt
- immunogenicity/neoag_candidates.tsv.gz: 1.36M untested candidates (Neopep not_tested)
- immunogenicity/hla_pop_freqs.tsv.gz: EUR/ASN/AFR class-I allele frequencies (AFND)
- removed benchmarks.tsv.gz (superseded by the split)
- DESCRIPTION.md: brief per-dataset index, now tracked

Pipeline, dashboard, methods & roadmap moved to private repseq/gamaleya-cancer.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

.gitignore

@@ -11,8 +11,5 @@ raw/
 gamaleya/
 tcga/
 
-# local-only deliverables (kept local for now)
-DESCRIPTION.md
-ROADMAP.md
-dashboard/
+# internal spec (not published); docs/dashboard live in repseq/gamaleya-cancer
 summary_all_datasets.tsv

DESCRIPTION.md

@@ -0,0 +1,40 @@
+# pMHC Data Compendium
+
+Harmonized data substrate for a personalized cancer-vaccine immunogenicity pipeline:
+epitope–MHC binding, immunogenicity labels & a tested-neoantigen workhorse DB, self/foreign
+similarity references, and HLA population frequencies. Public data is here; per-patient data
+stays private (gitignored). Pipeline, methods, roadmap & dashboard live in the private
+infrastructure repo (`repseq/gamaleya-cancer`).
+
+All tables are gzip-TSV. The immunogenicity tables share one schema: `peptide, mhc_a, mhc_b,
+mhc_class, mhc_species, source_species, host_species, assay_type, immunogenicity{1,0,null},
+expression, affinity, affinity_wt, agretopicity, foreignness, validated, dataset_origin,
+reference_id, n_references` (+ `patient_id, cancer_type` for the neoag tables). `affinity` is
+as-reported per source (units differ); MHC alleles are as-reported.
+
+## Public datasets (this repo)
+
+| Path | # | Dataset | One-line |
+|------|---|---------|----------|
+| `pmhc/pmhc_full.tsv.gz` | 6 | IEDB epitope–MHC | positive IEDB MHC-ligand binding records (human IMGT/HLA + mouse H-2) |
+| `pmhc/pmhc_shortlist.tsv.gz` | 6 | IEDB epitope–MHC (≥2 refs) | high-confidence pairs (≥2 references) |
+| `immunogenicity/iedb_labeled.tsv.gz` | 7 | IEDB immunogenicity | immunogenic (T-cell+) vs non-immunogenic (MHC-ligand+, healthy self) |
+| `immunogenicity/neoag_tested.tsv.gz` | 9 | Neoantigens — tested (workhorse) | tested patient-derived neoantigens, immunogenicity 0/1 (TESLA, Neopep, CEDAR, Gfeller, ITSNdb, GBM, VACCIMEL, Bjerregaard) |
+| `immunogenicity/neoag_candidates.tsv.gz` | 9 | Neoantigens — candidates | untested neoantigen candidates (Neopep `not_tested`) |
+| `immunogenicity/hla_pop_freqs.tsv.gz` | — | HLA population freqs | EUR/ASN/AFR class-I (A/B/C) allele frequencies (AFND) |
+| `proteome/human.fasta.gz` | 4 | Human proteome (UP000005640) | self-reference proteome for similarity search |
+| `proteome/mouse.fasta.gz` | 5 | Mouse proteome (UP000000589) | C57BL/6 self-reference proteome |
+| `ligandome/viral_foreign_iedb.tsv.gz` | 2 | Viral ligandome (IEDB) | viral-source presented peptides (foreign reference) |
+| `ligandome/viral_orfs_gse272406.tsv.gz` | 1 | Pan-viral ORFs (GSE272406) | translated novel viral ORF proteins (foreign; *not* thymus self — spec mislabel) |
+| `ligandome/cancer_targets_tsarina.tsv.gz` | 3 | Cancer-testis antigens | curated shared tumor-antigen genes (tsarina) |
+| `summary.tsv` | — | Pipeline stats | row counts & extraction metrics |
+
+## Private (gitignored — NOT in this repo)
+
+| Path | # | Dataset |
+|------|---|---------|
+| `gamaleya/patient_features.tsv.gz`, `gamaleya/hla_coverage.tsv.gz` | 8 | Gamaleya patient candidates + features (17 patients) |
+| `tcga/tcga_neoantigens.tsv.gz`, `tcga/hla_coverage.tsv.gz` | 10 | TCGA expressed neoantigen binders + tumor type (controlled-access) |
+
+Detailed schemas, methods, and caveats: see the private `gamaleya-cancer` repo
+(`DESCRIPTION` here is intentionally brief).

immunogenicity/{benchmarks.tsv.gz → hla_pop_freqs.tsv.gz}

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