Publish TCGA neoantigens; add data-catalog infographic

- TCGA neoantigen predictions are public (derived from open-access TCGA somatic + expression;
per-barcode HLA/neoantigens as published by TCIA / Thorsson 2018) — un-gitignored tcga/,
only the real Gamaleya patient cohort stays private
- catalog.html: self-contained infographic of the public datasets by species / MHC class /
category / tissue / source / downstream tool
- DESCRIPTION.md: TCGA moved to public table; link to catalog.html

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

Files changed (5) hide show

.gitignore +3 -2
DESCRIPTION.md +6 -4
catalog.html +63 -0
tcga/hla_coverage.tsv.gz +3 -0
tcga/tcga_neoantigens.tsv.gz +3 -0

.gitignore CHANGED Viewed

@@ -7,9 +7,10 @@ src/
 # raw downloads (never pushed)
 raw/
-# private data (never pushed)
 gamaleya/
-tcga/
 # internal spec (not published); docs/dashboard live in repseq/gamaleya-cancer
 summary_all_datasets.tsv

 # raw downloads (never pushed)
 raw/
+# private data (never pushed) — real patient cohort
 gamaleya/
+# NB: tcga/ is PUBLIC (neoantigen predictions derived from open-access TCGA somatic +
+# expression data; per-barcode HLA/neoantigens as published by TCIA / Thorsson 2018).
 # internal spec (not published); docs/dashboard live in repseq/gamaleya-cancer
 summary_all_datasets.tsv

DESCRIPTION.md CHANGED Viewed

@@ -32,6 +32,7 @@ the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive, and the mTEC-
 | `immunogenicity/iedb_labeled.tsv.gz` | 7 | IEDB immunogenicity — **ipred training set** | immunogenic (T-cell+, 34,362) vs non-immunogenic (MHC-ligand+ in healthy self, 756,506); `host_species` (human/mouse) is the cross-validation axis; ipred featurizes `peptide` (MJ/hydropathy/Kidera) |
 | `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 |
@@ -47,8 +48,9 @@ the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive, and the mTEC-
 | 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/iedb_labeled.tsv.gz` | 7 | IEDB immunogenicity — **ipred training set** | immunogenic (T-cell+, 34,362) vs non-immunogenic (MHC-ligand+ in healthy self, 756,506); `host_species` (human/mouse) is the cross-validation axis; ipred featurizes `peptide` (MJ/hydropathy/Kidera) |
 | `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`) |
+| `tcga/tcga_neoantigens.tsv.gz` | 10 | TCGA neoantigens | 2.24M expressed mutant-peptide–HLA binders across 8,505 TCGA donors (derived from open-access TCGA somatic + expression; per-barcode HLA/neoantigens as in TCIA / Thorsson 2018) |
 | `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 |
 | Path | # | Dataset |
 |------|---|---------|
+| `gamaleya/patient_features.tsv.gz`, `gamaleya/hla_coverage.tsv.gz` | 8 | Gamaleya patient candidates + features (17 patients) — real cohort, never published |
+An interactive, self-contained catalog of the public datasets (breakdowns by species, MHC
+class, source, category, tissue, and downstream tool) is in [`catalog.html`](catalog.html).
+Detailed schemas, methods, and caveats: see the private `gamaleya-cancer` repo (`DESCRIPTION`
+here is intentionally brief).

catalog.html ADDED Viewed

	@@ -0,0 +1,63 @@

+<!doctype html>
+<html lang=en><head><meta charset=utf-8>
+<meta name=viewport content="width=device-width,initial-scale=1">
+<title>pMHC Data Compendium — Catalog</title>
+<style>
+:root{--bg:#fbfbfc;--card:#fff;--ink:#16181d;--mut:#6b7280;--line:#e6e8ec;--accent:#2b8a7e}
+@media(prefers-color-scheme:dark){:root{--bg:#0f1114;--card:#171a1f;--ink:#e8eaed;--mut:#9aa0aa;--line:#262a31;--accent:#39c5a8}}
+*{box-sizing:border-box}
+body{margin:0;background:var(--bg);color:var(--ink);font:15px/1.5 -apple-system,BlinkMacSystemFont,"Segoe UI",Helvetica,Arial,sans-serif;-webkit-font-smoothing:antialiased}
+.wrap{max-width:1080px;margin:0 auto;padding:40px 22px 64px}
+header h1{font-size:26px;font-weight:700;margin:0 0 4px;letter-spacing:-.01em}
+header p{color:var(--mut);margin:0 0 26px;max-width:70ch}
+.kpis{display:grid;grid-template-columns:repeat(6,1fr);gap:12px;margin-bottom:30px}
+.kpi{background:var(--card);border:1px solid var(--line);border-radius:12px;padding:14px 12px}
+.kn{font-size:22px;font-weight:700;letter-spacing:-.02em}
+.kl{font-size:11px;text-transform:uppercase;letter-spacing:.05em;color:var(--mut);margin-top:2px}
+.grid{display:grid;grid-template-columns:1fr 1fr;gap:16px;margin-bottom:16px}
+.panel{background:var(--card);border:1px solid var(--line);border-radius:14px;padding:16px 18px}
+.panel h2{font-size:12px;text-transform:uppercase;letter-spacing:.06em;color:var(--mut);margin:0 0 12px;font-weight:600}
+.bars{display:flex;flex-direction:column;gap:7px}
+.brow{display:grid;grid-template-columns:118px 1fr auto;align-items:center;gap:10px;font-size:13px}
+.blab{color:var(--ink);white-space:nowrap;overflow:hidden;text-overflow:ellipsis}
+.btrack{height:10px;border-radius:6px;background:color-mix(in srgb,var(--line) 70%,transparent);overflow:hidden}
+.bfill{display:block;height:100%;border-radius:6px}
+.bval{color:var(--mut);font-variant-numeric:tabular-nums;font-size:12px;text-align:right;min-width:54px}
+.tablewrap{background:var(--card);border:1px solid var(--line);border-radius:14px;overflow-x:auto;margin-top:16px}
+table{border-collapse:collapse;width:100%;font-size:13px}
+th,td{text-align:left;padding:10px 12px;border-bottom:1px solid var(--line);white-space:nowrap}
+th{font-size:11px;text-transform:uppercase;letter-spacing:.05em;color:var(--mut);font-weight:600}
+tr:last-child td{border-bottom:none}
+td.num{text-align:right;font-variant-numeric:tabular-nums}
+td.src{color:var(--mut);white-space:normal}
+.dot{display:inline-block;width:8px;height:8px;border-radius:50%;margin-right:8px;vertical-align:middle}
+footer{color:var(--mut);font-size:12px;margin-top:26px;line-height:1.7}
+a{color:var(--accent)}
+@media(max-width:760px){.kpis{grid-template-columns:repeat(3,1fr)}.grid{grid-template-columns:1fr}}
+</style></head>
+<body><div class=wrap>
+<header>
+<h1>pMHC Data Compendium — Data Catalog</h1>
+<p>Harmonized public data for a personalized cancer-vaccine immunogenicity pipeline: epitope–MHC
+presentation, immunogenicity labels, thymic &amp; proteomic self references, foreign ligandomes,
+and HLA population frequencies. Per-patient cohort data is private and excluded here.</p>
+</header>
+<div class=kpis><div class="kpi"><div class="kn">15</div><div class="kl">datasets</div></div><div class="kpi"><div class="kn">7,423,658</div><div class="kl">records</div></div><div class="kpi"><div class="kn">5,263,507</div><div class="kl">distinct peptides</div></div><div class="kpi"><div class="kn">16</div><div class="kl">sources</div></div><div class="kpi"><div class="kn">5</div><div class="kl">tissues / origins</div></div><div class="kpi"><div class="kn">5</div><div class="kl">downstream tools</div></div></div>
+<div class=grid>
+<div class=panel><h2>Records by category</h2><div class="bars"><div class="brow"><span class="blab">Immunogenicity</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#c46ad0"></span></span><span class="bval">4,917,562</span></div><div class="brow"><span class="blab">Presentation</span><span class="btrack"><span class="bfill" style="width:45.5%;background:#3b82c4"></span></span><span class="bval">2,127,683</span></div><div class="brow"><span class="blab">Self reference</span><span class="btrack"><span class="bfill" style="width:9.2%;background:#39c5a8"></span></span><span class="bval">266,734</span></div><div class="brow"><span class="blab">Foreign reference</span><span class="btrack"><span class="bfill" style="width:6.0%;background:#e0873a"></span></span><span class="bval">104,508</span></div><div class="brow"><span class="blab">HLA frequencies</span><span class="btrack"><span class="bfill" style="width:4.1%;background:#8a8f98"></span></span><span class="bval">7,171</span></div></div></div>
+<div class=panel><h2>Peptide–MHC records by species</h2><div class="bars"><div class="brow"><span class="blab">Human</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#3b82c4"></span></span><span class="bval">7,084,713</span></div><div class="brow"><span class="blab">Mouse</span><span class="btrack"><span class="bfill" style="width:7.9%;background:#e0873a"></span></span><span class="bval">291,226</span></div></div></div>
+<div class=panel><h2>Peptide–MHC records by MHC class</h2><div class="bars"><div class="brow"><span class="blab">MHC class I</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#39c5a8"></span></span><span class="bval">6,456,191</span></div><div class="brow"><span class="blab">MHC class II</span><span class="btrack"><span class="bfill" style="width:14.7%;background:#c46ad0"></span></span><span class="bval">717,385</span></div></div></div>
+<div class=panel><h2>Records by tissue / origin</h2><div class="bars"><div class="brow"><span class="blab">Tumor</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#6e8bff"></span></span><span class="bval">4,127,087</span></div><div class="brow"><span class="blab">Viral</span><span class="btrack"><span class="bfill" style="width:6.0%;background:#6e8bff"></span></span><span class="bval">88,041</span></div><div class="brow"><span class="blab">Thymus</span><span class="btrack"><span class="bfill" style="width:5.5%;background:#6e8bff"></span></span><span class="bval">64,371</span></div><div class="brow"><span class="blab">Microbial / viral</span><span class="btrack"><span class="bfill" style="width:4.4%;background:#6e8bff"></span></span><span class="bval">16,467</span></div><div class="brow"><span class="blab">Population</span><span class="btrack"><span class="bfill" style="width:4.2%;background:#6e8bff"></span></span><span class="bval">7,171</span></div></div></div>
+<div class=panel><h2>Datasets per downstream tool</h2><div class="bars"><div class="brow"><span class="blab">mhcmatch</span><span class="btrack"><span class="bfill" style="width:45.1%;background:#39c5a8"></span></span><span class="bval">3 ds</span></div><div class="brow"><span class="blab">ipred</span><span class="btrack"><span class="bfill" style="width:31.4%;background:#39c5a8"></span></span><span class="bval">2 ds</span></div><div class="brow"><span class="blab">public-epitope</span><span class="btrack"><span class="bfill" style="width:17.7%;background:#39c5a8"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">seqtree</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#39c5a8"></span></span><span class="bval">7 ds</span></div><div class="brow"><span class="blab">model</span><span class="btrack"><span class="bfill" style="width:58.9%;background:#39c5a8"></span></span><span class="bval">4 ds</span></div></div></div>
+<div class=panel><h2>Datasets per source</h2><div class="bars"><div class="brow"><span class="blab">IEDB</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#8a8f98"></span></span><span class="bval">4 ds</span></div><div class="brow"><span class="blab">UniProt</span><span class="btrack"><span class="bfill" style="width:76.0%;background:#8a8f98"></span></span><span class="bval">3 ds</span></div><div class="brow"><span class="blab">NCI</span><span class="btrack"><span class="bfill" style="width:52.0%;background:#8a8f98"></span></span><span class="bval">2 ds</span></div><div class="brow"><span class="blab">HLA Ligand Atlas</span><span class="btrack"><span class="bfill" style="width:52.0%;background:#8a8f98"></span></span><span class="bval">2 ds</span></div><div class="brow"><span class="blab">TESLA</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">CEDAR</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">Gfeller</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">ITSNdb</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">GBM</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">VACCIMEL</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">Bjerregaard</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">TCGA</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">AFND</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">HPA</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">GSE272406</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">tsarina</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div></div></div>
+</div>
+<div class=tablewrap><table>
+<thead><tr><th>Dataset</th><th>Category</th><th>Species</th><th>MHC</th><th>Records</th>
+<th>Distinct&nbsp;peptides</th><th>Tissue</th><th>Source</th><th>Feeds</th></tr></thead>
+<tbody><tr><td><span class="dot" style="background:#3b82c4"></span>IEDB epitope–MHC</td><td>Presentation</td><td>human+mouse</td><td>I+II</td><td class=num>1,482,188</td><td class=num>689,421</td><td>—</td><td class=src>IEDB</td><td class=src>mhcmatch</td></tr><tr><td><span class="dot" style="background:#3b82c4"></span>IEDB epitope–MHC (≥2 refs)</td><td>Presentation</td><td>human+mouse</td><td>I+II</td><td class=num>645,102</td><td class=num>174,821</td><td>—</td><td class=src>IEDB</td><td class=src>mhcmatch</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>IEDB immunogenicity</td><td>Immunogenicity</td><td>human+mouse</td><td>I+II</td><td class=num>790,868</td><td class=num>516,092</td><td>—</td><td class=src>IEDB</td><td class=src>ipred, public-epitope</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>Neoantigens — tested</td><td>Immunogenicity</td><td>human</td><td>I+II</td><td class=num>525,989</td><td class=num>491,495</td><td>Tumor</td><td class=src>TESLA, NCI, CEDAR, Gfeller, ITSNdb, GBM, VACCIMEL, Bjerregaard</td><td class=src>model, ipred</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>Neoantigens — candidates</td><td>Immunogenicity</td><td>human</td><td>I</td><td class=num>1,355,926</td><td class=num>1,344,070</td><td>Tumor</td><td class=src>NCI</td><td class=src>model</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>TCGA neoantigens</td><td>Immunogenicity</td><td>human</td><td>I</td><td class=num>2,244,779</td><td class=num>1,948,737</td><td>Tumor</td><td class=src>TCGA</td><td class=src>model</td></tr><tr><td><span class="dot" style="background:#8a8f98"></span>HLA population freqs</td><td>HLA frequencies</td><td>—</td><td>—</td><td class=num>7,171</td><td class=num>—</td><td>Population</td><td class=src>AFND</td><td class=src>model</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Thymus self-peptidome</td><td>Self reference</td><td>human</td><td>I+II</td><td class=num>53,878</td><td class=num>53,878</td><td>Thymus</td><td class=src>HLA Ligand Atlas</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Thymus expression</td><td>Self reference</td><td>—</td><td>—</td><td class=num>10,493</td><td class=num>—</td><td>Thymus</td><td class=src>HPA, HLA Ligand Atlas</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Human proteome</td><td>Self reference</td><td>human</td><td>—</td><td class=num>147,506</td><td class=num>—</td><td>—</td><td class=src>UniProt</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Mouse proteome</td><td>Self reference</td><td>mouse</td><td>—</td><td class=num>54,857</td><td class=num>—</td><td>—</td><td class=src>UniProt</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#e0873a"></span>Bacterial + viral proteomes</td><td>Foreign reference</td><td>foreign</td><td>—</td><td class=num>16,467</td><td class=num>—</td><td>Microbial / viral</td><td class=src>UniProt</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#e0873a"></span>Viral ligandome (IEDB)</td><td>Foreign reference</td><td>human+mouse</td><td>I+II</td><td class=num>82,368</td><td class=num>44,993</td><td>Viral</td><td class=src>IEDB</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#e0873a"></span>Pan-viral ORFs (GSE272406)</td><td>Foreign reference</td><td>—</td><td>—</td><td class=num>5,673</td><td class=num>—</td><td>Viral</td><td class=src>GSE272406</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#3b82c4"></span>Cancer-testis antigens</td><td>Presentation</td><td>—</td><td>—</td><td class=num>393</td><td class=num>—</td><td>Tumor</td><td class=src>tsarina</td><td class=src>mhcmatch</td></tr></tbody></table></div>
+<footer>
+Generated by <code>pipeline/build_catalog.py</code> from the public compendium.
+Immunopeptidome self-reference (thymus) from the HLA Ligand Atlas (Marcu&nbsp;2021, CC-BY&nbsp;4.0);
+proteomes from UniProt; HLA frequencies from AFND. See <code>DESCRIPTION.md</code> for provenance.
+</footer>
+</div></body></html>

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