thymus: add human thymic self-peptidome (source #1 refill)

Fills the mislabeled source #1 (GSE272406 was viral ORFs, not thymus). Adds:
- thymus/thymus_immunopeptidome.tsv.gz: HLA Ligand Atlas thymus-eluted self peptides
(25.9k MHC-I + 28.0k MHC-II, human) — the drop-in seqtree self-similarity reference
- thymus/thymus_expression.tsv.gz: HPA thymus-cluster genes + atlas thymus source proteins

Human only; mouse thymus data is raw-only / journal-supplement-only (see DESCRIPTION.md).

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

DESCRIPTION.md

@@ -15,6 +15,14 @@ omits the feature columns IEDB doesn't populate. In `neoag_tested`/`neoag_candid
 primary datasets take precedence over the aggregated compendia (CEDAR, Neopep): a duplicate
 peptide–MHC already present in a primary dataset is dropped from CEDAR/Neopep.
 
+The `thymus/` tables use the reference-peptide schema (`peptide, mhc_a, mhc_class, mhc_species,
+source_protein, species, dataset_origin`; `mhc_a` is null — the HLA Ligand Atlas gives
+donor-level candidate alleles, not a per-peptide deconvolution, and the seqtree self-similarity
+use is peptide-level). Thymus data is **human only**: the mouse thymic immunopeptidome (Schuster
+PXD008733) is deposited as raw MS with the processed peptides on the now-defunct SysteMHC atlas,
+the mouse thymus proteome (PXD007288) is a 12 GB MaxQuant archive, and the mTEC-TRA gene list
+(Sansom GSE53111) is journal-supplement-only — a mouse pass would require reprocessing raw spectra.
+
 ## Public datasets (this repo)
 
 | Path | # | Dataset | One-line |
@@ -28,6 +36,8 @@ peptide–MHC already present in a primary dataset is dropped from CEDAR/Neopep.
 | `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 |
 | `proteome/*_UP*.fasta.gz` | — | 16 bacterial + viral reference proteomes | foreign-antigen references for molecular-mimicry scans and peptide-flank extraction; see `proteome/README.md` |
+| `thymus/thymus_immunopeptidome.tsv.gz` | 1 | Thymus self-peptidome (human) | HLA Ligand Atlas thymus-eluted self peptides (25.9k MHC-I + 28.0k MHC-II) — central-tolerance "self" reference for seqtree; fills the mislabeled source #1 |
+| `thymus/thymus_expression.tsv.gz` | 1 | Thymus expression (human) | thymically expressed self: HPA thymus-cluster genes (126) + atlas thymus source proteins (10.4k) |
 | `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) |

thymus/thymus_expression.tsv.gz

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thymus/thymus_immunopeptidome.tsv.gz

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