Add v1 data compendium: immunogenicity labels/benchmarks + similarity references

- pmhc/: IEDB epitope-MHC binding moved into folder (#6)
- immunogenicity/: IEDB-derived labels (#7, 790,868 rows: 34,362 immunogenic /
756,506 non-immunogenic) + 9 harmonized public benchmark sets (#9, 526,152 rows)
- proteome/: human UP000005640 + mouse UP000000589 self-reference proteomes (#4, #5)
- ligandome/: IEDB viral peptides (#2), pan-viral ORFs GSE272406 (#1), tsarina CTA targets (#3)
- summary.tsv: compendium-level counts

Private data (Gamaleya patients #8, TCGA neoantigens #10) is gitignored and not included.

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

.gitignore

@@ -3,3 +3,16 @@ src/
 .claude/
 .DS_Store
 **/.DS_Store
+
+# raw downloads (never pushed)
+raw/
+
+# private data (never pushed)
+gamaleya/
+tcga/
+
+# local-only deliverables (kept local for now)
+DESCRIPTION.md
+ROADMAP.md
+dashboard/
+summary_all_datasets.tsv

immunogenicity/benchmarks.tsv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:921b1530dae81bd0c0169271a1e5c3e39c8652ee9583ff82520d97251d1027d3
+size 6226745

immunogenicity/iedb_labeled.tsv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f91e95566d4c6fabf02cdcdc8eb3f17ce5eb6afe7e51944eb24e41df0c08459f
+size 9893733

ligandome/cancer_targets_tsarina.tsv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:dbddaa46e98d45d38af7b8b39df5e1cb7914f670745865c4e898ba8688e2aaf2
+size 26883

ligandome/viral_foreign_iedb.tsv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5c84c152df4095f08a4978cfc6bd1e690eb8420813376ffe23b0ee1b32fb0587
+size 997271

ligandome/viral_orfs_gse272406.tsv.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3b6c6d204103cd29add8a2d3bc1717611a2595e5bd89638ab8a46a4331cc0cb0
+size 789117

proteome/human.fasta.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6068b7ad09ebc57f1b7335abd936d74e7fdd58a67e9019efe8a30968d10e04b6
+size 38512271

proteome/mouse.fasta.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0e3ca4d8f01504c968ae9e2550484ad3adec32b5e0a50b7a4c74f89efabd1b75
+size 14956114

summary.tsv

@@ -1,19 +1,33 @@
 metric	value
-total_rows	5571576
-positive_assays	4967638
-positive_with_pmid	4843093
-positive_pmid_peptide	4581551
+distinct_references_pmid	2601
+rows_proteome_human	147506
 mhc_matchable_rows	1859913
-full_records	1482188
-full_human	1368118
-full_mouse	114070
-full_MHCI	1138232
-full_MHCII	343956
 distinct_epitopes	689421
-distinct_epitope_mhc	1054347
-distinct_references_pmid	2601
-rows_with_uniprot	1402640
+full_MHCII	343956
+rows_iedb_labeled	790868
+full_mouse	114070
 uniprot_pct	94.6
-shortlist_rows	645102
+compendium_public_rows	3735107
 shortlist_combos	217261
+distinct_epitope_mhc	1054347
+rows_gamaleya	15213
+positive_assays	4967638
+total_rows	5571576
 shortlist_max_references	70
+rows_with_uniprot	1402640
+rows_cta_tsarina	393
+positive_pmid_peptide	4581551
+compendium_datasets	11
+full_human	1368118
+shortlist_rows	645102
+full_MHCI	1138232
+compendium_private_rows	2259992
+full_records	1482188
+rows_tcga	2244779
+rows_pmhc_full	1482188
+rows_benchmarks	526152
+rows_viral_orfs	5673
+rows_pmhc_shortlist	645102
+positive_with_pmid	4843093
+rows_viral_iedb	82368
+rows_proteome_mouse	54857