# `pmhc/` — sources

The reference ligand panel every `mhcmatch.Store` is built from. **Experimental**: positive IEDB
MHC-ligand records, harmonised; nothing here is predicted.

| file | rows | what it is |
|---|--:|---|
| `pmhc_full.tsv.gz` | 1,482,188 | every positive IEDB epitope–MHC record |
| `pmhc_shortlist.tsv.gz` | 645,102 | the subset supported by **≥2 references** |

Schema: `epitope`, `gene`, `species`, `mhc_a`, `mhc_b`, `mhc_class`, `mhc_species`, `reference_id`,
`n_references`.

`pmhc_full.tsv.gz` composition:

| class | host | rows |
|---|---|--:|
| MHCI | HomoSapiens | 1,040,631 |
| MHCII | HomoSapiens | 327,487 |
| MHCI | MusMusculus | 97,601 |
| MHCII | MusMusculus | 16,469 |

**The two tiers are a precision/recall choice, not a quality ranking.** `shortlist` drops
single-reference pairs, which removes both the noise and the rare alleles that only one study ever
reported — so it is the better background and the worse coverage. `full` is the default;
`Store.from_pmhc(tier="shortlist")` selects the other.

```zsh
mhcmatch bootstrap --tier all      # fetches both, ~16 MB
```