| # `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 |
| ``` |
|
|
