| --- |
| license: cc-by-4.0 |
| pretty_name: PRISM Antibody Training Data |
| language: |
| - en |
| tags: |
| - biology |
| - protein |
| - antibody |
| - immunology |
| - OAS |
| size_categories: |
| - 10M<n<100M |
| --- |
| |
| # PRISM Antibody Training Data |
|
|
| Training data for **PRISM** ([RomeroLab-Duke/prism-antibody](https://huggingface.co/RomeroLab-Duke/prism-antibody)), |
| a germline/non-germline-aware antibody language model. This repository contains the curated |
| unpaired and paired antibody sequence datasets and the exact OAS download manifest used to |
| build them. |
|
|
| ## Files |
|
|
| | File | Rows | Description | |
| |------|------|-------------| |
| | `unpaired_anarci_relabeled.parquet` | 66,435,576 | Unpaired heavy/light chains (pretraining set) | |
| | `paired_anarci_relabeled.parquet` | 763,989 | Paired VH+VL antibodies (fine-tuning set) | |
| | `bulk_download.sh` | 14,433 URLs | Exact OAS download manifest used (see caveat below) | |
|
|
| Splits are encoded in the `split` column (`train` / `valid` / `test`). |
|
|
| ## Provenance & pipeline |
|
|
| - **Source**: [Observed Antibody Space (OAS)](https://opig.stats.ox.ac.uk/webapps/oas/), human studies only |
| (70 studies, 2021–2022 data freeze). |
| - **Pipeline**: download → QC filter (missing conserved cysteine / heavy fragmentation / |
| non-canonical AA) → exact sequence deduplication → **NGL mutation filter** → CDR3 + whole-sequence |
| identity clustering/dedup → ANARCI re-numbering. |
|
|
| ## ⚠️ Important caveats (read before reproducing) |
|
|
| 1. **This is NOT the full OAS human set.** Most of the largest study, **Briney_2019 heavy** |
| (~1,100 files), was excluded from the unpaired set for download/disk size reasons |
| (these lines are commented out in `bulk_download.sh`, and the loader skips `# wget` lines). |
| This is why the unpaired heavy count is ~58M rather than the full OAS human heavy total. |
| 2. **NGL (somatic) mutation filter**: sequences are kept only if |
| `num_ngl_muts_hc > 3` (heavy) and `num_ngl_muts_lc > 2` (light). Applied to both sets. |
| 3. **CDR3 clustering caveat**: the CDR3-identity clustering step used a fixed ANARCI CSV |
| column window that can be shifted by IMGT insertion codes (affects heavy more than light). |
| Treat `*_cdr3_cluster_id` / dedup counts with this in mind. |
| |
| ## Column dictionary |
| |
| `HEAVY_CHAIN_AA_SEQUENCE`, `LIGHT_CHAIN_AA_SEQUENCE` (AA), `*_NT_SEQUENCE` (nucleotide), |
| `*_AA_GERMLINE_ALIGNMENT` (germline-aligned AA), `BType` (B-cell type), `Source_File` (OAS origin), |
| `hc_mut_codes` / `lc_mut_codes` (somatic mutation codes), `num_ngl_muts_hc` / `num_ngl_muts_lc` / |
| `total_num_ngl_muts` (somatic mutation counts), `*_cdr3_cluster_id` / `*_whole_seq_cluster_id` |
| (clustering IDs), `v_gene_*` / `j_gene_*` (V/J gene calls — decode with `gene_vocabulary.json` |
| in the model repo), `region_mask_*` (IMGT region masks), `split` (train/valid/test), |
| `oas_*_mut_codes` (original OAS mutation codes before ANARCI relabel). |
| |
| ## License & citation |
| |
| Derived from OAS (CC-BY 4.0). Please cite OAS (Olsen et al. 2022, *Protein Science*) and PRISM. |
| |
| Model: https://huggingface.co/RomeroLab-Duke/prism-antibody |
| |
