RomeroLab-Duke/prism-antibody-data

PRISM Antibody Training Data

Training data for PRISM (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), 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