README.md

---
pretty_name: IEDB Assay Export
license: cc-by-4.0
tags:
- biology
- immunology
- epitopes
- assays
- iedb
- parquet
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*.parquet
  - split: test
    path: data/test-*.parquet
---

# IEDB Assay Export

IEDB is a curated database of experimentally characterized immune epitopes, including B cell, T cell, and MHC-binding data across infectious, allergic, autoimmune, and transplant contexts.

## Splits

| Split | Rows |
|---|---:|
| train | 6,705,467 |
| test | 745,344 |
| total | 7,450,811 |

The split is deterministic and epitope-aware: `sha256(epitope_id) % 10 == 0` goes to `test`; buckets `1` through `9` go to `train`. If an assay lacks an epitope ID, the script falls back to reference ID, assay ID, then XML filename.

## Dataset Statistics

| Metric | Value |
|---|---:|
| XML files parsed | 26,785 |
| XML parse-error files | 0 |
| Assay rows | 7,450,811 |
| Unique references with assays | 26,785 |
| Unique epitopes with assays | 2,320,500 |
| Uncompressed XML bytes | 26.32 GB |
| Compressed XML bytes | 605.58 MB |

Assay category counts:

| Assay category | Rows |
|---|---:|
| MhcLigandElution | 4,635,502 |
| BCell | 1,419,468 |
| MhcBinding | 825,450 |
| TCell | 570,391 |

Top qualitative measurements:

| Measurement | Rows |
|---|---:|
| Positive | 5,239,946 |
| Negative | 1,967,175 |
| Positive-Low | 118,346 |
| Positive-High | 69,648 |
| Positive-Intermediate | 55,696 |

Top epitope chemical types:

| Chemical type | Rows |
|---|---:|
| Peptide from protein | 6,773,619 |
| Peptide, no natural source | 591,652 |
| Discontinuous protein residues | 51,083 |
| Other Non-Sequence | 14,279 |
| Carbohydrate fragment | 5,650 |

## Load With `datasets`

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/IEDB")
print(ds)

row = ds["train"][0]
print(row)
```

Load one split directly:

```python
from datasets import load_dataset

train = load_dataset("LiteFold/IEDB", split="train")
test = load_dataset("LiteFold/IEDB", split="test")
```

Stream rows without materializing the full table locally:

```python
from datasets import load_dataset

streamed = load_dataset("LiteFold/IEDB", split="train", streaming=True)
first_row = next(iter(streamed))
```

Filter to positive T-cell assays:

```python
from datasets import load_dataset

train = load_dataset("LiteFold/IEDB", split="train")
positive_tcell = train.filter(
    lambda row: row["assay_category"] == "TCell" and row["is_positive"]
)
```

For large jobs, prefer streaming or process the Parquet files with a columnar engine such as DuckDB, PyArrow, Polars, or Spark.

## Main Columns

| Column | Description |
|---|---|
| `xml_file` | Source XML file inside `iedb_export.zip`. |
| `reference_id`, `pubmed_id`, `article_year`, `article_title`, `journal_title`, `authors` | Reference/article metadata. |
| `epitope_id`, `epitope_name` | IEDB epitope identifiers and names. |
| `epitope_structure_type`, `epitope_chemical_type` | Parsed XML structure type and chemical type. |
| `linear_sequence`, `linear_sequence_length` | Linear peptide/protein sequence when present. |
| `discontinuous_residues` | Discontinuous residue string when present. |
| `starting_position`, `ending_position` | Natural-sequence coordinates when present. |
| `source_organism_id`, `source_molecule_genbank_id` | Source organism and molecule identifiers parsed from epitope structure. |
| `assay_category`, `assay_id`, `assay_type_id` | Assay type and identifiers. |
| `qualitative_measurement`, `is_positive`, `quantitative_measurement` | Assay outcome fields. |
| `host_organism_id`, `host_sex`, `host_age`, `disease_state` | Host and disease context when present. |
| `mhc_allele_id`, `mhc_allele_types_present` | MHC information when present. |
| `cell_type`, `cell_tissue_type`, `cell_culture_conditions` | Effector-cell context when present. |
| `antigen_evidence_code`, `immunogen_evidence_code`, `assay_comments` | Additional assay curation metadata. |
| `split_bucket` | Deterministic hash bucket; bucket 0 is test. |

# Citation

```
@article{vita2025iedb,
  title   = {The Immune Epitope Database ({IEDB}): 2024 update},
  author  = {Vita, Randi and others},
  journal = {Nucleic Acids Research},
  volume  = {53},
  number  = {D1},
  pages   = {D436--D443},
  year    = {2025},
  doi     = {10.1093/nar/gkae1092}
}
```