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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}
}
``` |