| --- |
| pretty_name: DisProt Protein Disorder Annotations |
| license: cc-by-4.0 |
| tags: |
| - biology |
| - proteins |
| - intrinsic-disorder |
| - disprot |
| - annotation |
| - parquet |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/train-*.parquet |
| - split: test |
| path: data/test-*.parquet |
| --- |
| |
| # DisProt Protein Disorder Annotations |
|
|
| DisProt is a manually curated database of intrinsically disordered proteins and regions, including experimental evidence and functional annotations for protein disorder. |
|
|
| ## Splits |
|
|
| The split is deterministic by DisProt ID: `sha256(disprot_id) % 10`. Bucket `0` is `test`; buckets `1` through `9` are `train`. |
|
|
| | Split | Rows | |
| |---|---:| |
| | train | 2,875 | |
| | test | 324 | |
| | total | 3,199 | |
|
|
| ## Dataset Statistics |
|
|
| | Field | Value | |
| |---|---:| |
| | Protein entries | 3,199 | |
| | Curated region rows | 13,396 | |
|
|
| ## Usage |
|
|
| ```bash |
| pip install datasets |
| ``` |
|
|
| Load all splits: |
|
|
| ```python |
| from datasets import load_dataset |
| |
| ds = load_dataset("LiteFold/DisProt") |
| print(ds) |
| print(ds["train"][0]["disprot_id"]) |
| ``` |
|
|
| Load one split: |
|
|
| ```python |
| from datasets import load_dataset |
| |
| train = load_dataset("LiteFold/DisProt", split="train") |
| ``` |
|
|
| Filter proteins with high disorder content: |
|
|
| ```python |
| from datasets import load_dataset |
| |
| ds = load_dataset("LiteFold/DisProt", split="train") |
| high_disorder = ds.filter(lambda row: row["disorder_content"] is not None and row["disorder_content"] >= 0.5) |
| print(high_disorder[0]) |
| ``` |
|
|
| Load the region-level metadata: |
|
|
| ```python |
| import pandas as pd |
| from huggingface_hub import hf_hub_download |
| |
| path = hf_hub_download( |
| repo_id="LiteFold/DisProt", |
| repo_type="dataset", |
| filename="metadata/regions.parquet", |
| ) |
| regions = pd.read_parquet(path) |
| print(regions.head()) |
| ``` |
|
|
| ## Key Columns |
|
|
| | Column | Description | |
| |---|---| |
| | `disprot_id` | DisProt protein identifier. | |
| | `accession` | UniProt accession. | |
| | `name` | Protein name. | |
| | `organism` | Organism name. | |
| | `ncbi_taxon_id` | NCBI taxonomy ID. | |
| | `length` | Protein sequence length. | |
| | `disorder_content` | Fraction of sequence annotated as disordered. | |
| | `dataset_labels` | DisProt dataset labels. | |
| | `sequence` | Protein sequence. | |
| | `region_count` | Number of curated region annotations. | |
| | `region_ids` | Curated region IDs. | |
| | `region_starts` | Region start positions. | |
| | `region_ends` | Region end positions. | |
| | `region_terms` | Region term names. | |
| | `evidence_codes` | Region evidence codes. | |
| | `reference_ids` | Region reference IDs. | |
| | `cross_refs` | Region cross-references such as PDB IDs. | |
| | `feature_databases` | Feature sources such as Pfam or Gene3D. | |
| | `feature_ids` | Feature IDs. | |
| | `gene_names` | Gene names and synonyms. | |
| | `split_bucket` | Deterministic split bucket from `sha256(disprot_id) % 10`. | |
|
|
| # Citation |
|
|
| ``` |
| @article{quaglia2022disprot, |
| title = {{DisProt} in 2022: improved quality and accessibility of protein intrinsic disorder annotation}, |
| author = {Quaglia, Federica and M{\'e}sz{\'a}ros, B{\'a}lint and Salladini, Elisa and others}, |
| journal = {Nucleic Acids Research}, |
| volume = {50}, |
| number = {D1}, |
| pages = {D480--D487}, |
| year = {2022}, |
| doi = {10.1093/nar/gkab1082} |
| } |
| ``` |
