---
pretty_name: SwissTest
license: mit
language:
- en
task_categories:
- text-generation
tags:
- biology
- protein-design
- protein-sequence
- interpro
- gene-ontology
- benchmark
size_categories:
- 1K<n<10K
configs:
- config_name: go
  data_files:
  - split: test
    path: data/go/test-00000-of-00001.parquet
- config_name: ipr
  data_files:
  - split: test
    path: data/ipr/test-00000-of-00001.parquet
- config_name: ipr_go
  default: true
  data_files:
  - split: test
    path: data/ipr_go/test-00000-of-00001.parquet
---

# SwissTest

SwissTest contains English instructions for function-guided protein sequence design,
reference protein sequences, and GO molecular function or InterPro annotations.
It is a test dataset used in PDFBench. The three subsets (Hugging Face configurations) represent different
conditioning information for overlapping sets of reference sequences.

The dataset is packaged as one repository, `Knlife/SwissTest`, with three selectable
subsets: `go`, `ipr`, and `ipr_go`. The default subset is `ipr_go`.

## Subsets and splits

| Subset (configuration) | Split | Task records | Unique reference sequences | Excess exact duplicate records |
| --- | --- | ---: | ---: | ---: |
| `go` | test | 693 | 689 | 3 |
| `ipr` | test | 870 | 865 | 5 |
| `ipr_go` | test | 674 | 670 | 3 |

`go` provides GO molecular function annotations, `ipr` provides InterPro annotations,
and `ipr_go` provides both. Only `test` is supplied; no training or validation split
has been created. The default configuration is `ipr_go`.

The 2,237 task records contain 884 distinct reference sequences across all configurations.
The sets for `go` and `ipr` share 670 distinct sequences. All 670 distinct sequences
in `ipr_go` also occur in both other configurations. Configurations must not be treated
as disjoint train/test partitions. Annotations present in multiple configurations agree
for their shared reference sequences.

## Loading

Select a subset by passing its name as the second argument:

```python
from datasets import load_dataset

test = load_dataset("Knlife/SwissTest", "ipr_go", split="test")
go_test = load_dataset("Knlife/SwissTest", "go", split="test")
ipr_test = load_dataset("Knlife/SwissTest", "ipr", split="test")
```

For a local copy, pass its directory instead of the repository ID. The README declares
the data files for each configuration, so the original JSON archives and audit metadata
are excluded from loading.

## Record schema

All configurations use the same schema. Unavailable annotation types are empty lists;
annotations are never copied from another configuration to fill those lists.

| Field | Type | Meaning |
| --- | --- | --- |
| `id` | string | Configuration and zero-based source row, such as `go-000000`. Unique per task record in this snapshot. |
| `source_index` | int64 | Zero-based row index in the corresponding original JSON array. |
| `protein_id` | string | `sha256:` followed by the SHA-256 digest of the exact reference sequence. Shared by identical sequences; not a UniProt accession. |
| `instruction` | string | Original design instruction, including whitespace and punctuation. |
| `reference` | string | Original reference protein sequence. |
| `sequence_length` | int64 | Number of characters in `reference`. |
| `go_molecular_function` | list of structs | GO annotations with string fields `id` and `name`. |
| `interpro` | list of structs | InterPro annotations with string fields `id`, `name`, `type` and int64 fields `begin`, `end`. |

GO fields are renamed from `GO-ID` and `GO-Name`. InterPro fields are renamed from
`InterPro-ID`, `InterPro-Name`, `InterPro-Type`, `Beg`, and `End`. Their values and list
order are preserved. Coordinate values are retained exactly as supplied; no offset
conversion is applied. They satisfy `1 <= begin <= end <= sequence_length` in these files.
These locations describe annotations on the reference sequence.

The original `response#1` field equals `reference` in every one of the 2,237 records.
It is omitted from the normalized table. It must not be interpreted as a model-generated
prediction in these source files. The complete original records remain available in
`original/`.

## Preservation and validation

The conversion preserves every task record, its source order, the exact reference
sequence and instruction, and all annotation values and ordering. Exact duplicate
records are retained to preserve the original benchmark size and weighting.
Distinct reference proteins can share the same instruction.

All 2,930 GO annotation names contain leading or trailing whitespace. This whitespace
is preserved, together with the original punctuation and repeated terms in instructions.
Reference sequences range from 10 to 7,785 characters. The `ipr` configuration includes
the unknown residue symbol `X`; sequences are not truncated, filtered, or rewritten.
Several InterPro hits can refer to the same entry at different locations; these are retained.

Each Parquet file was reloaded with `datasets.load_dataset`, and every field was checked
against the normalized records. Reversing the field renaming and restoring `response#1`
reconstructed all original records. Archived JSON files match their source SHA-256 hashes.
Counts, duplicate row indices, sequence overlaps, checksums, and validation results are
recorded in [metadata/audit.json](metadata/audit.json).

## Repository files

```text
README.md
data/
  go/test-00000-of-00001.parquet
  ipr/test-00000-of-00001.parquet
  ipr_go/test-00000-of-00001.parquet
original/
  go.json
  ipr.json
  ipr_go.json
metadata/
  audit.json
  upstream_comparison.json
```

## Source and construction

These records match the test files in
[Knlife/SwiwwProtIPG](https://huggingface.co/datasets/Knlife/SwiwwProtIPG/tree/888930029b5c9ea0a0801f3d86732173c987056c),
at revision `888930029b5c9ea0a0801f3d86732173c987056c`:
`go_test.json`, `ipr_test.json`, and `ipr_go_test.json`.
The local source files replace the upstream `sequence` field with identical
`reference` and `response#1` fields. All other fields and the record order match.
The comparison and file hashes are recorded in
[metadata/upstream_comparison.json](metadata/upstream_comparison.json).

The [upstream card](https://huggingface.co/datasets/Knlife/SwiwwProtIPG/blob/888930029b5c9ea0a0801f3d86732173c987056c/README.md)
reports selection from UniProt/SwissProt between 2025-01-01 and 2025-08-25, with
InterPro and GO molecular function annotations. It describes constructing instructions
from annotation descriptions following Mol-Instructions. This construction history
is reported by the upstream publisher; it has not been independently reproduced here.
The task files contain no UniProt accessions or exact database release identifiers.

## License

This dataset is released under the MIT license, following the upstream dataset card.

## Citation

The upstream card provides the following PDFBench citation:

```bibtex
@misc{kuang2025pdfbenchbenchmarknovoprotein,
  title={PDFBench: A Benchmark for De novo Protein Design from Function},
  author={Jiahao Kuang and Nuowei Liu and Changzhi Sun and Tao Ji and Yuanbin Wu},
  year={2025},
  eprint={2505.20346},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url={https://arxiv.org/abs/2505.20346}
}
```

See the [PDFBench project](https://pdfbench.github.io/) for project context.