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:

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.

Repository files

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, 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.

The upstream card 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:

@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 for project context.