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ssp_q3_rag

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Error code:   ConfigNamesError
Exception:    RuntimeError
Message:      Dataset scripts are no longer supported, but found ssp_q3_rag.py
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 67, in compute_config_names_response
                  config_names = get_dataset_config_names(
                      path=dataset,
                      token=hf_token,
                  )
                File "/usr/local/lib/python3.14/site-packages/datasets/inspect.py", line 161, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                      path,
                  ...<4 lines>...
                      **download_kwargs,
                  )
                File "/usr/local/lib/python3.14/site-packages/datasets/load.py", line 1217, in dataset_module_factory
                  raise e1 from None
                File "/usr/local/lib/python3.14/site-packages/datasets/load.py", line 1177, in dataset_module_factory
                  raise RuntimeError(f"Dataset scripts are no longer supported, but found {filename}")
              RuntimeError: Dataset scripts are no longer supported, but found ssp_q3_rag.py

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Dataset Card for Secondary Structure Prediction (Q3) Dataset for RAGProtein

Dataset Summary

The study of a protein’s secondary structure (Sec. Struc. P.) forms a fundamental cornerstone in understanding its biological function. This secondary structure, comprising helices, strands, and various turns, bestows the protein with a specific three-dimensional configuration, which is critical for the formation of its tertiary structure. In the context of this work, a given protein sequence is classified into three distinct categories, each representing a different structural element: H - Helix (includes alpha-helix, 3-10 helix, and pi helix), E - Strand (includes beta-strand and beta-bridge), C - Coil (includes turns, bends, and random coils).

Dataset Structure

Data Instances

For each instance, there is a string of the protein sequences, a sequence for the strucutral labels. See the Secondary structure prediction dataset viewer to explore more examples.

{'seq':'MRGSHHHHHHGSVKVKFVSSGEEKEVDTSKIKKVWRNLTKYGTIVQFTYDDNGKTGRGYVRELDAPKELLDMLARAEGKLN'
'label':[ 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 0, 0, 0, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2 ]
'msa':     'MRGSHHHHHHGSVKVKFVSSGEEKEVDTSKIKKVWRNLTKYGTIVQFTYDDNGKTGRGYVRELDAPKELLDMLARAEGKLN|MRGSHHHHHHGSVKVKFVSSGEEKEVDTSKIKKVWRNLTKYGTIVQFTYDDNGKTGRGYVRELDAPKELLDMLARAEGKLN...',
'str_emb': [seq_len, 384]
}

The average for the seq and the label are provided below:

Feature Mean Count
seq 256
label (0) 109
label (1) 54
label (2) 92

Data Fields

  • seq: a string containing the protein sequence
  • label: a sequence containing the structural label of each residue.
  • msa: "|" seperated MSA sequences
  • str_emb: GB.StructureTokenizer generated structure embedding from AF2 predicted structures

Data Splits

The secondary structure prediction dataset has 2 splits: train and test. Below are the statistics of the dataset.

Dataset Split Number of Instances in Split
Train 10,848
Test 667

Source Data

Initial Data Collection and Normalization

The datasets applied in this study were originally published by NetSurfP-2.0.

Licensing Information

The dataset is released under the Apache-2.0 License.

Processed data collection

Single sequence data are collected from this paper:

@misc{chen2024xtrimopglm,
  title={xTrimoPGLM: unified 100B-scale pre-trained transformer for deciphering the language of protein},
  author={Chen, Bo and Cheng, Xingyi and Li, Pan and Geng, Yangli-ao and Gong, Jing and Li, Shen and Bei, Zhilei and Tan, Xu and Wang, Boyan and Zeng, Xin and others},
  year={2024},
  eprint={2401.06199},
  archivePrefix={arXiv},
  primaryClass={cs.CL},
  note={arXiv preprint arXiv:2401.06199}
}
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