| | --- |
| | dataset_info: |
| | features: |
| | - name: seq |
| | dtype: string |
| | - name: label |
| | dtype: int64 |
| | splits: |
| | - name: train |
| | num_bytes: 7657550 |
| | num_examples: 23375 |
| | - name: test |
| | num_bytes: 1550597 |
| | num_examples: 4791 |
| | download_size: 9032101 |
| | dataset_size: 9208147 |
| | configs: |
| | - config_name: default |
| | data_files: |
| | - split: train |
| | path: data/train-* |
| | - split: test |
| | path: data/test-* |
| | license: apache-2.0 |
| | task_categories: |
| | - text-classification |
| | tags: |
| | - chemistry |
| | - biology |
| | - medical |
| | size_categories: |
| | - 10K<n<100K |
| | --- |
| | |
| |
|
| | # Dataset Card for Cloning CLF Dataset |
| |
|
| | ### Dataset Summary |
| |
|
| | Protein structure determination includes a series of experimental stages to yield stable proteins for X-ray crystallography. Specifically, the proteins are first selected and expressed, then purified for crystal structure determination. Each step corresponds to a "stage tag" to denote whether the protein is stable under a certain stage. |
| |
|
| |
|
| | ## Dataset Structure |
| |
|
| | ### Data Instances |
| | For each instance, there is a string representing the protein sequence and an integer label indicating whether a protein sequence is stable under a certain stage. See the [Cloning CLF dataset viewer](https://huggingface.co/datasets/Bo1015/cloning_clf/viewer) to explore more examples. |
| |
|
| | ``` |
| | {'seq':'MEHVIDNFDNIDKCLKCGKPIKVVKLKYIKKKIENIPNSHLINFKYCSKCKRENVIENL' |
| | 'label':1} |
| | ``` |
| |
|
| | The average for the `seq` and the `label` are provided below: |
| |
|
| | | Feature | Mean Count | |
| | | ---------- | ---------------- | |
| | | seq | 315 | |
| | | label (0) | 0.6 | |
| | | label (1) | 0.4 | |
| |
|
| |
|
| |
|
| |
|
| | ### Data Fields |
| |
|
| | - `seq`: a string containing the protein sequence |
| | - `label`: a float value indicating the $k_cat$ score of the protein sequence. |
| | |
| | ### Data Splits |
| | |
| | The cloning clf dataset has 2 splits: _train_ and _test_. Below are the statistics of the dataset. |
| |
|
| | | Dataset Split | Number of Instances in Split | |
| | | ------------- | ------------------------------------------- | |
| | | Train | 23,375 | |
| | | Test | 4,791 | |
| |
|
| | ### Source Data |
| |
|
| | #### Initial Data Collection and Normalization |
| | The dataset is collected from [PredPPCrys](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105902), which manually annotated thousands of proteins with different experimental procedures. |
| |
|
| | ### Licensing Information |
| |
|
| | The dataset is released under the [Apache-2.0 License](http://www.apache.org/licenses/LICENSE-2.0). |
| |
|
| | ### Citation |
| | If you find our work useful, please consider citing the following 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} |
| | } |
| | ``` |
