
![image.png](./OPI_logo.png)
# Dataset Card for Open Protein Instructions (OPI)

## Dataset Description

- **Homepage:** 
- **Repository:** 
- **Paper:** 
- **Leaderboard:** 
- **Point of Contact:** 

### Dataset Summary

Open Protein Instructions(OPI) is the initial part of Open Biology Instructions(OBI) project, together with the subsequent Open Molecule Instructions(OMI), Open DNA Instructions(ODI), Open RNA Instructions(ORI) and Open Single-cell Instructions (OSCI). OBI is a project which aims to fully leverage the potential ability of Large Language Models(LLMs), especially the scientific LLMs like Galactica, to facilitate research in AI for Life Science community. While OBI is still in an early stage, we hope to provide a starting point for the community to bridge LLMs and biological domain knowledge.

## Dataset Structure

### Data Instances

```
instruction: 
    What is the EC classification of the input protein sequence based on its biological function?
input:                         
    MGLVSSKKPDKEKPIKEKDKGQWSPLKVSAQDKDAPPLPPLVVFNHLTPPPPDEHLDEDKHFVVALYDYTAMNDRDLQMLKGEKLQVLKGTGDWWLARS
    LVTGREGYVPSNFVARVESLEMERWFFRSQGRKEAERQLLAPINKAGSFLIRESETNKGAFSLSVKDVTTQGELIKHYKIRCLDEGGYYISPRITFPSL
    QALVQHYSKKGDGLCQRLTLPCVRPAPQNPWAQDEWEIPRQSLRLVRKLGSGQFGEVWMGYYKNNMKVAIKTLKEGTMSPEAFLGEANVMKALQHERLV
    RLYAVVTKEPIYIVTEYMARGCLLDFLKTDEGSRLSLPRLIDMSAQIAEGMAYIERMNSIHRDLRAANILVSEALCCKIADFGLARIIDSEYTAQEGAK
    FPIKWTAPEAIHFGVFTIKADVWSFGVLLMEVVTYGRVPYPGMSNPEVIRNLERGYRMPRPDTCPPELYRGVIAECWRSRPEERPTFEFLQSVLEDFYT
    ATERQYELQP
output: 
    2.7.10.2
```

### Data Splits
The OPI dataset folder structure is as follows:
```
./OPI_DATA/
├── AP
│   ├── Function
│   │   ├── test
│   │   │   ├── CASPSimilarSeq_function_test.jsonl
│   │   │   ├── IDFilterSeq_function_test.jsonl
│   │   │   └── UniProtSeq_function_test.jsonl
│   │   └── train
│   │       ├── function_description_train.json
│   │       └── function_description_train_0.01.json
│   ├── GO
│   │   ├── test
│   │   │   ├── CASPSimilarSeq_go_test.jsonl
│   │   │   ├── IDFilterSeq_go_test.jsonl
│   │   │   └── UniProtSeq_go_test.jsonl
│   │   └── train
│   │       ├── go_terms_train.json
│   │       └── go_terms_train_0.01.json
│   └── Keywords
│       ├── test
│       │   ├── CASPSimilarSeq_keywords_test.jsonl
│       │   ├── IDFilterSeq_keywords_test.jsonl
│       │   └── UniProtSeq_keywords_test.jsonl
│       └── train
│           ├── keywords_train.json
│           └── keywords_train_0.01.json
├── KM
│   ├── gSymbol2Cancer
│   │   ├── test
│   │   │   └── gene_symbol_to_cancer_test.jsonl
│   │   └── train
│   │       └── gene_symbol_to_cancer_train.json
│   ├── gName2Cancer
│   │   ├── test
│   │   │   └── gene_name_to_cancer_test.jsonl
│   │   └── train
│   │       └── gene_name_to_cancer_train.json
│   └── gSymbol2Tissue
│       ├── test
│       │   └── gene_symbol_to_tissue_test.jsonl
│       └── train
│           └── gene_symbol_to_tissue_train.json
└── SU
    ├── EC_number
    │   ├── test
    │   │   ├── CLEAN_EC_number_new_test.jsonl
    │   │   └── CLEAN_EC_number_price_test.jsonl
    │   └── train
    │       ├── CLEAN_EC_number_train.json
    ├── Fold_type-Remote
    │   ├── test
    │   │   └── Remote_test.jsonl
    │   └── train
    │       └── Remote_train.json
    └── Subcellular_location
        ├── test
        │   ├── location_test.jsonl
        └── train
            └── location_train.json
```

## Dataset Creation

The OPI dataset is curated on our own by extracting key information from [Swiss-Prot](https://www.uniprot.org/uniprotkb?facets=reviewed%3Atrue&query=%2A) database. The detailed construction pipeline is depicted in the supplementary material of our manuscript which has been submitted to NeurIPS 2023 Datasets and Benchmarks. The following figure shows the general construction process.
![image.png](./OPI_data.png)

## License
The dataset is licensed under a Creative Commons Attribution Non Commercial 4.0 License. The use of this dataset should also abide by the original [License & Disclaimer](https://www.uniprot.org/help/license) and [Privacy Notice](https://www.uniprot.org/help/privacy) of UniProt.
size_categories:1M<n<10M language:en license:cc-by-nc-4.0 biology region:us
{"language": ["en"], "license": "cc-by-nc-4.0", "size_categories": ["1M<n<10M"], "pretty_name": "OPI", "extra_gated_heading": "Acknowledge license to accept the repository", "extra_gated_prompt": "The Beijing Academy of Artificial Intelligence (hereinafter referred to as \"we\" or \"BAAI\") provides you with an open-source dataset (hereinafter referred to as \"dataset\") through the OPI HuggingFace repository (https://huggingface.co/datasets/BAAI/OPI). You can download the dataset you need and use it for purposes such as learning and research while abiding by the usage rules of each original dataset.\nBefore you acquire the open-source dataset (including but not limited to accessing, downloading, copying, distributing, using, or any other handling of the dataset), you should read and understand this \"OPI Open-Source Dataset Usage Notice and Disclaimer\" (hereinafter referred to as \"this statement\"). Once you acquire the open-source dataset, regardless of your method of acquisition, your actions will be regarded as acknowledgment of the full content of this statement.\n1. Ownership and Operation Rights\nYou should fully understand that the ownership and operation rights of the OPI HuggingFace repository (including the current and all previous versions) belong to BAAI. BAAI has the final interpretation and decision rights over this platform/tool and the open-source dataset plan.\nYou acknowledge and understand that due to updates and improvements in relevant laws and regulations and the need to fulfill our legal compliance obligations, we reserve the right to update, maintain, or even suspend or permanently terminate the services of this platform/tool from time to time. We will notify you of possible situations mentioned above reasonably such as through an announcement or email within a reasonable time. You should make corresponding adjustments and arrangements in a timely manner. However, we do not bear any responsibility for any losses caused to you by any of the aforementioned situations.\n2. Claim of Rights to Open-Source Datasets\nFor the purpose of facilitating your dataset acquisition and use for learning, and research, we have performed necessary steps such as format integration, data cleaning, labeling, categorizing, annotating, and other related processing on the third-party original datasets to form the open-source datasets for this platform/tool's users.\nYou understand and acknowledge that we do not claim the proprietary rights of intellectual property to the open-source datasets. Therefore, we have no obligation to actively recognize and protect the potential intellectual property of the open-source datasets. However, this does not mean that we renounce the personal rights to claim credit, publication, modification, and protection of the integrity of the work (if any) of the open-source datasets. The potential intellectual property and corresponding legal rights of the original datasets belong to the original rights holders.\nIn addition, providing you with open-source datasets that have been reasonably arranged, processed, and handled does not mean that we acknowledge the authenticity, accuracy, or indisputability of the intellectual property and information content of the original datasets. You should filter and carefully discern the open-source datasets you choose to use. You understand and agree that BAAI does not undertake any obligation or warranty responsibility for any defects or flaws in the original datasets you choose to use.\n3. Usage Restrictions for Open-Source Datasets\nYour use of the dataset must not infringe on our or any third party's legal rights and interests (including but not limited to copyrights, patent rights, trademark rights, and other intellectual property and other rights).\nAfter obtaining the open-source dataset, you should ensure that your use of the open-source dataset does not exceed the usage rules explicitly stipulated by the rights holders of the original dataset in the form of a public notice or agreement, including the range, purpose, and lawful purposes of the use of the original data. We kindly remind you here that if your use of the open-source dataset exceeds the predetermined range and purpose of the original dataset, you may face the risk of infringing on the legal rights and interests of the rights holders of the original dataset, such as intellectual property, and may bear corresponding legal responsibilities.\n4. Personal Information Protection\nDue to technical limitations and the public welfare nature of the open-source datasets, we cannot guarantee that the open-source datasets do not contain any personal information, and we do not bear any legal responsibility for any personal information that may be involved in the open-source datasets.\nIf the open-source dataset involves personal information, we do not bear any legal responsibility for any personal information processing activities you may involve when using the open-source dataset. We kindly remind you here that you should handle personal information in accordance with the provisions of the \"Personal Information Protection Law\" and other relevant laws and regulations.\nTo protect the legal rights and interests of the information subject and to fulfill possible applicable laws and administrative regulations, if you find content that involves or may involve personal information during the use of the open-source dataset, you should immediately stop using the part of the dataset that involves personal information and contact us as indicated in \"6. Complaints and Notices.\"\n5. Information Content Management\nWe do not bear any legal responsibility for any illegal and bad information that may be involved in the open-source dataset.\nIf you find that the open-source dataset involves or may involve any illegal and bad information during your use, you should immediately stop using the part of the dataset that involves illegal and bad information and contact us in a timely manner as indicated in \"6. Complaints and Notices.\"\n6. Complaints and Notices\nIf you believe that the open-source dataset has infringed on your legal rights and interests, you can contact us at 010-50955974, and we will handle your claims and complaints in accordance with the law in a timely manner.\nTo handle your claims and complaints, we may need you to provide contact information, infringement proof materials, and identity proof materials. Please note that if you maliciously complain or make false statements, you will bear all legal responsibilities caused thereby (including but not limited to reasonable compensation costs).\n7. Disclaimer\nYou understand and agree that due to the nature of the open-source dataset, the dataset may contain data from different sources and contributors, and the authenticity, accuracy, and objectivity of the data may vary, and we cannot make any promises about the availability and reliability of any dataset.\nIn any case, we do not bear any legal responsibility for any risks such as personal information infringement, illegal and bad information dissemination, and intellectual property infringement that may exist in the open-source dataset.\nIn any case, we do not bear any legal responsibility for any loss (including but not limited to direct loss, indirect loss, and loss of potential benefits) you suffer or is related to the open-source dataset.\n8. Others\nThe open-source dataset is in a constant state of development and change. We may update, adjust the range of the open-source dataset we provide, or suspend, pause, or terminate the open-source dataset service due to business development, third-party cooperation, changes in laws and regulations, and other reasons.\n", "extra_gated_fields": {"Name": "text", "Affiliation": "text", "Country": "text", "I agree to accept the license": "checkbox"}, "extra_gated_button_content": "Acknowledge license", "tags": ["biology"]}
TAGS
#size_categories-1M<n<10M #language-English #license-cc-by-nc-4.0 #biology #region-us 


!URL
# Dataset Card for Open Protein Instructions (OPI)

## Dataset Description

- Homepage: 
- Repository: 
- Paper: 
- Leaderboard: 
- Point of Contact: 

### Dataset Summary

Open Protein Instructions(OPI) is the initial part of Open Biology Instructions(OBI) project, together with the subsequent Open Molecule Instructions(OMI), Open DNA Instructions(ODI), Open RNA Instructions(ORI) and Open Single-cell Instructions (OSCI). OBI is a project which aims to fully leverage the potential ability of Large Language Models(LLMs), especially the scientific LLMs like Galactica, to facilitate research in AI for Life Science community. While OBI is still in an early stage, we hope to provide a starting point for the community to bridge LLMs and biological domain knowledge.

## Dataset Structure

### Data Instances



### Data Splits
The OPI dataset folder structure is as follows:


## Dataset Creation

The OPI dataset is curated on our own by extracting key information from Swiss-Prot database. The detailed construction pipeline is depicted in the supplementary material of our manuscript which has been submitted to NeurIPS 2023 Datasets and Benchmarks. The following figure shows the general construction process.
!URL

## License
The dataset is licensed under a Creative Commons Attribution Non Commercial 4.0 License. The use of this dataset should also abide by the original License & Disclaimer and Privacy Notice of UniProt.
# Dataset Card for Open Protein Instructions (OPI) ## Dataset Description

- Homepage: 
- Repository: 
- Paper: 
- Leaderboard: 
- Point of Contact: ### Dataset Summary

Open Protein Instructions(OPI) is the initial part of Open Biology Instructions(OBI) project, together with the subsequent Open Molecule Instructions(OMI), Open DNA Instructions(ODI), Open RNA Instructions(ORI) and Open Single-cell Instructions (OSCI). OBI is a project which aims to fully leverage the potential ability of Large Language Models(LLMs), especially the scientific LLMs like Galactica, to facilitate research in AI for Life Science community. While OBI is still in an early stage, we hope to provide a starting point for the community to bridge LLMs and biological domain knowledge. ## Dataset Structure ### Data Instances ### Data Splits
The OPI dataset folder structure is as follows: ## Dataset Creation

The OPI dataset is curated on our own by extracting key information from Swiss-Prot database. The detailed construction pipeline is depicted in the supplementary material of our manuscript which has been submitted to NeurIPS 2023 Datasets and Benchmarks. The following figure shows the general construction process.
!URL ## License
The dataset is licensed under a Creative Commons Attribution Non Commercial 4.0 License. The use of this dataset should also abide by the original License & Disclaimer and Privacy Notice of UniProt.
TAGS
#size_categories-1M<n<10M #language-English #license-cc-by-nc-4.0 #biology #region-us 
 # Dataset Card for Open Protein Instructions (OPI) ## Dataset Description

- Homepage: 
- Repository: 
- Paper: 
- Leaderboard: 
- Point of Contact: ### Dataset Summary

Open Protein Instructions(OPI) is the initial part of Open Biology Instructions(OBI) project, together with the subsequent Open Molecule Instructions(OMI), Open DNA Instructions(ODI), Open RNA Instructions(ORI) and Open Single-cell Instructions (OSCI). OBI is a project which aims to fully leverage the potential ability of Large Language Models(LLMs), especially the scientific LLMs like Galactica, to facilitate research in AI for Life Science community. While OBI is still in an early stage, we hope to provide a starting point for the community to bridge LLMs and biological domain knowledge. ## Dataset Structure ### Data Instances ### Data Splits
The OPI dataset folder structure is as follows: ## Dataset Creation

The OPI dataset is curated on our own by extracting key information from Swiss-Prot database. The detailed construction pipeline is depicted in the supplementary material of our manuscript which has been submitted to NeurIPS 2023 Datasets and Benchmarks. The following figure shows the general construction process.
!URL ## License
The dataset is licensed under a Creative Commons Attribution Non Commercial 4.0 License. The use of this dataset should also abide by the original License & Disclaimer and Privacy Notice of UniProt.