zERExtractor:An Automated Platform for Enzyme-Catalyzed Reaction Data Extraction from Scientific Literature
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arXiv
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| Autores principales: | , , , , , , , , , , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| Materias: | |
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| _version_ | 1866912537106186240 |
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| author | Zhou, Rui Ma, Haohui Xin, Tianle Zou, Lixin Hu, Qiuyue Cheng, Hongxi Lin, Mingzhi Guo, Jingjing Wang, Sheng Zhang, Guoqing Wei, Yanjie Zheng, Liangzhen |
| author_facet | Zhou, Rui Ma, Haohui Xin, Tianle Zou, Lixin Hu, Qiuyue Cheng, Hongxi Lin, Mingzhi Guo, Jingjing Wang, Sheng Zhang, Guoqing Wei, Yanjie Zheng, Liangzhen |
| contents | The rapid expansion of enzyme kinetics literature has outpaced the curation capabilities of major biochemical databases, creating a substantial barrier to AI-driven modeling and knowledge discovery. We present zERExtractor, an automated and extensible platform for comprehensive extraction of enzyme-catalyzed reaction and activity data from scientific literature. zERExtractor features a unified, modular architecture that supports plug-and-play integration of state-of-the-art models, including large language models (LLMs), as interchangeable components, enabling continuous system evolution alongside advances in AI. Our pipeline combines domain-adapted deep learning, advanced OCR, semantic entity recognition, and prompt-driven LLM modules, together with human expert corrections, to extract kinetic parameters (e.g., kcat, Km), enzyme sequences, substrate SMILES, experimental conditions, and molecular diagrams from heterogeneous document formats. Through active learning strategies integrating AI-assisted annotation, expert validation, and iterative refinement, the system adapts rapidly to new data sources. We also release a large benchmark dataset comprising over 1,000 annotated tables and 5,000 biological fields from 270 P450-related enzymology publications. Benchmarking demonstrates that zERExtractor consistently outperforms existing baselines in table recognition (Acc 89.9%), molecular image interpretation (up to 99.1%), and relation extraction (accuracy 94.2%). zERExtractor bridges the longstanding data gap in enzyme kinetics with a flexible, plugin-ready framework and high-fidelity extraction, laying the groundwork for future AI-powered enzyme modeling and biochemical knowledge discovery. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2508_09995 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | zERExtractor:An Automated Platform for Enzyme-Catalyzed Reaction Data Extraction from Scientific Literature Zhou, Rui Ma, Haohui Xin, Tianle Zou, Lixin Hu, Qiuyue Cheng, Hongxi Lin, Mingzhi Guo, Jingjing Wang, Sheng Zhang, Guoqing Wei, Yanjie Zheng, Liangzhen Biomolecules Emerging Technologies Machine Learning The rapid expansion of enzyme kinetics literature has outpaced the curation capabilities of major biochemical databases, creating a substantial barrier to AI-driven modeling and knowledge discovery. We present zERExtractor, an automated and extensible platform for comprehensive extraction of enzyme-catalyzed reaction and activity data from scientific literature. zERExtractor features a unified, modular architecture that supports plug-and-play integration of state-of-the-art models, including large language models (LLMs), as interchangeable components, enabling continuous system evolution alongside advances in AI. Our pipeline combines domain-adapted deep learning, advanced OCR, semantic entity recognition, and prompt-driven LLM modules, together with human expert corrections, to extract kinetic parameters (e.g., kcat, Km), enzyme sequences, substrate SMILES, experimental conditions, and molecular diagrams from heterogeneous document formats. Through active learning strategies integrating AI-assisted annotation, expert validation, and iterative refinement, the system adapts rapidly to new data sources. We also release a large benchmark dataset comprising over 1,000 annotated tables and 5,000 biological fields from 270 P450-related enzymology publications. Benchmarking demonstrates that zERExtractor consistently outperforms existing baselines in table recognition (Acc 89.9%), molecular image interpretation (up to 99.1%), and relation extraction (accuracy 94.2%). zERExtractor bridges the longstanding data gap in enzyme kinetics with a flexible, plugin-ready framework and high-fidelity extraction, laying the groundwork for future AI-powered enzyme modeling and biochemical knowledge discovery. |
| title | zERExtractor:An Automated Platform for Enzyme-Catalyzed Reaction Data Extraction from Scientific Literature |
| topic | Biomolecules Emerging Technologies Machine Learning |
| url | https://arxiv.org/abs/2508.09995 |