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Bioinformatics and biomedical informatics with ChatGPT: year one review: Biomedical Database Access

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Authors:

(1) Jinge Wang, Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA;

(2) Zien Cheng, Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA;

(3) Qiuming Yao, School of Computing, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;

(4) Li Liu, College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA and Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA;

(5) Dong Xu, Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;

(6) Gangqing Hu, Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA ([email protected]).

Table of Links

Abstract and 1. Introduction

2. Omics

3. Genetics

4. Biomedical Text Mining and 4.1. Performance Assessments across typical tasks

4.2. Biological pathway mining

5. Drug Discovery

5.1. Human-in-the-Loop and 5.2. In-context Learning

5.2 Instruction Finetuning

6. Biomedical Image Understanding

7. Bioinformatics Programming

7.1 Application in Applied Bioinformatics

7.2. Biomedical Database Access

7.2. Online tools for Coding with ChatGPT

7.4 Benchmarks for Bioinformatics Coding

8. Chatbots in Bioinformatics Education

9. Discussion and Future Perspectives

Author Contributions, Acknowledgements, Conflict of Interest Statement, Ethics Statement, and References


This paper is available on arxiv under CC BY 4.0 DEED license.


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