CurateGPT: A flexible language-model assisted biocuration tool
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arXiv
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| Main Authors: | , , , , , , , , , , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866912099487186944 |
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| author | Caufield, Harry Kroll, Carlo O'Neil, Shawn T Reese, Justin T Joachimiak, Marcin P Hegde, Harshad Harris, Nomi L Krishnamurthy, Madan McLaughlin, James A Smedley, Damian Haendel, Melissa A Robinson, Peter N Mungall, Christopher J |
| author_facet | Caufield, Harry Kroll, Carlo O'Neil, Shawn T Reese, Justin T Joachimiak, Marcin P Hegde, Harshad Harris, Nomi L Krishnamurthy, Madan McLaughlin, James A Smedley, Damian Haendel, Melissa A Robinson, Peter N Mungall, Christopher J |
| contents | Effective data-driven biomedical discovery requires data curation: a time-consuming process of finding, organizing, distilling, integrating, interpreting, annotating, and validating diverse information into a structured form suitable for databases and knowledge bases. Accurate and efficient curation of these digital assets is critical to ensuring that they are FAIR, trustworthy, and sustainable. Unfortunately, expert curators face significant time and resource constraints. The rapid pace of new information being published daily is exceeding their capacity for curation. Generative AI, exemplified by instruction-tuned large language models (LLMs), has opened up new possibilities for assisting human-driven curation. The design philosophy of agents combines the emerging abilities of generative AI with more precise methods. A curator's tasks can be aided by agents for performing reasoning, searching ontologies, and integrating knowledge across external sources, all efforts otherwise requiring extensive manual effort. Our LLM-driven annotation tool, CurateGPT, melds the power of generative AI together with trusted knowledge bases and literature sources. CurateGPT streamlines the curation process, enhancing collaboration and efficiency in common workflows. Compared to direct interaction with an LLM, CurateGPT's agents enable access to information beyond that in the LLM's training data and they provide direct links to the data supporting each claim. This helps curators, researchers, and engineers scale up curation efforts to keep pace with the ever-increasing volume of scientific data. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2411_00046 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | CurateGPT: A flexible language-model assisted biocuration tool Caufield, Harry Kroll, Carlo O'Neil, Shawn T Reese, Justin T Joachimiak, Marcin P Hegde, Harshad Harris, Nomi L Krishnamurthy, Madan McLaughlin, James A Smedley, Damian Haendel, Melissa A Robinson, Peter N Mungall, Christopher J Computation and Language Artificial Intelligence Databases Quantitative Methods Effective data-driven biomedical discovery requires data curation: a time-consuming process of finding, organizing, distilling, integrating, interpreting, annotating, and validating diverse information into a structured form suitable for databases and knowledge bases. Accurate and efficient curation of these digital assets is critical to ensuring that they are FAIR, trustworthy, and sustainable. Unfortunately, expert curators face significant time and resource constraints. The rapid pace of new information being published daily is exceeding their capacity for curation. Generative AI, exemplified by instruction-tuned large language models (LLMs), has opened up new possibilities for assisting human-driven curation. The design philosophy of agents combines the emerging abilities of generative AI with more precise methods. A curator's tasks can be aided by agents for performing reasoning, searching ontologies, and integrating knowledge across external sources, all efforts otherwise requiring extensive manual effort. Our LLM-driven annotation tool, CurateGPT, melds the power of generative AI together with trusted knowledge bases and literature sources. CurateGPT streamlines the curation process, enhancing collaboration and efficiency in common workflows. Compared to direct interaction with an LLM, CurateGPT's agents enable access to information beyond that in the LLM's training data and they provide direct links to the data supporting each claim. This helps curators, researchers, and engineers scale up curation efforts to keep pace with the ever-increasing volume of scientific data. |
| title | CurateGPT: A flexible language-model assisted biocuration tool |
| topic | Computation and Language Artificial Intelligence Databases Quantitative Methods |
| url | https://arxiv.org/abs/2411.00046 |