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arXiv · 2306.08486

Collection of prokaryotic genome contents expectation rules from scientific literature

Serena Lam·Giorgio Gonnella
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Abstract

Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny, metabolic or morphological traits, geographical proximity, or habitat features are likely to exhibit similarities in their genomes. These similarities give rise to expectations about the content of genomes within these organism groups. Such expectations are often informally expressed in scientific literature, focusing on the analysis of individual genomes or comparisons among related groups of organisms. Our objective is to develop a system for formalized expectations as rules, facilitating automated verification, and evaluation of newly sequenced genomes. In this study, we present a database comprising rules manually extracted from scientific literature. Furthermore, we explore the feasibility of automatizing the extraction and analysis process using large language models, such as GPT3.5 and GPT4. We have developed a web application, EGCWebApp, which enables users to visualize and edit the rules. Additionally, we provided a Python library and command-line tools collection, egctools, to further extend the functionality for processing and managing these rules.

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Serena Lam, Giorgio Gonnella. 2023-06-14. Collection of prokaryotic genome contents expectation rules from scientific literature. https://arxiv.org/abs/2306.08486

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