OligoM-Cancer: A multidimensional information platform for deep phenotyping of heterogenous oligometastatic cancer

Rongrong Wu; Hui Zong; Weizhe Feng; Ke Zhang; Jiakun Li; Erman Wu; Tong Tang; Chaoying Zhan; Xingyun Liu; Yi Zhou; Chi Zhang; Yingbo Zhang; Mengqiao He; Shumin Ren; Bairong Shen

Computational and Structural Biotechnology Journal (Dec 2024)

OligoM-Cancer: A multidimensional information platform for deep phenotyping of heterogenous oligometastatic cancer

Rongrong Wu,
Hui Zong,
Weizhe Feng,
Ke Zhang,
Jiakun Li,
Erman Wu,
Tong Tang,
Chaoying Zhan,
Xingyun Liu,
Yi Zhou,
Chi Zhang,
Yingbo Zhang,
Mengqiao He,
Shumin Ren,
Bairong Shen

Affiliations

Rongrong Wu: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Hui Zong: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Weizhe Feng: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Ke Zhang: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Jiakun Li: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Erman Wu: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Tong Tang: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Department of Computer Science and Information Technologies, Elviña Campus, University of A Coruña, A Coruña, Spain
Chaoying Zhan: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Xingyun Liu: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Department of Computer Science and Information Technologies, Elviña Campus, University of A Coruña, A Coruña, Spain
Yi Zhou: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Chi Zhang: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
Yingbo Zhang: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Mengqiao He: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Shumin Ren: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
Bairong Shen: Department of Urology and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Correspondence to: Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan, China.

Journal volume & issue: Vol. 24
pp. 561 – 570

Abstract

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Patients with oligometastatic cancer (OMC) exhibit better response to local therapeutic interventions and a more treatable tendency than those with polymetastatic cancers. However, studies on OMC are limited and lack effective integration for systematic comparison and personalized application, and the diagnosis and precise treatment of OMC remain controversial. The application of large language models in medicine remains challenging because of the requirement of high-quality medical data. Moreover, these models must be enhanced using precise domain-specific knowledge. Therefore, we developed the OligoM-Cancer platform (http://oligo.sysbio.org.cn), pioneering knowledge curation that depicts various aspects of oligometastases spectrum, including markers, diagnosis, prognosis, and therapy choices. A user-friendly website was developed using HTML, FLASK, MySQL, Bootstrap, Echarts, and JavaScript. This platform encompasses comprehensive knowledge and evidence of phenotypes and their associated factors. With 4059 items of literature retrieved, OligoM-Cancer includes 1345 valid publications and 393 OMC-associated factors. Additionally, the included clinical assistance tools enhance the interpretability and credibility of clinical translational practice. OligoM-Cancer facilitates knowledge-guided modeling for deep phenotyping of OMC and potentially assists large language models in supporting specialised oligometastasis applications, thereby enhancing their generalization and reliability.

Published in Computational and Structural Biotechnology Journal

ISSN: 2001-0370 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Technology: Chemical technology: Biotechnology
Website: https://www.journals.elsevier.com/computational-and-structural-biotechnology-journal

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