CodLncScape Provides a Self‐Enriching Framework for the Systematic Collection and Exploration of Coding LncRNAs

• Published in: Advanced science 2024-06, Vol.11 (22), p.e2400009-n/a
• Main Authors: Liu, Tianyuan, Qiao, Huiyuan, Wang, Zixu, Yang, Xinyan, Pan, Xianrun, Yang, Yu, Ye, Xiucai, Sakurai, Tetsuya, Lin, Hao, Zhang, Yang
• Format: Article
• Language: English
• Subjects: Cancer; Chatbots; Clustering; coding lncRNAs; computational biology; Computational Biology - methods; computational precision health; data collection; Humans; Knowledge; machine learning; Neoplasms - genetics; Peptides; Physiology; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Signal transduction; Software; Spermatogenesis; Squamous cell carcinoma; Visualization
• ISSN: 2198-3844; 2198-3844
• DOI: 10.1002/advs.202400009

Recent studies have revealed that numerous lncRNAs can translate proteins under specific conditions, performing diverse biological functions, thus termed coding lncRNAs. Their comprehensive landscape, however, remains elusive due to this field's preliminary and dispersed nature. This study introduces codLncScape, a framework for coding lncRNA exploration consisting of codLncDB, codLncFlow, codLncWeb, and codLncNLP. Specifically, it contains a manually compiled knowledge base, codLncDB, encompassing 353 coding lncRNA entries validated by experiments. Building upon codLncDB, codLncFlow investigates the expression characteristics of these lncRNAs and their diagnostic potential in the pan‐cancer context, alongside their association with spermatogenesis. Furthermore, codLncWeb emerges as a platform for storing, browsing, and accessing knowledge concerning coding lncRNAs within various programming environments. Finally, codLncNLP serves as a knowledge‐mining tool to enhance the timely content inclusion and updates within codLncDB. In summary, this study offers a well‐functioning, content‐rich ecosystem for coding lncRNA research, aiming to accelerate systematic studies in this field. codLncScape consists of a set of interconnected tools that work together to create a self‐sustaining loop of knowledge expansion in coding lncRNA research. The cycle begins with codLncDB, moves on to codLncFlow, and then to codLncWeb, which leads to codLncNLP, before returning to codLncDB. Specifically, it includes a knowledge base, analysis workflow, online platform, and NLP model.