Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz051.
Gastrointestinal (GI) cancer is common, characterized by high mortality, and includes oesophagus, gastric, liver, bile duct, pancreas, rectal and colon cancers. The insufficient specificity and sensitivity of biomarkers is still a key clinical hindrance for GI cancer diagnosis and successful treatment. The emergence of precision medicine', basket trial' and `field cancerization' concepts calls for an urgent need and importance for the understanding of how organ system cancers occur at the molecular levels. Knowledge from both the literature and data available in public databases is informative in elucidating the molecular alterations underlying GI cancer. Currently, most available cancer databases have not offered a comprehensive discovery of gene-disease associations, molecular alterations and clinical information by integrated text mining and data mining in GI cancer. We develop GIDB, a panoptic knowledge database that attempts to automate the curation of molecular signatures using natural language processing approaches and multidimensional analyses. GIDB covers information on 8730 genes with both literature and data supporting evidence, 248 miRNAs, 58 lncRNAs, 320 copy number variations, 49 fusion genes and 2381 semantic networks. It presents a comprehensive database, not only in parallelizing supporting evidence and data integration for signatures associated with GI cancer but also in providing the timeline feature of major molecular discoveries. It highlights the most comprehensive overview, research hotspots and the development of historical knowledge of genes in GI cancer. Furthermore, GIDB characterizes genomic abnormalities in multilevel analysis, including simple somatic mutations, gene expression, DNA methylation and prognosis. GIDB offers a user-friendly interface and two customizable online tools (Heatmap and Network) for experimental researchers and clinicians to explore data and help them shorten the learning curve and broaden the scope of knowledge. More importantly, GIDB is an ongoing research project that will continue to be updated and improve the automated method for reducing manual work.
胃肠道（GI）癌症很常见，其特点是死亡率高，包括食道癌、胃癌、肝癌、胆管癌、胰腺癌、直肠癌和结肠癌。生物标志物的特异性和敏感性不足仍然是 GI 癌症诊断和成功治疗的关键临床障碍。精准医学、篮子试验和肿瘤异质性概念的出现，迫切需要和重视了解器官系统癌症在分子水平上是如何发生的。来自文献和公共数据库中可用数据的知识有助于阐明 GI 癌症的分子变化。目前，大多数可用的癌症数据库尚未通过综合文本挖掘和数据挖掘在 GI 癌症中提供对基因-疾病关联、分子变化和临床信息的全面发现。我们开发了 GIDB，这是一个全景知识数据库，试图使用自然语言处理方法和多维分析来自动整理分子特征。GIDB 涵盖了 8730 个基因的信息，这些基因既有文献支持证据，也有数据支持证据，包括 248 个 miRNA、58 个 lncRNA、320 个拷贝数变异、49 个融合基因和 2381 个语义网络。它提供了一个全面的数据库，不仅平行提供了与 GI 癌症相关的特征的支持证据和数据集成，还提供了主要分子发现的时间线特征。它突出了 GI 癌症中基因最全面的概述、研究热点和历史知识的发展。此外，GIDB 在多层次分析中描述了基因组异常，包括简单的体细胞突变、基因表达、DNA 甲基化和预后。GIDB 提供了一个用户友好的界面和两个可定制的在线工具（Heatmap 和 Network），供实验研究人员和临床医生探索数据，帮助他们缩短学习曲线，拓宽知识范围。更重要的是，GIDB 是一个正在进行的研究项目，将继续更新和改进自动方法，以减少手动工作。
