To date, research on inflammatory bowel disease (IBD, encompassing Crohn’s disease and ulcerative colitis), a chronic complex disorder, has generated a large amount of data scattered across published literature (1 06 333) listed in PubMed on 14 October 2020, and no dedicated database currently exists that catalogues information on genes associated with IBD. We aimed to manually curate 289 genes that are experimentally validated to be linked with IBD and its known phenotypes. Furthermore, we have developed an integrated platform providing information about different aspects of these genes by incorporating several resources and an extensive text-mined knowledgebase. The curated IBD database (IBDDB) allows the selective display of collated 34 subject-specific concepts (listed as columns) exportable through a user-friendly IBDDB portal. The information embedded in concepts was acquired via text-mining of PubMed (manually cleaned and curated), accompanied by data-mining from varied resources. The user can also explore different biomedical entities and their co-occurrence with other entities (about one million) from 11 curated dictionaries in the indexed PubMed records. This functionality permits the user to generate and cross-examine a new hypothesis that is otherwise not easy to comprehend by just reading the published abstracts and papers. Users can download required information using various file formats and can display information in the form of networks. To our knowledge, no curated database of IBD-related genes is available so far. IBDDB is free for academic users and can be accessed at https://www.cbrc.kaust.edu.sa/ibd/.

中文翻译：

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IBDDB：一个手动策划和文本挖掘增强的炎症性肠病相关基因数据库

迄今为止，关于炎症性肠病（IBD，包括克罗恩病和溃疡性结肠炎）这种慢性复杂疾病的研究已经产生了大量数据，这些数据散布在 2020 年 10 月 14 日 PubMed 上列出的已发表文献 (1 06 333) 中，并且没有目前存在专门的数据库，该数据库对与 IBD 相关的基因信息进行编目。我们旨在手动管理 289 个经过实验验证与 IBD 及其已知表型相关的基因。此外，我们开发了一个集成平台，通过整合多种资源和广泛的文本挖掘知识库，提供有关这些基因不同方面的信息。策划的 IBD 数据库 (IBDDB) 允许有选择地显示整理的 34 个特定主题的概念（列为列），可通过用户友好的 IBDDB 门户导出。嵌入在概念中的信息是通过 PubMed 的文本挖掘（手动清理和整理）获得的，同时从各种资源中进行数据挖掘。用户还可以从 PubMed 索引记录中的 11 个精选词典中探索不同的生物医学实体及其与其他实体（约一百万）的共现。此功能允许用户生成和交叉检查一个新假设，否则仅通过阅读已发表的摘要和论文就不容易理解。用户可以使用各种文件格式下载所需的信息，并可以网络形式显示信息。据我们所知，目前还没有经过整理的 IBD 相关基因数据库。IBDDB 对学术用户免费，可通过 https://www.cbrc.kaust.edu.sa/ibd/ 访问。