Abstract
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/.
Highlights
Inflammatory bowel disease (IBD) is a complex intestinal disorder with two notable phenotypes: Crohn’s disease (CD) and ulcerative colitis (UC) [1]
A global index is created by matching the titles and the abstracts retrieved from PubMed against the dictionaries to create a KB index, which links each concept to its occurrences in the PubMed records
The nodes represent the entities from the selected dictionaries and are colour-coded, while numbering on the edges or links represents the number of PubMed records (Figure 2B) showing co-occurrence of the entities
Summary
Inflammatory bowel disease (IBD) is a complex intestinal disorder with two notable phenotypes: Crohn’s disease (CD) and ulcerative colitis (UC) [1]. The incidence and prevalence of IBD are highest in westernized nations. Increased incidence of IBD, especially UC, has been found among sub-Saharan Africans [8]. Population-specific differences have been identified, e.g. in South Africa, the incidence of CD in 194 investigated patients was 18% [35] in whites, 78% [152] in mixed race and 4% [7] in blacks [9]. IBD does not present itself as an isolated disease but exhibits several extraintestinal manifestations and complications. These manifestations include arthropathies, mucocutaneous, hepatobiliary, ophthalmological and peripheral arthritis [10, 11].
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