Inflammatory Bowel Disease (IBD) Interactome: text database and analyzed data of experimental research in humans between 1990-2020

We present the corpus of abstracts (database), raw and analyzed data tables as well as MATLAB™ custom code associated to our paper "Network analysis of inflammatory bowel disease research: towards the interactome". In our work we quantitatively analyze, through text mining of scientific abstracts and network analysis, how representativeness of components from the different functional levels (i.e. immune-endocrine cells, molecules, genes and biological processes and modulating factors) involved in the human Inflammatory Bowel Disease (IBD) interactome and their relations have changed over time. We expected to understand how knowledge in this field has been constructed and provide insights on the principal challenges for approaching the interactome of this disease. Tables Supporting Table S1_Raw corpus of abstracts: we present the raw set of abstracts and associated metadata retrieved as a result of our PubMed query and dowloading through the bibliographic manager Zotero 5.0. Rows represent each abstract and columns metadata associated to each one of them. Specifically, the eleventh column, named "AbstractNote", contains the text of the abstract itself. Also important, the third column named "PublicationYear", contains the year of publication of the abstract. Supporting Table S2_Curated corpus of abstracts: we present the set of abstracts as detailed for Supporting Table S1 but after curation steps (namely, elimination of duplicates and abstracts only studying animal models). Supporting Table S3_Target Matrix of Cells, Supporting Table S4_Target Matrix of Molecules, Supporting Table S5_Target Matrix of Genes, Supporting Table S6_Target Matrix of Biological Processes and Modulating Factors: we present the set of immune-endocrine cells, molecules, genes and biological processes and modulating factors that have been involved in human IBD in recent reviews (Graham, D.B., Xavier, R.J. Nature 578, 527–539 (2020); Konstantina E. Vennou et al. Genomics 112(2), 1761-1767 (2020); Lahue, K.G. et al. Genes Immun 21, 311–325 (2020)). Rows show each of the immune-endocrine cells, molecules, genes and biological processes and modulating factors of interest and columns the semantic synonyms of each one of them. Semantic synonyms were constructed using domain-knowledge and catalogues (GeneCards, HGNG, HUGO, UniProt, Genetics Home Reference from the NIH). The occurrence of these set of immune-endocrine cells, molecules, genes and biological processes and modulating factors an