emiRIT: A text-mining based resource for microRNA information

Abstract

Motivation: microRNAs (miRNAs) are essential gene regulators and their dysregulation often leads to diseases. Easy access to miRNA information is crucial for interpreting generated experimental data, connecting facts across publications, and developing new hypotheses built on previous knowledge. Here, we present emiRIT, a text mining-based resource, which presents miRNA information mined from the literature through a user-friendly interface. Results: We collected 149,233 miRNA-PubMed ID pairs from Medline between January 1997 to May 2020. emiRIT currently contains miRNA-gene regulation (60,491 relations); miRNA-disease (cancer) (12,300 relations); miRNA-biological process and pathways (23,390 relations); and circulatory miRNAs in extracellular locations (3,782 relations). Biological entities and their relation to miRNAs were extracted from Medline abstracts using publicly available and in-house developed text mining tools, and the entities were normalized to facilitate querying and integration. We built a database and an interface to store and access the integrated data, respectively. Conclusion: We provide an up-to-date and user-friendly resource to facilitate access to comprehensive miRNA information from the literature on a large-scale, enabling users to navigate through different roles of miRNA and examine them in a context specific to their information needs. To assess our resource's information coverage, in the absence of gold standards, we have conducted two case studies focusing on the target and differential expression information of miRNAs in the context of diseases. Database URL: https://research.bioinformatics.udel.edu/emirit/

Student biocuration projects as a learning environment

“…For microRNA projects the HGNC symbol of the microRNA target is used to search either miRTarBase 49 or emiRIT. 50 If no suitable articles are identified, then PubMed is searched with the HGNC symbol and key words such as microRNA (Supplementary Table S10, Extended data 46 ). Articles are only curated if there is evidence that the microRNA binds to the target mRNA that encodes for one of the prioritised proteins (usually this is provided by a reporter assay) and there is sufficient information about the species of the microRNA and mRNA used in the experiments.…”

“…Articles are only curated if there is sufficient information about the species of the protein used in the experiments and the article provides experimental data that describes the role of the protein in the disease or process that the student is curating. For microRNA projects the HGNC symbol of the microRNA target is used to search either miRTarBase 49 or emiRIT 50 . If no suitable articles are identified, then PubMed is searched with the HGNC symbol and key words such as microRNA (Supplementary Table S10).…”