ABSTRACT
Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analyzing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images. OnTheFly2.0 can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform named entity recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms. Multiple files can be analyzed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein-protein and protein-chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0 currently supports 197 species and is available at http://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info.
ABSTRACT
Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.
