PHILM2Web: A high-throughput database of macromolecular host –pathogen interactions on the Web

AbstractDuring infection, the pathogen ’s entry into the host organism, breaching the host immune defense, spread and multiplication are frequently mediated by multiple interactions between the host and pathogen proteins. Systematic studying of host–pathogen interactions (HPIs) is a challenging task for both experimental and computat ional approaches and is critically dependent on the previously obtained knowledge about these interactions found in the biomedical literature. While several HPI databases exist that manually filter HPI protein–protein interactions from the generic databases and curated experimental interactomic st udies, no comprehensive database on HPIs obtained from the biomedical literature is currently available. Here, we introduce a high-throughput literature-mining platform for extracting HPI data that includes the most comprehensive to date collection of HPIs obtained from the PubMed abstracts. Our HPI data portal, PHILM2Web (Pathogen–Host Interactions by Literature Mining on the Web), integrates an automatically generated database of interactions extracted by PHILM, our high-precision HPI literature-mining algorithm. Currently, the database contains 23 581 generic HPIs between 157 host and 4 03 pathogen organisms from 11 609 abstracts. The interactions were obtained from processing 608 972 PubMed abstracts, each containing mentions of at least one host and one pathogen organisms. In response to the coronavirus disease 2019 (COVID-19) pandemi...
Source: Database : The Journal of Biological Databases and Curation - Category: Databases & Libraries Source Type: research