DVIDS - News - Mining the literature to improve our ability to counter biothreats

"The amount of genome data in the published literature has increased exponentially as the price of genomic sequencing has continued to fall. With that, a key question arises: How can all this data be used to enhance biomedical research and enhance warfighter capabilities? Researchers from Los Alamos National Laboratory (LANL) in New Mexico are finding new ways to mine that data, which could provide clues that will enable more effective countermeasures to biothreats. DTRA CB/JSTO-funded researchers managed by Dr. Dan Wolfe are leading the way by developing methods to mine underutilized data published as text. New methods to search for data in published text and supplemental information will have the potential to facilitate studies of microbial genomes, which will provide insight into how they cause disease and how we might protect warfighters and first responders against those diseases. The problem is, as the scientific literature grows, medical professionals are having increasing difficulty locating important information to respond rapidly to biothreats and emergent infectious diseases. In fact, the scientific literature now identifies millions of microbial genes and associated data. This text data rarely is loaded into public sequence databases that can be rapidly searched ... The group demonstrated their data-mining program by identifying gene locus tags of Burkholderia pseudomallei as a model organism. Their results show that the locus tags found in unindexed supplementary tables and within ranges like genomic islands contain the majority of locus tags. Significantly, their software provided access to data resources that are not accessed by conventional PubMed searches. The LANL group published their methods in BMC Bioinformatics journal article 'Mining locus tags in PubMed Central to improve microbial gene annotation.'  Researchers hope to convert a full text database into a functional gene annotation database that would be a valuable reference for most microbial genomes that don’t have recent or updated annotations available in public sequence databases. This innovative approach will make it easier to identify the biothreats to warfighters and first responders and thus rapidly develop successful countermeasures."