Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories.

MOTIVATION: As the number of public data resources continues to proliferate, identifying relevant datasets across heterogenous repositories is becoming critical to answering scientific questions. To help researchers navigate this data landscape, we developed Dug: a semantic search tool for biomedical datasets utilizing evidence-based relationships from curated knowledge graphs to find relevant datasets and explain why those results are returned. RESULTS: Developed through the National Heart, Lung and Blood Institute's (NHLBI) BioData Catalyst ecosystem, Dug has indexed more than 15 911 study variables from public datasets. On a manually curated search dataset, Dug's total recall (total relevant results/total results) of 0.79 outperformed default Elasticsearch's total recall of 0.76. When using synonyms or related concepts as search queries, Dug (0.36) far outperformed Elasticsearch (0.14) in terms of total recall with no significant loss in the precision of its top results. AVAILABILITY AND IMPLEMENTATION: Dug is freely available at https://github.com/helxplatform/dug. An example Dug deployment is also available for use at https://search.biodatacatalyst.renci.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Emerald ash borer intensifies harvest regimes on private land.

Invasive forest insects have significant direct impacts on forest ecosystems and they are also generating new risks, uncertainties, and opportunities for forest landowners. The growing prevalence and inexorable spread of invasive insects across the United States, combined with the fact that the majority of the nation's forests are controlled by thousands of autonomous private landowners, raises an important question: To what extent will private landowners alter their harvest practices in response to insect invasions? Using a quasi-experimental design, we conducted a causal analysis to investigate the influence of the highly impactful emerald ash borer (EAB) on (1) annual probability of harvest; (2) intensity of harvest; and (3) diameter of harvested trees, for both ash and non-ash species on private land throughout the Midwest and mid-Atlantic regions of the United States. We found that EAB detection had a negative impact on annual harvest probability and a positive impact on harvest intensity, resulting in a net increase in harvested biomass. Furthermore, our estimates suggest that EAB detection will influence private landowners to harvest greater quantities of ash, relative to non-ash species. We also found that harvested trees in EAB-infested areas had smaller diameters, on average, compared with those unaffected by EAB. These results can help policymakers, forest managers, and extension programs to anticipate and better advise landowners and managers about their options and the associated outcomes for forests.