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.

Rewriting the history of an extinction-was a population of Steller's sea cows (Hydrodamalis gigas) at St Lawrence Island also driven to extinction?

The Kommandorskiye Islands population of Steller's sea cow (Hydrodamalis gigas) was extirpated ca 1768 CE. Until now, Steller's sea cow was thought to be restricted in historic times to Bering and Copper Islands, Russia, with other records in the last millennium from the western Aleutian Islands. However, Steller's sea cow bone has been obtained by the authors from St Lawrence Island, Alaska, which is significantly further north. Bone identity was verified using analysis of mitochondrial DNA. The nitrogen-15 (δ(15)N)/carbon-13 (δ(13)C) values for bone samples from St Lawrence Island were significantly (p ≤ 0.05) different from Bering Island samples, indicating a second population. Bone samples were dated to between 1030 and 1150 BP (approx. 800-920 CE). The samples date from close to the beginning of the mediaeval warm period, which could indicate that the population at St Lawrence Island was driven to extinction by climate change. A warming of the climate in the area may have changed the availability of kelp; alternatively or in addition, the animals may have been driven to extinction by the expansion of the Inuit from the Bering Strait region, possibly due to opening waterways, maybe following bowhead whales (Balaena mysticetus), or searching for iron and copper. This study provides evidence for a previously unknown population of sea cows in the North Pacific within the past 1000 years and a second Steller's sea cow extirpation event in recent history.