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.

COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database.

SUMMARY: In response to the COVID-19 pandemic, we established COVID-KOP, a new knowledgebase integrating the existing Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP) biomedical knowledge graph with information from recent biomedical literature on COVID-19 annotated in the CORD-19 collection. COVID-KOP can be used effectively to generate new hypotheses concerning repurposing of known drugs and clinical drug candidates against COVID-19 by establishing respective confirmatory pathways of drug action. AVAILABILITY AND IMPLEMENTATION: COVID-KOP is freely accessible at https://covidkop.renci.org/. For code and instructions for the original ROBOKOP, see: https://github.com/NCATS-Gamma/robokop.

Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface.

BACKGROUND: Efforts are underway to semantically integrate large biomedical knowledge graphs using common upper-level ontologies to federate graph-oriented application programming interfaces (APIs) to the data. However, federation poses several challenges, including query routing to appropriate knowledge sources, generation and evaluation of answer subsets, semantic merger of those answer subsets, and visualization and exploration of results. OBJECTIVE: We aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs. METHODS: We developed a biomedical query language and web application interphase-termed as Translator Query Language (TranQL)-to query semantically federated knowledge graphs and explore query results. TranQL uses the Biolink data model as an upper-level biomedical ontology and an API standard that has been adopted by the Biomedical Data Translator Consortium to specify a protocol for expressing a query as a graph of Biolink data elements compiled from statements in the TranQL query language. Queries are mapped to federated knowledge sources, and answers are merged into a knowledge graph, with mappings between the knowledge graph and specific elements of the query. The TranQL interactive web application includes a user interface to support user exploration of the federated knowledge graph. RESULTS: We developed 2 real-world use cases to validate TranQL and address biomedical questions of relevance to translational science. The use cases posed questions that traversed 2 federated Translator API endpoints: Integrated Clinical and Environmental Exposures Service (ICEES) and Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ICEES provides open access to observational clinical and environmental data, and ROBOKOP provides access to linked biomedical entities, such as "gene," "chemical substance," and "disease," that are derived largely from curated public data sources. We successfully posed queries to TranQL that traversed these endpoints and retrieved answers that we visualized and evaluated. CONCLUSIONS: TranQL can be used to ask questions of relevance to translational science, rapidly obtain answers that require assertions from a federation of knowledge sources, and provide valuable insights for translational research and clinical practice.

COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database.

In response to the COVID-19 pandemic, we established COVID-KOP, a new knowledgebase integrating the existing ROBOKOP biomedical knowledge graph with information from recent biomedical literature on COVID-19 annotated in the CORD-19 collection. COVID-KOP can be used effectively to test new hypotheses concerning repurposing of known drugs and clinical drug candidates against COVID-19. COVID-KOP is freely accessible at https://covidkop.renci.org/. For code and instructions for the original ROBOKOP, see: https://github.com/NCATS-Gamma/robokop.

ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources.

A proliferation of data sources has led to the notional existence of an implicit Knowledge Graph (KG) that contains vast amounts of biological knowledge contributed by distributed Application Programming Interfaces (APIs). However, challenges arise when integrating data across multiple APIs due to incompatible semantic types, identifier schemes, and data formats. We present ROBOKOP KG ( http://robokopkg.renci.org ), which is a KG that was initially built to support the open biomedical question-answering application, ROBOKOP (Reasoning Over Biomedical Objects linked in Knowledge-Oriented Pathways) ( http://robokop.renci.org ). Additionally, we present the ROBOKOP Knowledge Graph Builder (KGB), which constructs the KG and provides an extensible framework to handle graph query over and integration of federated data sources.

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.

SUMMARY: Knowledge graphs (KGs) are quickly becoming a common-place tool for storing relationships between entities from which higher-level reasoning can be conducted. KGs are typically stored in a graph-database format, and graph-database queries can be used to answer questions of interest that have been posed by users such as biomedical researchers. For simple queries, the inclusion of direct connections in the KG and the storage and analysis of query results are straightforward; however, for complex queries, these capabilities become exponentially more challenging with each increase in complexity of the query. For instance, one relatively complex query can yield a KG with hundreds of thousands of query results. Thus, the ability to efficiently query, store, rank and explore sub-graphs of a complex KG represents a major challenge to any effort designed to exploit the use of KGs for applications in biomedical research and other domains. We present Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways as an abstraction layer and user interface to more easily query KGs and store, rank and explore query results. AVAILABILITY AND IMPLEMENTATION: An instance of the ROBOKOP UI for exploration of the ROBOKOP Knowledge Graph can be found at http://robokop.renci.org. The ROBOKOP Knowledge Graph can be accessed at http://robokopkg.renci.org. Code and instructions for building and deploying ROBOKOP are available under the MIT open software license from https://github.com/NCATS-Gamma/robokop. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.