KG-Hub -- Building and Exchanging Biological Knowledge Graphs

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of knowledge graphs is lacking. Here we present KG-Hub, a platform that...

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Published inarXiv.org
Main Authors Caufield, J Harry, Putman, Tim, Schaper, Kevin, Unni, Deepak R, Hegde, Harshad, Callahan, Tiffany J, Cappelletti, Luca, Sierra AT Moxon, Ravanmehr, Vida, Carbon, Seth, Chan, Lauren E, Cortes, Katherina, Shefchek, Kent A, Glass Elsarboukh, Balhoff, James P, Fontana, Tommaso, Matentzoglu, Nicolas, Bruskiewich, Richard M, Thessen, Anne E, Harris, Nomi L, Munoz-Torres, Monica C, Haendel, Melissa A, Robinson, Peter N, Joachimiak, Marcin P, Mungall, Christopher J, Reese, Justin T
Format Paper
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 31.01.2023
Subjects
Exchanging
Feature extraction
Graph theory
Graphs
Knowledge representation
Machine learning
Microorganisms
Ontology
Tooling
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Summary:Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of knowledge graphs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of knowledge graphs. Features include a simple, modular extract-transform-load (ETL) pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate knowledge graphs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph machine learning, including node embeddings and training of models for link prediction and node classification.
ISSN:2331-8422