Reproducible Mapping of Tabular Data into Semantic Knowledge Graphs with OntoWeaver and BioCypher
Johann Dréo, Claire Laudy, Sebastian Lobentanzer, Marko Baric, Ekaterina Gaydukova, Benno Schwikowski · 2024
Large-scale high-level information fusion and data integration is a pressing need in several scientific domains. Recently, the biomedical community established BioCypher, a tool to help create large Semantic Knowledge Graphs (SKGs) in a simple and reproducible way. In this article, we introduce OntoWeaver, a companion tool to BioCypher that allows to easily extract tabular data into SKGs by using a simple declarative mapping. OntoWeaver allows implementing reproducible mappings from tabular data to SKGs with a simple declarative configuration. The use of OntoWeaver and BioCypher is demonstrated in two different use cases: cancer database integration and invasive species monitoring. We believe that OntoWeaver and BioCypher, both free and open-source software, can help several scientific communities working on SKGs and high-level information fusion problems.