F1000Res.: auth.: group Dessimoz

F1000Res. 2019 Oct 29;8:1822.

doi: 10.12688/f1000research.21027.1. eCollection 2019.

A Hands-On Introduction to Querying Evolutionary Relationships Across Multiple Data Sources Using SPARQL


The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative analyses, combining information from multiple sources. However, analyzing evolutionary data in RDF is not trivial, due to the steep learning curve required to understand both the data models adopted by different RDF data sources, as well as the SPARQL query language. In this article, we provide a hands-on introduction to querying evolutionary data across multiple sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD). We present four protocols in increasing order of complexity. In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups. Finally, we show how orthology information in different sources can be compared, through the use of federated SPARQL queries.

Keywords: Comparative Genomics; Orthology; Resource Description Framework (RDF); SPARQL; Sequence Homology.