A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

Details

Serval ID
serval:BIB_EF5C14AC5C45
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL
Journal
F1000Research
Author(s)
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Mendes de Farias Tarcisio
ISSN
2046-1402
ISSN-L
2046-1402
Publication state
Published
Issued date
29/10/2019
Peer-reviewed
Oui
Volume
8
Pages
1822
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
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
Pubmed
Open Access
Yes
Create date
23/01/2020 15:29
Last modification date
18/08/2020 5:21
Usage data