Combining neXtProt and WikiPathways strengths using SPARQL federated queries
Wednesday, 12 June 2019, 20:00 CEST
Presenter: Dr. Lydie Lane, CALIPHO group, SIB Swiss Institute of Bioinformatics
neXtProt is the SIB knowledge resource on human proteins. It aims to document the inter- and intra-individual diversity of human proteins at genomic, transcriptomic and proteomic levels, and to support applications specifically relevant to human proteins. It integrates curated information from UniProtKB/Swiss-Prot and other high-quality resources, and has been chosen as the reference knowledgebase for the HUPO Human Protein Project. Since 2019, neXtProt is part of the European Joint Project on Rare Disease. By providing FAIR molecular data on human genes it will contribute in improving the interoperability of the whole rare disease resource ecosystem.
For every human gene, neXtProt provides comprehensive annotation of population genomic variation, levels of expression in healthy tissues, detailed mass spectrometry data on gene products, and functional annotation. All annotations are triples that make use of community-approved standards. neXtProt has an intuitive web interface, dedicated tools for the proteomics community, a SPARQL endpoint allowing advanced data querying and an API allowing easy connection with other life science resources and tools.
In order to extend our current gene/protein-centric view to a more systemic view, we started to build federated SPARQL queries with WikiPathways. These queries allow to answer questions such as “how many pathways have at least one protein detected in the mitochondrial matrix?” or “how many proteins listed in WikiPathways are still lacking experimental evidence in human cells”? These queries can be used for internal quality control of both resources, and could serve as ground work to develop a common graphic interface to make the most of our respective contents.
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