Querying SIB resources with SPARQL

Presentation of the SIB Swiss Institute of Bioinformatics + quick introductions to RDF and SPARQL in general.

Rhea is a comprehensive expert-curated resource of biochemical transformations, transport reactions, and spontaneous reactions of biological interest.

Accompanying Jupyter Notebook (hands-on introduction to querying metabolism related data across multiple data sources using SPARQL).

MetaNetX/MNXref is a resource for systems biology and metabolomics

The neXtProt knowledgebase is an integrative resource providing both data on human protein and the tools to explore these.

In this tutorial, you will learn how to query and retrieve orthology and paralogy information from the OMA database with SPARQL.

In this tutorial, you will learn how to query gene expression patterns from the Bgee database with SPARQL.

GlyConnect is a platform integrating sources of information to help characterise the molecular components of protein glycosylation.

HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is used to annotate protein records in UniProtKB via UniProt's automatic annotation pipeline.

The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.

In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data.