Topic Name Description
Course material File Introduction: querying SIB Swiss Institute of Bioinformatics resources with SPARQL (slides)

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

File SPARQLing Rhea (slides)

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

URL SPARQLing Rhea (queries)

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

File SPARQLing MetaNetX/MNXref (slides)

MetaNetX/MNXref is a resource for systems biology and metabolomics

File SPARQLing neXtprot (slides)

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

File SPARQLing OMA (slides)

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


File SPARQLing Bgee (slides)

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


File SPARQLing GlyConnect (slides)

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

File SPARQLing HAMAP (slides)

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.

File SPARQLing UniProt (slides)

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.

File SPARQLing OrthoDB (slides)

OrthoDB: The hierarchical catalog of orthologs
mapping genomics to functional data

File SPARQLing Elixir friends: IDSM, Ensembl & DisGeNet (slides)

IDSM (Elixir Czech node): Integrated Database of Small Molecules

Ensembl (EBI RDF platform): Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation

DisGeNET: genes and variants associated to human diseases