Skip to content

RDF

Home BioGateway Querying
Querying BGW with SPARQL PDF Print E-mail
This form lets you query the ontology-driven knowledge base through a SPARQL endpoint hosted by the Systems Biology group at the Norwegian University of Science and Technology ( NTNU ) . The underlying triple store contains close to 0.5 billon RDF triples of information.

Select a query and run it. Modify the parameters accordingly. Alternatively, enter SPARQL code in the query box below.
The graphs available for querying could be listed with the query Ont3 and are described below the query box.

Sample queries:


Query:


Graphs with asserted triples only
ontology - contains BFO-2.0, SIO and 113 ontologies from 'http://purl.obolibrary.org/obo/' (loaded as OWL). All of these 115 ontologies are availble as separate graphs as well.
go-basic - Gene Ontology basic version
intact - Protein-protein interactions from IntAct
The graphs below are limited to the 147 Reference Proteomes 'http://www.ebi.ac.uk/reference_proteomes'.
uniprot.animals - Protein information from the UniProt knowledge base for animals
uniprot.plants - Protein information from the UniProt knowledge base for plants
uniprot.fungi - Protein information from the UniProt knowledge base for fungi
uniprot.bacteria - Protein information from the UniProt knowledge base for bacteria
uniprot.archaea - Protein information from the UniProt knowledge base for archaea
goa.animals - Gene Ontology Annotations for animals
goa.plants - Gene Ontology Annotations for plants
goa.fungi - Gene Ontology Annotations for fungi
goa.bacteria - Gene Ontology Annotations for bacteria
goa.archaea - Gene Ontology Annotations for archaea
entrez.animals - Gene information from NCBI Entrez for animals
entrez.plants - Gene information from NCBI Entrez for plants
entrez.fungi - Gene information from NCBI Entrez for fungi
entrez.bacteria - Gene information from NCBI Entrez for bacteria
entrez.archaea - Gene information from NCBI Entrez for archaea
Graphs with asserted and inferred triples
go-basic-if
ncbitaxon-if(loaded as OWL)

Last Updated on Wednesday, 08 January 2014 14:59
 

Newsflash

Doctoral Degree for Aravind Venkatesan On 13th Feb 2014, Aravind Venkatesan successfully defended his Ph.D. thesis "Application of Semantic Web Technology to establish knowledge management and discovery in the Life Sciences"  and was awarded the title of Doctor in Sciences by NTNU.

 
BioGateway 2.00
Major revision
1. Local URIs replaced with external resolvable URIs
2. Data from SwissProt extended to UniProt
3. Data from IntAct added
4. Scope limited to 147 Reference Proteomes
5. Inferred triples limited to those supported explicitly by the ontology plus 'priority over is_a'
 
Genes2GO: Gene Ontology matrix builder
Genes2GO builds a binary matrix with genes and GO IDs/Terms.

Cell Cycle Ontology v.2.01 and Gene Expression Knowledge Base V.1.01
Streamlined modelling of post-translational protein modifications which makes querying for modifications straightforward (e.g. query APO4)
 

Main Menu