The BioGateway Resource
A Semantic Systems Biology Database
BioGateway consists of a graph-based database built on Semantic Web principles, a SPARQL endpoint allowing users to query it, and a Cytoscape app which integrates the query functionality directly into your network building workflow.
What is BioGateway?
BioGateway is an initiative that enables a Semantic Systems Biology approach. It provides an entry point to access a data warehouse where biological data is gathered in the form of triples (using RDF). The systems can be queried using SPARQL. The BioGateway system can also be explored using the SPARQL browser. With this browser, SPARQL results can be visually seen as a network of resources.
The Cytoscape App
We have developed an app for Cytoscape to allow you to directly integrate the power of our Semantic Knowledge Base into your network building workflow. With the Query Builder tool, you can formulate the topology of what you are looking for, and it will generate the SPARQL query for you.
The query result can then be imported directly into the Cytoscape network you are building – without having to deal with result file formats, incompatible column standards or identifiers.
The BioGateway Database
BioGateway contains several datasets, in the form of bridge graphs, from various sources. Each of these bridge graphs has a set of relation types, describing different types of relationships between entities. The different graphs, the most important relation types in them, and their meaning is described below.
Protein → Taxon
Refers to the taxon that the subject protein is part of.
INVOLVED IN DISEASE
Protein → Disease
Refers to the diseases that the subject protein is involved in.
MOLECULARLY INTERACTS WITH
Protein → Protein
This relation is based on Protein-Protein Interactions (PPIs) from the IntAct dataset, and refers to curated direct relationships between the subject protein and any other protein.
ENABLES MOLECULAR FUNCTION / INVOLVED IN BIOLOGICAL PROCESS / PART OF CELLULAR COMPONENT
Protein → GO Term
Refers to the GO Terms that the subject protein is annotated with.
This also includes parent GO Terms.
Gene → Taxon
Annotates the taxon that the subject gene is part of.
Gene → Protein
Annotates the proteins that the subject gene is encoding.
Note: some genes encode multiple proteins.
Is related to
Protein → Gene
Refers to the interaction between a Transcription Factor and a Target Gene. Usually this interaction results in a regulation of the target gene. BioGateway contains TF2TG relations both from curated resources (TRRUST, TFactS, HTRIdb, SIGNOR) and from a text mining effort carried out between CNIO/BSC, Spain, and NTNU (to be published soon).
Please let us know if you have any questions, or if something is not working correctly for you.