We have developed the BioGateway App, a Cytoscape plugin that supports the building of a wish list of questions that are translated to SPARQL queries, which are launched against the BioGateway server. We demonstrate the functionality of the BioGateway App both in simple and more complex use cases, taken from our website https://www.biogateway.eu/examples/
1.1.
Introduction
The BioGateway (BGW) triple store [
The main feature of the BioGateway App is the Query Builder, which supports the
design of queries that are built from definitions of proteins or genes and a relationship
to either an ontology term or another protein or gene. By adding additional query parts
line by line, increasingly complex and restrictive or inclusive queries can be composed.
The Run Query command converts these to native SPARQL queries that are launched
against the BioGateway 3.0 SPARQL endpoint [
The main information that is subject to the query is obtained from IntAct [
Copyright © 2019 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0). The selection of terms of interest such as genes, proteins, ontology terms and relation types is facilitated by an autocomplete function that is driven by a REST API of a NoSQL database loaded with all the entity names and metadata from the BioGateway server, to allow quick response times. To ensure compatibility between the App and the BioGateway data, upon startup the App fetches an XML-based configuration file from our webserver. This file contains the relation types and their URIs, default settings and the default layout style for BioGateway graphs, as well as available metadata types and the query constraints that this metadata enables, allowing some updates to the App without requiring the user to reinstall it. User preferences set in the BioGateway tab of the Cytoscape Control Panel are stored between sessions, such as the default query constraints related to species, data sources, and additional selection criteria for querying the BioGateway content. 2.2.
Next to specifying the results through the definition of restrictive queries, the Query Constraints section of the BioGateway tab in the Control Panel allows additional constraints for specific relations, such as setting a minimum confidence score for ProteinProtein Interactions, as provided by IntAct (Orchard et al. 2013). This control panel also allows the selection of extra types of metadata to be loaded together with the results, but as this may significantly increase query time, this metadata can also be added after the network is complete (Reload Metadata), so that it can be used for filtering and display options. 3.
We will demonstrate the functionality of the BioGateway App both in simple and more complex use cases, taken from https://www.biogateway.eu/examples/. While BGW 3.0.0 contains only human data, BGW 3.0.1 (release date expected in December 2019) will include data for 25 best-studied eukaryotes. 4.