Table 1.

Software and resources using OLS Client and/or OLS Dialog (by June 2017)

Name	Description	URL	Tools
ProteomeXchange Submission Tool7	Stand‐alone submission tool for the PRIDE database	https://github.com/proteomexchange/px-submission-tool	OLS Client OLS Dialog
Reactome Annotation Tool13	Pathway annotation tool	http://www.reactome.org	OLS Client
IntAct10	Curated molecular interactions database	http://www.ebi.ac.uk/intact	OLS Client
PeptideShaker14	Search engine independent platform for the interpretation of proteomics identification results	http://compomics.github.io/projects/peptide-shaker	OLS Client
Omics Discovery Index11	A multi‐omics dataset discovery resource	http://www.omicsdi.org	OLS Client
Colims	A LIMS system to automate and expedite proteomics data management, processing and analysis	http://compomics.github.io/projects/colims	OLS Client OLS Dialog
BioSamples(7)	Resource that stores and supplies descriptions and metadata about biological samples	https://www.ebi.ac.uk/biosamples	OLS Client
CySBML(8)	Cytoscape plugin for importing and visualizing SBML annotations	https://sourceforge.net/projects/cysbml	OLS Client
BioModels Database12	BioModels Database is a repository of computational models of biological processes.	http://www.ebi.ac.uk/biomodels-main	OLS Client