OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Yasset Perez-Riverol,Maximilian Koch,Juan Antonio Vizcaíno,Harald Barsnes,Olga Vrousgou,Tobias Ternent,Simon Jupp

doi:10.1002/pmic.201700244

Yasset Perez-Riverol, Maximilian Koch + Show 5 more

Open Access

https://doi.org/10.1002/pmic.201700244

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Abstract

The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open‐source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog.

Highlights

Modern systems biology and bioinformatics approaches rely on the integration and experimental details is becoming essential in data management practices, of large amounts of potentially disparate both in local storage systems and in public databases
We introduce an updated version of the Ontology Lookup Service (OLS) Dialog, a Java graphical user interface that can be plugged into Java desktop formation
We present an update of the OLS Dialog, a Java graphical user interface (GUI) built on top of the OLS Client that can be plugged into Java desktop applications

Summary

TECHNICAL BRIEF

Yasset Perez-Riverol,* Tobias Ternent, Maximilian Koch, Harald Barsnes, Olga Vrousgou, Simon Jupp, and Juan Antonio Vizcaıno*. The API is composed of two functional components: (i) the data models, incorporating all data structures (terms, identifiers, ontologies, annotations and synonyms); and (ii) the OLS Client query interface, providing a set of functionalities to query, browse and retrieve the ontology’s related information. Searched text; (ii) “Term ID Search”, which selects a term by its accession number; (iii) “Browse Ontology” enables users to browse the selected ontology tree structure to select the desired term; and (iv) the “PSI-MOD Mass Search”, which uses the PSI-MOD ontology [6] and UNIMOD to select protein modifications using the delta mass corresponding to a given modification (Fig. 2) The former more specific search functionality is used for instance in the ProteomeXchange (PX) Submission tool,[7] used by most submitters to the widely-used PRIDE database (as part of PX). API, application programming interface; CURIE, Compact URI; CV, controlled vocabulary; GUI, graphical user interface; LIMS, Laboratory Information Management System; OLS, Ontology Lookup Service; OWL, Web Ontology Language; PX, ProteomeXchange; URI, Uniform Resource Identifier

Curated molecular interactions database

OLS Client OLS Dialog OLS Client