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

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.

The PRIDE database and related tools and resources in 2019: improving support for quantification data

“…The aim is to improve the capture of the experimental design information and technical metadata (e.g. search parameters and relevant information contained in the raw files) (28,38). The improvement in annotation is also required to facilitate further data re-use for third parties.…”

“…The PX Submission tool (3) (available at https://github.com/proteomexchange/px-submission-tool) is a stand-alone tool used by most PRIDE submitters to perform data submissions. Some of the recent refinements done in the tool are: (i) the integration of the new OLS (Ontology Lookup Service) Client and OLS Dialog libraries (28), supporting the new version of the OLS, used to annotate datasets using controlled vocabulary terms; and (ii) the addition of a direct feedback system for users to report how the data submission went.…”

iProX: an integrated proteome resource

“…Adequate information on experimental design and MS/MS data generation must be provided in a standardized manner to ensure that an answer to a query with particular terms includes all relevant data. Thus, iProX makes extensive use of controlled vocabularies and ontologies embedded in the Ontology Lookup Service (OLS) system (27) to annotate the entries of proteomics datasets in the subproject information page, e.g. NCBITAXON (NCBI organismal classification) for organismal taxonomy, DOID (Human Disease Ontology) (28) for human disease states, BTO (BRENDA tissue/enzyme source) (29) for tissues, CL (Cell Ontology) (30) for cell types, and PRIDE CV (PRIDE Controlled Vocabulary), PSI-MS CV (MS ontology) (6), MOD (Protein modification) (31) and SEP (Sample processing and separations controlled vocabulary) for MS experiments and data analysis procedure annotation.…”

MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes

“…The disease phenotypes were annotated with official names, experimental factor terms, definitions, classifications, and cross references using EFO [30]. EFO provides a systematic description of many experimental variables across European Bioinformatics Institute (EMBL-EBI) databases and the National Human Genome Research Institute (NHGRI) genome-wide association study (GWAS) catalog [31]; it also combines parts of several popular ontologies, such as Orphanet Rare Disease Ontology [32], Human Phenotype Ontology [33], and Monarch Disease…”