ArticleProteomics2017
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
Article in Proteomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- The PRIDE database at 20 years: 2025 update.Nucleic acids research · 2025Article
- Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit.Database : the journal of biological databases and curation · 2024Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.Nucleic acids research · 2022Article
- A proteomics sample metadata representation for multiomics integration and big data analysis.Nature communications · 2021Review
- Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.Development (Cambridge, England) · 2021Article
- MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.Genomics, proteomics & bioinformatics · 2020Article
- An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder.International journal of molecular sciences · 2020Article
- OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database.Orphanet journal of rare diseases · 2019Article
- The PRIDE database and related tools and resources in 2019: improving support for quantification data.Nucleic acids research · 2019Article
- iProX: an integrated proteome resource.Nucleic acids research · 2019Article
- Eleven quick tips to build a usable REST API for life sciences.PLoS computational biology · 2018Article
- The European Bioinformatics Institute in 2017: data coordination and integration.Nucleic acids research · 2018Article
- Article
- Proteomic repository data submission, dissemination, and reuse: key messages.Expert review of proteomicsReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.