ArticleBioinformatics (Oxford, England)2019
Automated workflow composition in mass spectrometry-based proteomics.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- A framework for reproducibly managing coupled research software and data assets based on shared transformation functions.Patterns (New York, N.Y.) · 2026Article
- Quality Control in the Mass Spectrometry Proteomics Core: A Practical Primer.Journal of biomolecular techniques : JBT · 2024Article
- Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine.Annual review of pharmacology and toxicology · 2024Review
- An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.Journal of the American Society for Mass Spectrometry · 2023Article
- Automation to Enable High-Throughput Chemical Proteomics.Journal of proteome research · 2023Review
- Ten Topics to Get Started in Medical Informatics Research.Journal of medical Internet research · 2023Article
- A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.Metabolites · 2022Review
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.Briefings in bioinformatics · 2021Article
- APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry.Journal of proteome research · 2021Article
- Loose programming of GIS workflows with geo-analytical concepts.Transactions in GIS : TG · 2021Article
- Article
- Tool recommender system in Galaxy using deep learning.GigaScience · 2021Article
- Community curation of bioinformatics software and data resources.Briefings in bioinformatics · 2020Article
- PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features.Molecular & cellular proteomics : MCP · 2020Article
- doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows.BMC bioinformatics · 2019Article
- The bio.tools registry of software tools and data resources for the life sciences.Genome biology · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationNumerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.
resultsWe provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools' semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logically and semantically equivalent workflows for four use cases representing frequent tasks in MS-based proteomics. Indeed we found that the results computed by the workflows could vary considerably, emphasizing the benefits of a framework that facilitates their systematic exploration. AVAILABILITY AND IMPLEMENTATION: The project files and workflows are available from https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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