ArticleJournal of proteome research2021
APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
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
6 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
- bio.tools: an expanded web service for research software in the life sciences.Nucleic acids research · 2026Article
- An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.Journal of the American Society for Mass Spectrometry · 2023Article
- Metabolomics meets systems immunology.EMBO reports · 2023Review
- A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research.Metabolites · 2022Review
- Perspectives on automated composition of workflows in the life sciences.F1000Research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The bio.tools registry is a main catalogue of computational tools in the life sciences. More than 17 000 tools have been registered by the international bioinformatics community. The bio.tools metadata schema includes semantic annotations of tool functions, that is, formal descriptions of tools' data types, formats, and operations with terms from the EDAM bioinformatics ontology. Such annotations enable the automated composition of tools into multistep pipelines or workflows. In this Technical Note, we revisit a previous case study on the automated composition of proteomics workflows. We use the same four workflow scenarios but instead of using a small set of tools with carefully handcrafted annotations, we explore workflows directly on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation and extension of the workflow composition method previously used. Moving "into the wild" opens up an unprecedented wealth of tools and a huge number of alternative workflows. Automated composition tools can be used to explore this space of possibilities systematically. Inevitably, the mixed quality of semantic annotations in bio.tools leads to unintended or erroneous tool combinations. However, our results also show that additional control mechanisms (tool filters, configuration options, and workflow constraints) can effectively guide the exploration toward smaller sets of more meaningful workflows.
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.