ArticleBioinformatics (Oxford, England)2018
Reactome diagram viewer: data structures and strategies to boost performance.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 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
117 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- NF-κB/RelA signaling required for CD40-induced humoral immunity depends on specific NEMO lysine residues in mice.The EMBO journal · 2026Article
- Children with Autism Spectrum Disorder and Chronic Gastrointestinal Symptoms Have Alterations in Intestinal Neurotransmitter Pathways.Digestive diseases and sciences · 2026Article
- Human brain and organoid transcriptomes reveal key receptor tyrosine kinase pathways and genetic signatures in Alzheimer's disease.Experimental & molecular medicine · 2026Article
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data.Cell reports methods · 2026Article
- Deciphering Stiffness-Driven Changes in Colorectal Cancer by Proteomics.Molecular & cellular proteomics : MCP · 2026Article
- Infection-driven proteomic signatures in immune cell-derived extracellular vesicles reflect hemorrhagic stroke outcome.Journal of neuroinflammation · 2025Observational
- Multi-omics dissection of RAD21-PON1 axis reveals metabolic-immune crosstalk and prognostic significance in hepatocellular carcinoma.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Diffusely metastatic glioblastoma with FGFR3::TACC3 fusion: cell-free DNA fragmentation analyses and molecular characterization of matched primary and metastatic tumor sites.Acta neuropathologica communications · 2025Article
- Quantitative Computed Tomographic Clusters in C-BIOPRED Asthma Cohort: Association with Sputum Proteomics.MedComm · 2025Article
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data.bioRxiv : the preprint server for biology · 2025Article
- Single-cell multiome and spatial profiling reveals pancreas cell type-specific gene regulatory programs of type 1 diabetes progression.Science advances · 2025Article
- Maternal plasma microRNAs as potential biomarkers for triaging pregnancies of unknown location and ectopic pregnancy diagnosis.Non-coding RNA research · 2025Article
- Genetic Parameters, Linear Associations, and Genome-Wide Association Study for Endotoxin-Induced Cortisol Response inAnimals : an open access journal from MDPI · 2025Article
- Effects of life-long hyperlipidaemia on age-dependent development of endothelial dysfunction in humanised dyslipidaemic mice.GeroScience · 2025Article
- A structural haplotype in the 17q21.31 MAPT region is associated with increased risk for chronic traumatic encephalopathy endophenotypes.Cell reports. Medicine · 2025Article
- Article
- Metabolic imaging distinguishes ovarian cancer subtypes and detects their early and variable responses to treatment.Oncogene · 2025Article
- Positive Selection on Mammalian Immune Genes-Effects of Gene Function and Selective Constraint.Molecular biology and evolution · 2025Article
- Exploring Synaptic Pathways in Traumatic Brain Injury: A Cross-Phenotype Genomics Approach.Journal of neurotrauma · 2025Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results: The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources. Availability and implementation: Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. Contact: fabregat@ebi.ac.uk or hhe@ebi.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.