ArticlePLoS computational biology2018
Reactome graph database: Efficient access to complex pathway data.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 2 of them syntheses that pooled it.
What it found
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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
156 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Graph-Representation of Patient Data: a Systematic Literature Review.Journal of medical systems · 2020Pooled it
- Inflammation and remodeling pathways and risk of cardiovascular events in patients with ischemic heart failure and reduced ejection fraction.Scientific reports · 2022Trial
- Dapagliflozin Attenuates NKCC2 Protein Expression and Alleviates Diabetic Kidney Disease in Salt Loaded-Hypertensive Diabetic Db/Db Mice.FASEB bioAdvances · 2026Article
- Article
- The physiological drivers of commercial broiler chicken performance uncovered with transcriptomics analyses and a novel pathway activation method.Poultry science · 2026Article
- Eras of bioinformatics technologies from command-line interfaces to artificial intelligence (AI) chatbots.Briefings in bioinformatics · 2026Review
- WayFindR: investigating feedback in biological pathways.NAR genomics and bioinformatics · 2026Article
- Children with Autism Spectrum Disorder and Chronic Gastrointestinal Symptoms Have Alterations in Intestinal Neurotransmitter Pathways.Digestive diseases and sciences · 2026Article
- The immunoproteome and multimorbidity: A Mendelian randomization study.Science advances · 2026Article
- Inducible CRISPR-Cas9 screening platform to interrogate non-proliferative cellular states.Nature protocols · 2026Review
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data.Cell reports methods · 2026Article
- A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer.Communications medicine · 2026Article
- Optic Nerve Head Spatial Transcriptomic Change in Nonhuman Primate Early Experimental Glaucoma.Investigative ophthalmology & visual science · 2026Article
- Application of Large Language Models for Annotating Genes into Reactome Pathways.bioRxiv : the preprint server for biology · 2025Article
- 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
- 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
- Identifying congestion phenotypes using unsupervised machine learning in acute heart failure.European heart journal. Digital health · 2025Article
- Gene expression and molecular pathway analyses differentiate immunotherapy-induced myositis from spontaneous dermatomyositis.Scientific reports · 2025Article
96 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
10 authors.
Funding
Abstract
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.
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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.