ArticleNPJ systems biology and applications2019
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases.
Article in NPJ systems biology and applications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation.Bioinformatics (Oxford, England) · 2026Article
- Chr:17q21.31 locus risk haplotype H1 susceptibility to ferroptosis is mediated by endolysosomal pathway.Cell death & disease · 2025Article
- BioMedGraphica: An All-in-One Platform for Joint Textual Biomedical Prior Knowledge and Numeric Graph Generation.bioRxiv : the preprint server for biology · 2025Article
- One path, two solutions: Network-based analysis identifies targetable pathways for the treatment of comorbid type II diabetes and neuropsychiatric disorders.Computational and structural biotechnology journal · 2024Article
- PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful.Nucleic acids research · 2024Article
- Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations.Orphanet journal of rare diseases · 2023Article
- Differential gene expression in the contralateral hemisphere of the rat brain after focal ischemia.Scientific reports · 2023Article
- Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis.Frontiers in genetics · 2023Article
- PathIN: an integrated tool for the visualization of pathway interaction networks.Computational and structural biotechnology journal · 2023Article
- Nanopublication-based semantic publishing and reviewing: a field study with formalization papers.PeerJ. Computer science · 2023Article
- Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque.Nature communications · 2022Article
- On the influence of several factors on pathway enrichment analysis.Briefings in bioinformatics · 2022Review
- A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism.Patterns (New York, N.Y.) · 2022Article
- Article
- DecoPath: a web application for decoding pathway enrichment analysis.NAR genomics and bioinformatics · 2021Article
- Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis.PLoS computational biology · 2021Article
- A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization.Scientific reports · 2021Article
- Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations.BMC bioinformatics · 2021Article
- Genome-wide association study of psychiatric and substance use comorbidity in Mexican individuals.Scientific reports · 2021Article
- WikiPathways: connecting communities.Nucleic acids research · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson's disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at https://compath.scai.fraunhofer.de/.
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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.