ArticleNucleic acids research2020
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 196 papers, 4 of them syntheses 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
196 citing papers in PubMed, 4 syntheses or guidelines pooled it, 325 citations in OpenAlex.
- Meta-analysis and in-silico functional characterization of the SNCA variant rs356220 in Parkinson's disease.Scientific reports · 2025Pooled it
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Sparse canonical correlation to identify breast cancer related genes regulated by copy number aberrations.PloS one · 2022Pooled it
- Pooled it
- Sex-specific molecular signatures in persistent pain after whiplash injury: an exploratory analysis.Pain reports · 2026Article
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- Enhancing link prediction in biomedical knowledge graphs with BioPathNet.Nature biomedical engineering · 2026Article
- Evolutionary convergence and niche-specific regulation of core HIF1A pathway genes synergistically drive divergent hypoxia adaptation in mammals.BMC ecology and evolution · 2026Article
- VITAGRAPH: building a knowledge graph for biologically relevant learning tasks.Scientific data · 2026Article
- Applying prior knowledge of regulatory signaling to investigate macrophage cAMP dynamics during Mycobacterium tuberculosis infection.Scientific reports · 2026Article
- Addressing multiple facets of ligand-receptor network inference including single-cell proteomics.Nucleic acids research · 2026Article
- A data-driven framework reconstructs the molecular continuum of human MASLD progression.Nature metabolism · 2026Article
- drGT: interpretable drug response prediction with attention-guided gene attribution on a drug-cell-gene heterogeneous graph.BMC bioinformatics · 2026Article
- Mapping cross-domain drivers of Alzheimer's disease risk through integrated network analysis.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Toward a Common Set of Interface Requirements for Genomic Data Management: Scoping Review.Journal of medical Internet research · 2026Article
- GPU-accelerated modeling of biological regulatory networks.Scientific reports · 2026Article
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- From SNPs to pathways: a genome-wide benchmark of annotation discrepancies and their impact on protein- and pathway-level inference.BMC genomics · 2026Article
- VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs.bioRxiv : the preprint server for biology · 2026Article
136 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
25 authors at 6 institutions in 4 countries.
Funding
Abstract
Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.
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.