ArticleNature biotechnology2010
The BioPAX community standard for pathway data sharing.
Article in Nature biotechnology, 2010. 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 361 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
361 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Enhancing link prediction in biomedical knowledge graphs with BioPathNet.Nature biomedical engineering · 2026Article
- VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs.bioRxiv : the preprint server for biology · 2026Article
- CladeOScope-GSA: Revealing Evolutionary Associations Across Gene Sets.International journal of molecular sciences · 2026Article
- KGG: a fully automated workflow for creating disease-specific knowledge graphs.Bioinformatics (Oxford, England) · 2025Article
- PathoGraph: A Graph-Based Method for Standardized Representation of Pathology Knowledge.Scientific data · 2025Article
- Saccharomyces Genome Database: advances in genome annotation, expanded biochemical pathways, and other key enhancements.Genetics · 2025Article
- Sustainable software development in science - insights from 20 years of Vanted.Journal of integrative bioinformatics · 2025Article
- Leveraging public AI tools to explore systems biology resources in mathematical modeling.NPJ systems biology and applications · 2025Article
- Updates implemented in version 4 of the GlyCosmos Glycoscience Portal.Analytical and bioanalytical chemistry · 2025Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions.Frontiers in immunology · 2025Review
- BioPAX in 2024: Where we are and where we are heading.Computational and structural biotechnology journal · 2024Review
- Immune digital twins for complex human pathologies: applications, limitations, and challenges.NPJ systems biology and applications · 2024Review
- Article
- The BioRECIPE Knowledge Representation Format.ACS synthetic biology · 2024Article
- Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer.Briefings in bioinformatics · 2024Article
- MetSim: Integrated Programmatic Access and Pathway Management for Xenobiotic Metabolism Simulators.Chemical research in toxicology · 2024Article
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Article
301 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issuedReubenacker, Oliver [corrected to Ruebenacker, Oliver]
Authors and funding
91 authors.
Funding
Abstract
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
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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.