ArticleDatabase : the journal of biological databases and curation2018
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.
Article in Database : the journal of biological databases and curation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- momapy: a Python library to work with molecular maps.Bioinformatics (Oxford, England) · 2026Article
- Nanopublication-based semantic publishing and reviewing: a field study with formalization papers.PeerJ. Computer science · 2023Article
- Maximizing the utility of public data.Frontiers in genetics · 2023Article
- Exploring the Complex Network of Heme-Triggered Effects on the Blood Coagulation System.Journal of clinical medicine · 2022Article
- BioTAGME: A Comprehensive Platform for Biological Knowledge Network Analysis.Frontiers in genetics · 2022Article
- A Functional Network Model of the Metastasis Suppressor PEBP1/RKIP and Its Regulators in Breast Cancer Cells.Cancers · 2021Article
- LINPS: a database for cancer-cell-specific perturbations of biological networks.Database : the journal of biological databases and curation · 2021Article
- Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.Molecular systems biology · 2021Article
- A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders.Frontiers in bioengineering and biotechnology · 2020Article
- Using a Large Margin Context-Aware Convolutional Neural Network to Automatically Extract Disease-Disease Association from Literature: Comparative Analytic Study.JMIR medical informatics · 2019Article
- NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks.BMC bioinformatics · 2019Article
- PathMe: merging and exploring mechanistic pathway knowledge.BMC bioinformatics · 2019Article
- Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.Database : the journal of biological databases and curation · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid accumulation of knowledge in the field of systems and networks biology during recent years requires complex, but user-friendly and accessible web applications that allow from visualization to complex algorithmic analysis. While several web applications exist with various focuses on creation, revision, curation, storage, integration, collaboration, exploration, visualization and analysis, many of these services remain disjoint and have yet to be packaged into a cohesive environment.Here, we present BEL Commons: an integrative knowledge discovery environment for networks encoded in the Biological Expression Language (BEL). Users can upload files in BEL to be parsed, validated, compiled and stored with fine granular permissions. After, users can summarize, explore and optionally shared their networks with the scientific community. We have implemented a query builder wizard to help users find the relevant portions of increasingly large and complex networks and a visualization interface that allows them to explore their resulting networks. Finally, we have included a dedicated analytical service for performing data-driven analysis of knowledge networks to support hypothesis generation.
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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.