ArticleBioinformatics (Oxford, England)2019
MINERVA API and plugins: opening molecular network analysis and visualization to the community.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 42 citations in OpenAlex.
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- Non-small cell lung cancer map and analysis: exploring interconnected oncogenic signal integrators.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- An explorable model of an adverse outcome pathway of cytokine release syndrome related to the administration of immunomodulatory biotherapeutics and cellular therapies.Frontiers in immunology · 2025Article
- Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer.NPJ systems biology and applications · 2024Article
- Exploration and comparison of molecular mechanisms across diseases using MINERVA Net.Protein science : a publication of the Protein Society · 2023Article
- The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease.Frontiers in immunology · 2023Article
- Visualization of automatically combined disease maps and pathway diagrams for rare diseases.Frontiers in bioinformatics · 2023Article
- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Article
- Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps.NPJ systems biology and applications · 2022Article
- CyFi-MAP: an interactive pathway-based resource for cystic fibrosis.Scientific reports · 2021Article
- Mapping Compound Databases to Disease Maps-A MINERVA Plugin for CandActBase.Journal of personalized medicine · 2021Article
- Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation.BioData mining · 2021Article
- COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Molecular systems biology · 2021Article
- Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map.Journal of personalized medicine · 2021Article
- Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Briefings in bioinformatics · 2021Review
- WikiPathways: connecting communities.Nucleic acids research · 2021Article
- The Atlas of Inflammation Resolution (AIR).Molecular aspects of medicine · 2020Review
- RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis.Database : the journal of biological databases and curation · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryThe complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform's visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. AVAILABILITY AND IMPLEMENTATION: Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.
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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.