ArticleBriefings in bioinformatics2020
Closing the gap between formats for storing layout information in systems biology.
Article in Briefings in bioinformatics, 2020. 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 17 papers.
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Who cites it
17 citing papers in PubMed.
- A standardized workflow for kinetic metabolic model curation and dissemination.PLoS computational biology · 2026Article
- HIDmap: a physiology-based map of human immune system development to support animal-free research and regulatory innovation.Frontiers in immunology · 2026Article
- Cardiotoxicity adverse outcome pathway network: towards mechanistic and quantitative modelling.Frontiers in toxicology · 2026Article
- SBMLNetwork: A framework for standards-based visualization of biochemical models.PLoS computational biology · 2025Article
- Non-small cell lung cancer map and analysis: exploring interconnected oncogenic signal integrators.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- FAIR assessment of Disease Maps fosters open science and scientific crowdsourcing in systems biomedicine.Scientific data · 2025Article
- Unlocking liver physiology: comprehensive pathway maps for mechanistic understanding.Frontiers in toxicology · 2025Article
- Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer.NPJ systems biology and applications · 2024Article
- BioKC: a collaborative platform for curation and annotation of molecular interactions.Database : the journal of biological databases and curation · 2024Article
- 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
- 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
- Ten simple rules for creating reusable pathway models for computational analysis and visualization.PLoS computational biology · 2021Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation.BMC bioinformatics · 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
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.
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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.