ArticleBMC systems biology2013
Translation of SBGN maps: Process Description to Activity Flow.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Sustainable software development in science - insights from 20 years of Vanted.Journal of integrative bioinformatics · 2025Article
- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Design considerations for representing systems biology information with the Systems Biology Graphical Notation.Journal of integrative bioinformatics · 2022Article
- Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Molecular systems biology · 2022Review
- Reactome and the Gene Ontology: digital convergence of data resources.Bioinformatics (Oxford, England) · 2021Article
- SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.Briefings in bioinformatics · 2021Article
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- Automated inference of Boolean models from molecular interaction maps using CaSQ.Bioinformatics (Oxford, England) · 2020Article
- Qualitative dynamics semantics for SBGN process description.BMC systems biology · 2016Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration.
resultsTo solve this problem we define translations of SBGN PD maps into the more abstract SBGN AF maps. We present a template-based translation which allows the user to focus on different aspects of the underlying biological system. We also discuss aspects of laying out the AF map and of interactive navigation between both the PD and the AF map. The methods developed here have been implemented as part of SBGN-ED ( http://www.sbgn-ed.org).
conclusionsSBGN PD maps become much smaller and more manageable when translated into SBGN AF. The flexible translation of PD into AF and related interaction methods are an initial step in translating the different SBGN languages and open the path to future research for translation methods between other SBGN languages.
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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.