ArticleBMC bioinformatics2013
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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
7 citing papers in PubMed.
- Sustainable software development in science - insights from 20 years of Vanted.Journal of integrative bioinformatics · 2025Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- Design considerations for representing systems biology information with the Systems Biology Graphical Notation.Journal of integrative bioinformatics · 2022Article
- Closing the gap between formats for storing layout information in systems biology.Briefings in bioinformatics · 2020Article
- Mental-Map Preserving Visualisation of Partitioned Networks in Vanted.Journal of integrative bioinformatics · 2019Article
- MINERVA-a platform for visualization and curation of molecular interaction networks.NPJ systems biology and applications · 2016Article
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiologists make frequent use of databases containing large and complex biological networks. One popular database is the Kyoto Encyclopedia of Genes and Genomes (KEGG) which uses its own graphical representation and manual layout for pathways. While some general drawing conventions exist for biological networks, arbitrary graphical representations are very common. Recently, a new standard has been established for displaying biological processes, the Systems Biology Graphical Notation (SBGN), which aims to unify the look of such maps. Ideally, online repositories such as KEGG would automatically provide networks in a variety of notations including SBGN. Unfortunately, this is non-trivial, since converting between notations may add, remove or otherwise alter map elements so that the existing layout cannot be simply reused.
resultsHere we describe a methodology for automatic translation of KEGG metabolic pathways into the SBGN format. We infer important properties of the KEGG layout and treat these as layout constraints that are maintained during the conversion to SBGN maps.
conclusionsThis allows for the drawing and layout conventions of SBGN to be followed while creating maps that are still recognizably the original KEGG pathways. This article details the steps in this process and provides examples of the final result.
Indexed as
Identifiers
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.