ArticleBioinformatics (Oxford, England)2010
Editing, validating and translating of SBGN maps.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed.
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- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.Frontiers in immunology · 2023Article
- Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality.Journal of integrative bioinformatics · 2022Article
- GraphML-SBGN bidirectional converter for metabolic networks.Journal of integrative bioinformatics · 2022Article
- SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more.PLoS computational biology · 2022Article
- 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
- COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Molecular systems biology · 2021Article
- QSDB-a graphical Quorum Sensing Database.Database : the journal of biological databases and curation · 2021Article
- SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.Briefings in bioinformatics · 2021Article
- Ten simple rules for creating reusable pathway models for computational analysis and visualization.PLoS computational biology · 2021Article
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
- Cholesterol Homeostasis: An In Silico Investigation into How Aging Disrupts Its Key Hepatic Regulatory Mechanisms.Biology · 2020Article
- Closing the gap between formats for storing layout information in systems biology.Briefings in bioinformatics · 2020Article
- 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable.
resultsWe present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats. AVAILABILITY: SBGN-ED is freely available from http://vanted.ipk-gatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files.
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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.