ArticleBioinformatics (Oxford, England)2011
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- MecCog: a knowledge representation framework for genetic disease mechanism.Bioinformatics (Oxford, England) · 2021Article
- A graphical and computational modeling platform for biological pathways.Nature protocols · 2018Article
- Data Sharing: Convert Challenges into Opportunities.Frontiers in public health · 2017Review
- Modelling the Structure and Dynamics of Biological Pathways.PLoS biology · 2016Article
- Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges.Database : the journal of biological databases and curation · 2015Review
- Methods and approaches in the topology-based analysis of biological pathways.Frontiers in physiology · 2013Review
- Bioinformatic approaches for functional annotation and pathway inference in metagenomics data.Briefings in bioinformatics · 2012Review
- Systems biology of host-fungus interactions: turning complexity into simplicity.Current opinion in microbiology · 2012Review
- PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.Bioinformatics (Oxford, England) · 2012Article
- graphite - a Bioconductor package to convert pathway topology to gene network.BMC bioinformatics · 2012Article
- Article
- Ten years of pathway analysis: current approaches and outstanding challenges.PLoS computational biology · 2012Review
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Authors and funding
9 authors.
Funding
Abstract
motivationMany models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions.
resultsThe Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. AVAILABILITY AND IMPLEMENTATION: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.
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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.