Dataset Information

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

ABSTRACT:

Motivation

Many 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.

Results

The 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.

SUBMITTER: Beltrame L

PROVIDER: S-EPMC3137220 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

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Publications

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

Beltrame Luca L Calura Enrica E Popovici Razvan R RR Rizzetto Lisa L Guedez Damariz Rivero DR Donato Michele M Romualdi Chiara C Draghici Sorin S Cavalieri Duccio D

Bioinformatics (Oxford, England) 20110607 15

<h4>Motivation</h4>Many 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.<h4>Results</h4>The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective ...[more]

PMID: 21653523

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Dataset Information

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

Motivation

Results

Availability and implementation

Publications

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

Similar Datasets

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