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.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways / Beltrame L;Calura E;Popovici RR;Rizzetto L;Guedez DR;Donato M;Romualdi C;Draghici S;Cavalieri D. - In: BIOINFORMATICS. - ISSN 1367-4803. - ELETTRONICO. - 27:(2011), pp. 2127-2133. [10.1093/bioinformatics/btr339]

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

BELTRAME, LUCA;CALURA, ENRICA;RIZZETTO, LISA;CAVALIERI, DUCCIO
2011

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.
2011
27
2127
2133
Beltrame L;Calura E;Popovici RR;Rizzetto L;Guedez DR;Donato M;Romualdi C;Draghici S;Cavalieri D
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/606398
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