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

被引：19

作者：

Beltrame, Luca ^{[2
]}

Calura, Enrica ^{[2
,3
]}

Popovici, Razvan R. ^{[4
]}

Rizzetto, Lisa ^{[2
]}

Guedez, Damariz Rivero ^{[2
]}

Donato, Michele ^{[1
]}

Romualdi, Chiara ^{[3
]}

Draghici, Sorin ^{[1
]}

Cavalieri, Duccio ^{[2
]}

机构：

[1] Wayne State Univ, Dept Comp Sci, Detroit, MI 48202 USA

[2] Univ Florence, Dept Pharmacol M Aiazzi Mancini, I-50139 Florence, Italy

[3] Univ Padua, Dept Biol, I-35121 Padua, Italy

[4] Miravtech Corp, Troy, MI 48083 USA

来源：

BIOINFORMATICS | 2011年 / 27卷 / 15期

关键词：

SYSTEMS BIOLOGY; GENE-EXPRESSION; TOOL;

D O I：

10.1093/bioinformatics/btr339

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：2127 / 2133

页数：7

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