ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining

• Published in: BMC Bioinformatics
• Main Authors: Sivachenko Andrey Y, Huan Tianxiao, Harrison Scott H, Chen Jake Y
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2008
• Subjects: Computer applications to medicine. Medical informatics; R858-859.7; Biology (General); QH301-705.5; DML
• Online Access: https://doi.org/10.1186/1471-2105-9-S9-S5; https://doaj.org/article/c28415bd1c1a4b84a5bbcc40b5e447af

Abstract Background New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. Results We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated ...