title: ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.
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 data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network.
  
  
  CONCLUSIONS
  The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.
authors.affiliation: School of Informatics, Indiana University - Purdue University, Indianapolis, IN 46202, USA. huant@iupui.edu
authors.forename: Tianxiao
authors.initials: T
authors.lastname: Huan
authors.forename: Andrey Y
authors.initials: AY
authors.lastname: Sivachenko
authors.forename: Scott H
authors.initials: SH
authors.lastname: Harrison
authors.forename: Jake Y
authors.initials: JY
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome
references.citation: BMC Med Genomics. 2008 Apr 25;1:12
references.pmid: 18439290
references.citation: Genome Res. 2002 Oct;12(10):1540-8
references.pmid: 12368246
references.citation: Nat Biotechnol. 2003 Jun;21(6):697-700
references.pmid: 12740586
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):248-50
references.pmid: 12519993
references.citation: Adv Protein Chem. 2002;61:1-8
references.pmid: 12461819
references.citation: Nat Genet. 2007 Nov;39(11):1338-49
references.pmid: 17922014
references.citation: Bioinformatics. 2007 Oct 15;23(20):2651-9
references.pmid: 17720984
references.citation: Bioinformatics. 2003 Nov 1;19(16):2155-7
references.pmid: 14594725
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W466-71
references.pmid: 16845051
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6
references.pmid: 18048412
references.citation: Bioinformatics. 2005 Jun 1;21(11):2730-8
references.pmid: 15797912
references.citation: Proc Natl Acad Sci U S A. 2007 May 22;104(21):8685-90
references.pmid: 17502601
references.citation: IEEE Eng Med Biol Mag. 2005 May-Jun;24(3):95-102
references.pmid: 15971847
references.citation: BMC Bioinformatics. 2006 Nov 18;7:508
references.pmid: 17112386
references.citation: Pac Symp Biocomput. 2006;:367-78
references.pmid: 17094253
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D433-7
references.pmid: 15608232
references.citation: BMC Bioinformatics. 2007 Sep 13;8:335
references.pmid: 17854489
references.citation: Genome Res. 2003 Oct;13(10):2363-71
references.pmid: 14525934
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W352-7
references.pmid: 15980487
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7
references.pmid: 15608251
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):303-5
references.pmid: 11752321
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W89-95
references.pmid: 15215357
references.citation: Chembiochem. 2002 Oct 4;3(10):928-44
references.pmid: 12362358
references.citation: Bioinformatics. 2001 Apr;17(4):359-63
references.pmid: 11301305
references.citation: Bioinformatics. 2005 May 1;21(9):2076-82
references.pmid: 15657099
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D590-4
references.pmid: 17158159
references.citation: Nat Biotechnol. 2007 Oct;25(10):1119-26
references.pmid: 17921997
references.citation: Nat Biotechnol. 2007 Oct;25(10):1110-1
references.pmid: 17921993