Visualizing omics and clinical data: Which challenges for dealing with their variety?

Life sciences are currently going through a great number of transformations raised by the in-going revolution in high-throughput technologies for the acquisition of data. The integration of their high dimensionality, ranging from omics to clinical data, is becoming one of the most challenging stages. It involves inter-disciplinary developments with the aim to move towards an enhanced understanding of human physiology for caring purposes. Biologists, bioinformaticians, physicians and other experts related to the healthcare domain have to accompany each step of the analysis process in order to investigate and expertise these various data. In this perspective, methods related to information visualization are gaining increasing attention within life sciences. The softwares based on these methods are now well recognized to facilitate expert users' success in carrying out their data analysis tasks. This article aims at reviewing the current methods and techniques dedicated to information visualisation and their current use in software development related to omics or/and clinical data.

[1]  Tim Berners-Lee,et al.  Linked Data - The Story So Far , 2009, Int. J. Semantic Web Inf. Syst..

[2]  Ben Shneiderman,et al.  Improving Healthcare with Interactive Visualization , 2013, Computer.

[3]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[4]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[5]  Aedín C. Culhane,et al.  Dimension reduction techniques for the integrative analysis of multi-omics data , 2016, Briefings Bioinform..

[6]  Eberechukwu Onukwugha,et al.  Understanding Adherence and Prescription Patterns Using Large-Scale Claims Data , 2016, PharmacoEconomics.

[7]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[8]  Riccardo Miotto,et al.  Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams , 2016, Briefings Bioinform..

[9]  Ed H. Chi,et al.  A taxonomy of visualization techniques using the data state reference model , 2000, IEEE Symposium on Information Visualization 2000. INFOVIS 2000. Proceedings.

[10]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[11]  Colin Ware,et al.  Information Visualization: Perception for Design , 2000 .

[12]  Edward M. Reingold,et al.  Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..

[13]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[14]  Robert D. Finn,et al.  The European Bioinformatics Institute in 2016: Data growth and integration , 2015, Nucleic Acids Res..

[15]  Patrice Degoulet,et al.  Translational research platforms integrating clinical and omics data: a review of publicly available solutions , 2014, Briefings Bioinform..

[16]  Jing Wang,et al.  Empowering biologists with multi-omics data: colorectal cancer as a paradigm , 2014, Bioinform..

[17]  William Stafford Noble,et al.  Software tools for visualizing Hi-C data , 2017, Genome Biology.

[18]  Romain Bourqui,et al.  Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks , 2014, Briefings Bioinform..

[19]  Chris North,et al.  The Value of Information Visualization , 2008, Information Visualization.

[20]  Josua Krause,et al.  Supporting Iterative Cohort Construction with Visual Temporal Queries , 2016, IEEE Transactions on Visualization and Computer Graphics.

[21]  Boris P. Hejblum,et al.  Group and sparse group partial least square approaches applied in genomics context , 2015, Bioinform..

[22]  Tamara Munzner,et al.  A Nested Model for Visualization Design and Validation , 2009, IEEE Transactions on Visualization and Computer Graphics.

[23]  Paul N. Schofield,et al.  The role of ontologies in biological and biomedical research: a functional perspective , 2015, Briefings Bioinform..

[24]  Inanç Birol,et al.  Hive plots - rational approach to visualizing networks , 2012, Briefings Bioinform..

[25]  L. Zhao,et al.  Big data visualization identifies the multidimensional molecular landscape of human gliomas , 2016, Proceedings of the National Academy of Sciences.

[26]  Eric Fleury,et al.  Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals , 2015, PLoS Comput. Biol..

[27]  Huan Liu,et al.  Resource description framework: metadata and its applications , 2001, SKDD.

[28]  Ilya Safro,et al.  Graph minimum linear arrangement by multilevel weighted edge contractions , 2006, J. Algorithms.

[29]  Boris P. Hejblum,et al.  Time-Course Gene Set Analysis for Longitudinal Gene Expression Data , 2015, PLoS Comput. Biol..

[30]  Wei Lin,et al.  Single-cell Transcriptome Study as Big Data , 2016, Genom. Proteom. Bioinform..

[31]  Edward R. Tufte,et al.  The Visual Display of Quantitative Information , 1986 .

[32]  Peter P. Chen.  The entity-relationship model: toward a unified view of data , 1975, VLDB '75.

[33]  Ben Shneiderman,et al.  LifeLines: using visualization to enhance navigation and analysis of patient records , 1998, AMIA.

[34]  Peer Bork,et al.  iPath2.0: interactive pathway explorer , 2011, Nucleic Acids Res..

[35]  Mark Gerstein,et al.  Closure of the NCBI SRA and implications for the long-term future of genomics data storage , 2011, Genome Biology.

[36]  Ben Shneiderman,et al.  Temporal Event Sequence Simplification , 2013, IEEE Transactions on Visualization and Computer Graphics.

[37]  Adriano Barbosa-Silva,et al.  SmartR: an open-source platform for interactive visual analytics for translational research data , 2017, Bioinform..

[38]  Patrick Madden,et al.  Circular Layout in the Graph Layout Toolkit , 1996, GD.

[39]  Robert L Cook,et al.  Evaluating Google, Twitter, and Wikipedia as Tools for Influenza Surveillance Using Bayesian Change Point Analysis: A Comparative Analysis , 2016, JMIR public health and surveillance.

[40]  Yves Grandvalet,et al.  Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm , 2015, BMC Bioinformatics.

[41]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[42]  C. Thermes,et al.  Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.

[43]  Romain Bourqui,et al.  rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining , 2017, BMC Bioinformatics.

[44]  Shareef M. Dabdoub,et al.  PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets , 2016, Scientific Reports.

[45]  Israel Steinfeld,et al.  BMC Bioinformatics BioMed Central , 2008 .

[46]  Y. Kestens,et al.  A GPS-Based Methodology to Analyze Environment-Health Associations at the Trip Level: Case-Crossover Analyses of Built Environments and Walking. , 2016, American journal of epidemiology.

[47]  John N. Weinstein,et al.  High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID) , 2005, BMC Bioinformatics.

[48]  Cole Trapnell,et al.  Single-cell transcriptome sequencing: recent advances and remaining challenges , 2016, F1000Research.

[49]  Alessandro Vespignani,et al.  influenza A(H1N1): a Monte Carlo likelihood analysis based on , 2009 .

[50]  Jordi Petit,et al.  Experiments on the minimum linear arrangement problem , 2003, ACM J. Exp. Algorithmics.

[51]  David Harel,et al.  A Multi-scale Algorithm for the Linear Arrangement Problem , 2002, WG.

[52]  John T. Stasko,et al.  Toward a Deeper Understanding of the Role of Interaction in Information Visualization , 2007, IEEE Transactions on Visualization and Computer Graphics.

[53]  Anton J. Enright,et al.  Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future , 2015, GigaScience.

[54]  Vivian West,et al.  Innovative information visualization of electronic health record data: a systematic review , 2014, J. Am. Medical Informatics Assoc..

[55]  Lucy T. Nowell,et al.  ThemeRiver: Visualizing Thematic Changes in Large Document Collections , 2002, IEEE Trans. Vis. Comput. Graph..

[56]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[57]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[58]  Mark D. Hoover,et al.  Use of the "Exposome" in the Practice of Epidemiology: A Primer on -Omic Technologies. , 2016, American journal of epidemiology.

[59]  Mathieu Bastian,et al.  Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.

[60]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[61]  Pietro Liò,et al.  CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks , 2015, Bioinform..

[62]  Roberto Therón,et al.  BicOverlapper: A tool for bicluster visualization , 2008, Bioinform..

[63]  Boudewijn P F Lelieveldt,et al.  Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data , 2016, Proceedings of the National Academy of Sciences.

[64]  Ben Shneiderman,et al.  Extracting Insights from Electronic Health Records: Case Studies, a Visual Analytics Process Model, and Design Recommendations , 2011, Journal of Medical Systems.

[65]  Andreas Ludwig,et al.  A Fast Adaptive Layout Algorithm for Undirected Graphs , 1994, GD.

[66]  Heidrun Schumann,et al.  Visualization of Time-Oriented Data , 2011, Human-Computer Interaction Series.

[67]  Jeffrey Heer,et al.  SpanningAspectRatioBank Easing FunctionS ArrayIn ColorIn Date Interpolator MatrixInterpola NumObjecPointI Rectang ISchedu Parallel Pause Scheduler Sequen Transition Transitioner Transiti Tween Co DelimGraphMLCon IData JSONCon DataField DataSc Dat DataSource Data DataUtil DirtySprite LineS RectSprite , 2011 .

[68]  Annick Lesne,et al.  Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition , 2011, Bioinform..

[69]  Jock D. Mackinlay,et al.  Automating the design of graphical presentations of relational information , 1986, TOGS.

[70]  Rodolphe Thiébaut,et al.  Dendritic cell‐based therapeutic vaccine elicits polyfunctional HIV‐specific T‐cell immunity associated with control of viral load , 2014, European journal of immunology.

[71]  Riccardo Bellazzi,et al.  The ONCO-I2b2 Project: Integrating Biobank Information and Clinical Data to Support Translational Research in Oncology , 2011, MIE.

[72]  Rodolphe Thiébaut,et al.  A new endpoint definition improved clinical relevance and statistical power in a vaccine trial. , 2009, Journal of clinical epidemiology.

[73]  Ben Shneiderman,et al.  Searching Electronic Health Records for Temporal Patterns in Patient Histories: A Case Study with Microsoft Amalga , 2008, AMIA.

[74]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[75]  Hiroyuki Kubota,et al.  Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers. , 2016, Trends in biotechnology.

[76]  Alexandru Telea,et al.  Data visualization - principles and practice , 2007 .

[77]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[78]  E. Perakslis,et al.  Effective knowledge management in translational medicine , 2010, Journal of Translational Medicine.