How are they different? A quantitative domain comparison of information visualization and data visualization (2000᾿014)
详细信息 查看全文
- 作者：Meen Chul Kim ; Yongjun Zhu ; Chaomei Chen
- 关键词：Visual analytics ; Domain analysis ; Information visualization ; Data visualization ; Data science ; Scientometrics
- 刊名：Scientometrics
- 出版年：2016
- 出版时间：April 2016
- 年：2016
- 卷：107
- 期：1
- 页码：123-165
- 全文大小：8,758 KB
- 参考文献：Aigner, W., Miksch, S., Schumann, H., & Tominski, C. (2011). Visualization of time-oriented data. London: Springer.CrossRef
Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11, R106.CrossRef
Andronis, C., Sharma, A., Virvilis, V., Deftereos, S., & Persidis, A. (2011). Literature mining, ontologies and information visualization for drug repurposing. Briefings in Bioinformatics, 12(4), 357–368.CrossRef
Asuncion, A., & Newman, D. (2007). UCI machine learning repository. http://www.ics.uci.edu/~mlearn/MLRepository.html . Accessed 30 June 2015.
Bederson, B., & Shneiderman, B. (2003). The craft of information visualization: Readings and reflections. San Francisco, CA: Morgan Kaufmann.
Belkin, M., & Niyogi, P. (2003). Laplacian eigenmaps for dimensionality reduction and data representation. Neural Computation, 15(6), 1373–1396.MATH CrossRef
Berkovitch, F., Nicolet, Y., Wan, J. T., Jarrett, J. T., & Drennan, C. L. (2004). Crystal structure of biotin synthase: An s-adenosylmethionine-dependent radical enzyme. Science, 303(5654), 76–79.CrossRef
Bino, R. J., Hall, R. D., Fiehn, O., Kopka, J., Saito, K., Draper, J., et al. (2004). Potential of metabolomics as a functional genomics tool. Trends in Plant Science, 9(9), 418–425.CrossRef
Blei, D. M., Ng, A. Y., & Jordan, M. I. (2003). Latent Dirichlet allocation. The Journal of Machine Learning Research, 3, 993–1022.MATH
Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry, 72(1–2), 248–254.CrossRef
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., et al. (2001). Minimum information about a microarray experiment (MIAME)—Toward standards for microarray data. Nature Genetics, 29, 365–371.CrossRef
Bui, B. T. S., Florentin, D., Fournier, F., Ploux, O., Méjean, A., & Marquet, A. (1998). Biotin synthase mechanism: On the origin of sulphur. FEBS Letters, 440(1–2), 226–230.
Bui, B. T. S., Florentin, D., Marquet, A., Benda, R., & Trautwein, A. X. (1999). Mössbauer studies of Escherichia coli biotin synthase: Evidence for reversible interconversion between [2Fe–2S](2+) and [4Fe–4S](2+) clusters. FEBS Letters, 459(3), 411–414.CrossRef
Card, S. K., Mackinlay, J. D., & Schneiderman, B. (1999). Readings in information visualization: Using vision to think. San Francisco, CA: Morgan Kaufmann.
Cheek, J., & Broderick, J. B. (2001). Adenosylmethionine-dependent iron–sulfur enzymes: Versatile clusters in a radical new role. Journal of Biological Inorganic Chemistry, 6(3), 209–226.CrossRef
Chen, C. (1999). Information visualisation and virtual environments. London: Springer.CrossRef
Chen, C. (2006). CiteSpace II: Detecting and visualizing emerging trends and transient patterns in scientific literature. Journal of the American Society for Information Science and Technology, 57(3), 359–377.CrossRef
Chen, C. (2010). Information visualization. Wiley Interdisciplinary Review: Computational Statistics, 2(4), 387–403.CrossRef
Chen, C., Dubin, R., & Kim, M. C. (2014a). Emerging trends and new developments in regenerative medicine: A scientometric update (2000–2014). Expert Opinion on Biological Therapy, 14(9), 1295–1317.CrossRef
Chen, C., Dubin, R., & Kim, M. C. (2014b). Orphan drugs and rare diseases: A scientometric review (2000–2014). Expert Opinion on Orphan Drugs, 2(7), 709–724.CrossRef
Chen, C. H., Härdle, W. K., & Unwin, A. (Eds.). (2008). Handbook of data visualization (Springer handbooks of computational statistics). Santa Clara, CA: Springer.
Chen, C., Hu, Z., Liu, S., & Tseng, H. (2012). Emerging trends in regenerative medicine: A scientometric analysis in CiteSpace. Expert Opinions on Biological Therapy, 12(5), 593–608.CrossRef
Chen, C., Ibekwe-SanJuan, F., & Hou, J. (2010). The structure and dynamics of co-citation clusters: A multiple-perspective co-citation analysis. Journal of the American Society for Information Science and Technology, 61(7), 1386–1409.CrossRef
Chen, C., & Leydesdorff, L. (2014). Patterns of connections and movements in dual-map overlays: A new method of publication portfolio analysis. Journal of the American Society for Information Science and Technology, 65(2), 334–351.CrossRef
Chinwalla, A. T., Cook, L. L., Delehaunty, K. D., et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520–562.CrossRef
Cleveland, W. S., & McGill, R. (1984). Graphical perception: Theory, experimentation, and application to the development of graphical methods. Journal of the American Statistical Association, 79(387), 521–554.MathSciNet CrossRef
Cobo, M. J., López-Herrera, A. G., Herrera-Viedma, E., & Herrera, F. (2011). Science mapping software tools: Review, analysis, and cooperative study among tools. Journal of the American Society for Information Science and Technology, 62(7), 1382–1402.MATH CrossRef
Cosper, N. J., Booker, S. J., Ruzicka, F., Frey, P. A., & Scott, R. A. (2000). Direct Fe–S cluster involvement in generation of a radical in lysine 2,3-aminomutase. Biochemistry, 39(51), 15668–15673.CrossRef
Davis, A. P., Murphy, C. G., Johnson, R., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., et al. (2013). The comparative toxicogenomics database: Update 2013. Nucleic Acids Research, 41(D1), D1104–D1114.CrossRef
Deerwester, S., Dumais, S. T., Furnas, G. W., Landauer, T. K., & Harshman, R. (1990). Indexing by latent semantic analysis. Journal of the American Society for Information Science, 41(6), 391–407.CrossRef
DellValle, M. (2010). Electronic tongues employing electrochemical sensors. Electroanalysis, 22(14), 1539–1555.
Delorme, A., & Makeig, S. (2004). EEGLAB: An open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. Journal of Neuroscience Methods, 134(1), 9–21.CrossRef
Duda, R. O., Hart, P. E., & Stork, D. G. (2001). Pattern classification. London: Wiley-Interscience.MATH
Duin, E. C., Lafferty, M. E., Crouse, B. R., Allen, R. M., Sanyal, I., Flint, D. H., et al. (1997). [2Fe–2S] to [4Fe–4S] cluster conversion in Escherichia coli biotin synthase. Biochemistry, 36(39), 11811–11820.CrossRef
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America, 95(25), 14863–14868.CrossRef
Ellis, G., & Dix, A. (2007). A taxonomy of clutter reduction for information visualisation. IEEE Transactions on Visualization and Computer Graphics, 13(6), 1216–1223.CrossRef
Elmqvist, N., Moere, A. V., Jetter, H. C., Cernea, D., Reiterer, H., & Jankun-Kelly, T. J. (2011). Fluid interaction for information visualization. Information Visualization, 10(4), 327–340.CrossRef
Fabrikant, S. I., & Buttenfield, B. P. (2001). Formalizing semantic spaces for information access. Annals of the Association of American Geographers, 91(2), 263–280.CrossRef
Faisal, S., Blandford, A., & Potts, H. W. (2013). Making sense of personal health information: Challenges for information visualization. Health Informatics Journal, 19(3), 198–217.CrossRef
Fekete, J. (2004). The infovis toolkit. In INFOVIS 2004 IEEE symposium on information visualization (pp. 167–174).
Fiehn, O. (2002). Metabolomics—The link between genotypes and phenotypes. Plant Molecular Biology, 48(1–2), 155–171.CrossRef
Fiehn, O., Kopka, J., Dörmann, P., Altmann, T., Trethewey, R. N., & Willmitzer, L. (2000). Metabolite profiling for plant functional genomics. Nature Biotechnology, 18, 1157–1161.CrossRef
Fontecave, M., Mulliez, E., & Ollagnier-de-Choudens, S. (2001). Adenosylmethionine as a source of 5′-deoxyadenosyl radicals. Current Opinion in Chemical Biology, 5(5), 506–512.CrossRef
Francisco, A. P., Vaz, C., Monteiro, P. T., Melo-Cristino, J., Ramirez, M., & Carriço, J. A. (2012). PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics, 13, 87.CrossRef
Frey, P. A. (2001). Radical mechanisms of enzymatic catalysis. Annual Review of Biochemistry, 70, 121–148.CrossRef
Frey, P. A., Hegeman, A. D., & Ruzicka, F. J. (2008). The radical SAM superfamily. Critical Reviews in Biochemistry and Molecular Biology, 43(1), 63–88.CrossRef
Frey, P. A., & Magnusson, O. T. (2003). s-Adenosylmethionine: A wolf in sheep’s clothing, or a rich man’s adenosylcobalamin? Chemical Reviews, 103(6), 2129–2148.CrossRef
Friendly, M. (2008). Milestones in the history of thematic cartography, statistical graphics, and data visualization. http://www.math.usu.edu/~symanzik/teaching/2009_stat6560/Downloads/Friendly_milestone.pdf . Accessed 7 February 2015.
Gaviria, A. R. (2008). When is information visualization art? Determining the critical criteria. Leonardo, 41(5), 479–482.CrossRef
Gehlenborg, N., O’Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M. A., Kitano, H., et al. (2010). Visualization of omics data for systems biology. Nature Methods, 7(3 Suppl), S56–S68.CrossRef
Grove, T. L., Benner, J. S., Radle, M. I., Ahlum, J. H., Landgraf, B. J., Krebs, C., et al. (2011). A radically different mechanism for s-adenosylmethionine—Dependent methyltransferases. Science, 332(6029), 604–607.CrossRef
Guianvarc’h, D., Florentin, D., Bui, B. T. S., Nunzi, F., & Marquet, A. (1997). Biotin synthase, a new member of the family of enzymes which uses s-adenosylmethionine as a source of deoxyadenosyl radical. Biochemical and Biophysical Research Communications, 236(2), 402–406.CrossRef
Henshaw, T. F., Cheek, J., & Broderick, J. B. (2000). The [4Fe–4S]1+ cluster of pyruvate formate-lyase activating enzyme generates the glycyl radical on pyruvate formate-lyase: EPR-detected single turnover. Journal of the American Chemistry Society, 122(34), 8331–8332.CrossRef
Herman, I., Melancon, G., & Marshall, M. S. (2000). Graph visualization and navigation in information visualization: A survey. IEEE Transactions on Visualization and Computer Graphics, 6(1), 24–43.CrossRef
Hewitson, K. S., Ollagnier-de-Choudens, S., Sanakis, Y., Shaw, N. M., Baldwin, J. E., Münck, E., et al. (2001). The iron–sulfur center of biotin synthase: Site-directed mutants. Journal of Biological Inorganic Chemistry, 7(1–2), 83–93.
Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science and Engineering, 9(3), 90–95.CrossRef
Inselberg, A., & Dimsdale, B. (1990). Parallel coordinates: A tool for visualizing multi-dimensional geometry. In Visualization ’90 proceedings of the first IEEE conference on visualization (pp. 361–378).
Isenberg, P. (2007). Interactive tree comparison for co-located collaborative information visualization. IEEE Transactions on Visualization and Computer Graphics, 13(6), 1232–1239.MathSciNet CrossRef
Isenberg, T., Isenberg, P., Chen, J., Sedlmair, M., & Moller, T. (2013). A systematic review on the practice of evaluating visualization. IEEE Transactions on Visualization and Computer Graphics, 19(12), 2818–2827.CrossRef
Jarrett, J. T. (2003). The generation of 5′-deoxyadenosyl radicals by adenosylmethionine-dependent radical enzymes. Current Opinion in Chemical Biology, 7(2), 174–182.CrossRef
Jenssen, T., Lægreid, A., Komorowski, J., & Hovig, E. (2001). A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics, 28, 21–28.
Jolliffe, I. T. (2002). Principal component analysis. Secaucus, NJ: Springer.MATH
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012). KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research, 40(D1), D109–D114.CrossRef
Kaul, S., Koo, H., Jenkins, J., et al. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814), 796–815.CrossRef
Kersten-Oertel, M., Jannin, P., & Collins, D. L. (2013). The state of the art of visualization in mixed reality image guided surgery. Computerized Medical Imaging and Graphics, 37(2), 98–112.CrossRef
Kim, M. C., & Chen, C. (2015). A scientometric review of emerging trends and new developments in recommendation systems. Scientometrics, 104(1), 239–263.CrossRef
Kleinberg, J. (2002). Bursty and hierarchical structure in streams. In KDD ’02 Proceedings of the eighth ACM SIGKDD international conference on knowledge discovery and data mining (pp. 91–101).
Kohonent, T. (1997). Self-organizing maps. Secaucus, NJ: Springer.CrossRef
Krzywinski, M. I., Schein, J. E., Birol, I., Connors, J., Gascoyne, R., Horsman, D., et al. (2009). Circos: An information aesthetic for comparative genomics. Genome Research, 19(9), 1639–1645.CrossRef
Külzer, R., Pils, T., Kappl, R., Hüttermann, J., & Knappe, J. (1998). Reconstitution and characterization of the polynuclear iron–sulfur cluster in pyruvate formate-lyase-activating enzyme. The Journal of biological chemistry, 273(9), 4897–4903.CrossRef
Lam, H., Bertini, E., Isenberg, P., Plaisant, C., & Carpendale, S. (2011). Empirical studies in information visualization: Seven scenarios. IEEE Transactions on Visualization and Computer Graphics, 18(9), 1520–1536.CrossRef
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.CrossRef
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.CrossRef
Layer, G., Moser, J., Heinz, D. W., Jahn, D., & Schubert, W. (2003). Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of radical SAM enzymes. The EMBO Journal, 22, 6214–6224.CrossRef
Lee, J. A., & Verleysen, M. (2007). Nonlinear dimensionality reduction. Berlin: Springer.MATH CrossRef
Leung, Y. K., & Apperley, M. D. (1994). A review and taxonomy of distortion-oriented presentation techniques. ACM Transactions on Computer-Human Interaction (TOCHI), 1(2), 126–160.CrossRef
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.CrossRef
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078–2079.CrossRef
Lieder, K. W., Booker, S., Ruzicka, F. J., Beinert, H., Reed, G. H., & Frey, P. A. (1998). s-Adenosylmethionine-dependent reduction of lysine 2,3-aminomutase and observation of the catalytically functional iron–sulfur centers by electron paramagnetic resonance. Biochemistry, 37(8), 2578–2585.CrossRef
Liu, S., Cui, W., Wu, Y., & Liu, M. (2014). A survey on information visualization: Recent advances and challenges. The Visual Computer, 30(12), 1373–1393.CrossRef
Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., et al. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology, 14(13), 1675–1680.CrossRef
Luck, S. J. (2005). An introduction to the event-related potential technique. Cambridge, MA: The MIT Press.
Maris, E., & Oostenveld, R. (2007). Nonparametric statistical testing of EEG- and MEG-data. Journal of Neuroscience Methods, 164(1), 177–190.CrossRef
Marquet, A. (2001). Enzymology of carbon–sulfur bond formation. Current Opinion in Chemical Biology, 5(5), 541–549.CrossRef
McKenna, A., Hanna, B., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., et al. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.CrossRef
Mehlan, H., Schmidt, F., Weiss, S., Schüler, J., Fuchs, S., Riedel, K., et al. (2013). Data visualization in environmental proteomics. Proteomics, 13(18–19), 2805–2821.
Miller, J. R., Busby, R. W., Jordan, S. W., Cheek, J., Henshaw, T. F., Ashley, G. W., et al. (2000). Escherichia coli LipA is a lipoyl synthase: In vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl–acyl carrier protein. Biochemistry, 39(49), 15166–15178.CrossRef
Moreland, J. L., Gramada, A., Buzko, O. V., Zhang, Q., & Bourne, P. E. (2005). The molecular biology toolkit (MBT): A modular platform for developing molecular visualization applications. BMC Bioinformatics, 6, 21.CrossRef
Morse, E., Lewis, M., & Olsen, K. A. (2000). Evaluating visualizations: Using a taxonomic guide. International Journal of Human-Computer Studies, 53(5), 637–662.MATH CrossRef
Munzner, T. (2009). A nested model for visualization design and validation. IEEE Transactions on Visualization and Computer Graphics, 15(6), 921–928.CrossRef
Ollagnier, S., Mulliez, E., Schmidt, P. P., Eliasson, R., Gaillardi, J., Deronzier, C., et al. (1997). Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The Journal of biological Chemistry, 272(39), 24216–24223.CrossRef
Ollagnier-De-Choudens, S., Mulliez, E., Hewitson, K. S., & Fontecave, M. (2002a). Biotin synthase is a pyridoxal phosphate-dependent cysteine desulfurase. Biochemistry, 41(29), 9145–9152.CrossRef
Ollagnier-de-Choudens, S., Sanakis, Y., Hewitson, K. S., Roach, P., Baldwin, J. E., Münck, E., et al. (2000). Iron–sulfur center of biotin synthase and lipoate synthase. Biochemistry, 39(14), 4165–4173.CrossRef
Ollagnier-de-Choudens, S., Sanakis, Y., Hewitson, K. S., Roach, P., Münck, E., & Fontecave, M. (2002b). Reductive cleavage of s-adenosylmethionine by biotin synthase from Escherichia coli. The Journal of biological chemistry, 277(16), 13449–13454.CrossRef
Oostenveld, R., Fries, P., Maris, E., & Schoffelen, J. (2011). FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data. Computational Intelligence and Neuroscience, 2011, Article ID 156869.
Orford, S., Harris, R., & Dorling, D. (1999). Geography: Information visualization in the social sciences. Social Science Computer Review, 17(3), 289–304.CrossRef
Penterman, R., Klink, S. I., de Koning, H., Nisato, G., & Broer, D. J. (2002). Single-substrate liquid–crystal displays by photo-enforced stratification. Nature, 417, 55–58.CrossRef
Pérez, F., & Granger, B. E. (2007). IPython: A system for interactive scientific computing. Computing in Science and Engineering, 9(3), 21–29.CrossRef
Polich, J. (2007). Updating P300: An integrative theory of P3a and P3b. Clinical Neurophysiology, 118(10), 2128–2148.CrossRef
Raamsdonk, L. M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M. C., et al. (2001). A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnology, 19, 45–50.CrossRef
Rabow, A. A., Shoemaker, R. H., Sausville, E. A., & Covell, D. G. (2002). Mining the national cancer institute’s tumor-screening database: Identification of compounds with similar cellular activities. Journal of Medical Chemistry, 45(4), 818–840.CrossRef
Rauber, A., Merkl, D., & Dittenbach, M. (2002). The growing hierarchical self-organizing map: Exploratory analysis of high-dimensional data. IEEE Transactions on Neural Networks, 13(6), 1331–1341.MATH CrossRef
Rhee, S. Y., Beavis, W., Berardini, T. Z., Chen, G., Dixon, D., Doyle, A., et al. (2003). The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research, 31(1), 224–228.CrossRef
Ripley, B. D. (1996). Pattern recognition and neural networks. Cambridge, MA: Cambridge University Press.MATH CrossRef
Riul, A., Jr, Dantas, C. A. R., Miyazakic, C. M., & Oliveira, O. N., Jr. (2010). Recent advances in electronic tongues. Analyst, 135, 2481–2495.CrossRef
Robertson, G. G., Card, S. K., & Mackinlay, J. D. (1993). Information visualization using 3D interactive animation. Communications of the ACM, 36(4), 57–71.CrossRef
Robertson, G. G., Mackinlay, J. D., & Card, S. K. (1991). Cone trees: Animated 3D visualizations of hierarchical information. In CHI ’91 Proceedings of the SIGCHI conference on human factors in computing systems (pp. 189–194).
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., et al. (2011). Integrative genomics viewer. Nature Biotechnology, 29, 24–26.CrossRef
Roessner, U., Luedemann, A., Brust, D., Fiehn, O., Linke, T., Willmitzer, L., et al. (2001). Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. The Plant Cell, 13(1), 11–29.CrossRef
Roessner, U., Wagner, C., Kopka, J., Trethewey, R. N., & Willmitzer, L. (2000). Simultaneous analysis of metabolites in potato tuber by gas chromatography–mass spectrometry. The Plant Journal, 23(1), 131–142.CrossRef
Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., et al. (2004). GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. Journal of Biomedical Informatics, 37(1), 43–53.CrossRef
Salomonis, N., Hanspers, K., Zambon, A. C., Vranizan, K., Lawlor, S. C., Dahlquist, K. D., et al. (2007). GenMAPP 2: New features and resources for pathway analysis. BMC Bioinformatics, 8, 217.CrossRef
Sanyal, I., Cohen, G., & Flint, D. H. (1994). Biotin synthase: Purification, characterization as a [2Fe–2S]cluster protein, and in vitro activity of the Escherichia coli bioB gene product. Biochemistry, 33(12), 3625–3631.CrossRef
Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270(5235), 467–470.CrossRef
Scherf, U., Ross, D. T., Waltham, M., Smith, L. H., Lee, J. K., Tanabe, L., et al. (2000). A gene expression database for the molecular pharmacology of cancer. Nature Genetics, 23(3), 236–244.CrossRef
Schneiderman, B. (1998). Designing the user interface: Strategies for effective human–computer interaction. Boston, MA: Addison-Wesley.
Segel, E. (2010). Narrative visualization: Telling stories with data. IEEE Transactions on Visualization and Computer Graphics, 16(6), 1139–1148.CrossRef
Shannon, P., Markiel, A., Ozier, W., Baliga, N. S., Wang, J. T., Ramage, D., et al. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.CrossRef
Sofia, H. D., Chen, G., Hetzler, B. G., Reyes-Spindola, J. F., & Miller, N. E. (2001). Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Research, 29(5), 1097–1106.CrossRef
Spence, B. (2000). Information visualization. New York, NY: ACM Press.
Stasko, J., Görg, C., & Liu, Z. (2008). Jigsaw: supporting investigative analysis through interactive visualization. Information Visualization, 7(2), 118–132.CrossRef
Su, A. I., Cooke, M. P., Ching, K. A., Hakak, Y., Walker, J. R., Wiltshire, T., et al. (2002). Large-scale analysis of the human and mouse transcriptomes. Proceedings of the National Academy of Sciences of the United States of America, 99(7), 4465–4470.CrossRef
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America, 101(16), 6062–6067.CrossRef
Sugiyama, M. (2007). Dimensionality reduction of multimodal labeled data by local fisher discriminant analysis. The Journal of Machine Learning Research, 8, 1027–1061.MATH
Sumner, L. W., Mendes, P., & Dixon, R. A. (2003). Plant metabolomics: Large-scale phytochemistry in the functional genomics era. Phytochemistry, 62(6), 817–836.CrossRef
Swayne, D. F., Cook, D., & Buja, A. (1998). XGobi: Interactive dynamic data visualization in the X window system. Journal of Computational and Graphical Statistics, 7(1), 113–130.
Tao, D., Li, X., Wu, X., & Maybank, S. J. (2008). Geometric mean for subspace selection. IEEE Transactions on Pattern Analysis and Machine Intelligence, 31(2), 260–274.
Tautenhahn, R., Patti, G. J., Rinehart, D., & Siuzdak, G. (2012). XCMS online: A web-based platform to process untargeted metabolomic data. Analytical Chemistry, 84(11), 5035–5039.CrossRef
Tenenbaum, J. B., de Silva, V., & Langford, J. C. (2000). A Global geometric framework for nonlinear dimensionality reduction. Science, 290(5500), 2319–2323.CrossRef
The ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74.CrossRef
Thomas, J. J., & Cook, K. A. (2005). Illuminating the path: The R&D agenda for visual analytics. USA: National Visualization and Analytics Center.
Thorvaldsdóttir, H., Robinson, J. T., & Mesirov, J. P. (2013). Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Briefings in Bioinformatics, 14(2), 178–192.CrossRef
Torgerson, W. S. (1952). Multidimensional scaling: I. Theory and method. Psychometrika, 17, 401–419.MathSciNet MATH CrossRef
Törönen, P., Kolehmainen, M., & Castrén, E. (1999). Analysis of gene expression data using self-organizing maps. FEBS Letters, 451(2), 142–146.CrossRef
Tory, M. (2005). Evaluating visualizations: Do expert reviews work? IEEE Computer Graphics and Applications, 25(5), 8–11.CrossRef
Tufte, E. (1983). The visual display of quantitative information. Cheshire, Connecticut: Graphics Press.
Tufte, E. (1990). Envisioning information. Cheshire, CT: Graphics Press.
Tukey, J. (1977). Exploratory data analysis. Boston, MA: Addison-Wesley.MATH
Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America, 98(9), 5116–5121.MATH CrossRef
Ugulava, N. B., Gibney, B. R., & Jarrett, J. T. (2001a). Biotin synthase contains two distinct iron–sulfur cluster binding sites: Chemical and spectroelectrochemical analysis of iron–sulfur cluster interconversions. Biochemistry, 40(28), 8343–8351.CrossRef
Ugulava, N. B., Sacanell, C. J., & Jarrett, J. T. (2001b). Spectroscopic changes during a single turnover of biotin synthase: Destruction of a [2Fe–2S] cluster accompanies sulfur insertion. Biochemistry, 40(28), 8352–8358.CrossRef
Ugulava, N. B., Surerus, K. K., & Jarrett, J. T. (2002). Evidence from Mössbauer spectroscopy for distinct [2Fe–2S]2+ and [4Fe–4S]2+ cluster binding sites in biotin synthase from Escherichia coli. Journal of the American Chemistry Society, 124(31), 9050–9051.CrossRef
Vaas, L. A. I., Sikorski, J., Michael, V., Göker, M., & Klenk, H. (2012). Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE, 7(4), e34846.CrossRef
van der Maaten, L., & Hinton, G. (2008). Visualizing data using t-SNE. The Journal of Machine Learning Research, 9, 2579–2605.MATH
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995). Serial analysis of gene expression. Science, 270(5235), 484–487.CrossRef
Venna, J., Peltonen, J., Nybo, K., Aidos, H., & Kaski, S. (2010). Information retrieval perspective to nonlinear dimensionality reduction for data visualization. The Journal of Machine Learning Research, 11, 451–490.MathSciNet MATH
Venter, J. C., Adams, M. D., & Myers, E. W. (2001). The sequence of the human genome. Science, 291(5507), 1304–1351.CrossRef
Vey, J. L., & Drennan, C. L. (2011). Structural insights into radical generation by the radical SAM superfamily. Chemical Reviews, 111(4), 2487–2506.CrossRef
Walsby, C. J., Hong, W., Broderick, W. E., Cheek, J., Ortillo, D., Broderick, J. B., et al. (2002a). Electron–nuclear double resonance spectroscopic evidence that s-adenosylmethionine binds in contact with the catalytically active [4Fe–4S]+ cluster of pyruvate formate-lyase activating enzyme. Journal of the American Chemistry Society, 124(12), 3143–3151.CrossRef
Walsby, C. J., Ortillo, D., Broderick, W. E., Broderick, J. B., & Hoffman, B. M. (2002b). An anchoring role for FeS clusters: Chelation of the amino acid moiety of s-adenosylmethionine to the unique iron site of the [4Fe–4S] cluster of pyruvate formate-lyase activating enzyme. Journal of the American Chemistry Society, 124(38), 11270–11271.CrossRef
Ware, C. (2000). Information visualization: Perception for design. San Francisco, CA: Morgan Kaufmann.
Ware, C. (2004). Information visualization: Perception for design. San Francisco, CA: Morgan Kaufmann.
Wicks, P., Massagli, M., Frost, J., Brownstein, C., Okun, S., Vaughan, T., et al. (2010). Sharing health data for better outcomes on PatientsLikeMe. Journal of Medical Internet Research, 12(2), e19.CrossRef
Yan, F., LaMarre, J. M., Röhrich, R., Wiesner, J., Jomaa, H., Mankin, A. S., et al. (2010). RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. Journal of the American Chemistry Society, 132(11), 3953–3964.CrossRef
Yi, J. S., Kang, Y. A., Stasko, J. T., & Jacko, J. A. (2007). Toward a deeper understanding of the role of interaction in information visualization. IEEE Transactions on Visualization and Computer Graphics, 13(6), 1224–1231.CrossRef
Yin, H. (2008). On multidimensional scaling and the embedding of self-organising maps. Neural Networks, 21(3), 160–169.CrossRef
Yin, H., & Huang, W. (2010). Adaptive nonlinear manifolds and their applications to pattern recognition. Information Sciences, 180(14), 2649–2662.MathSciNet MATH CrossRef
Zhang, B., Schmoyer, D., Kirov, S., & Snoddy, J. (2004). GOTree machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics, 5, 16.CrossRef
Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L., & Gruissem, W. (2004). GENEVESTIGATOR: Arabidopsis microarray database and analysis toolbox. Plant Physiology, 136(1), 2621–2632.CrossRef - 作者单位：Meen Chul Kim (1)
Yongjun Zhu (1)
Chaomei Chen (1)
1. Drexel University College of Computing and Informatics, Philadelphia, PA, USA - 刊物主题：Information Storage and Retrieval; Library Science; Interdisciplinary Studies;
- 出版者：Springer Netherlands
- ISSN：1588-2861
文摘
Information visualization and data visualization are often viewed as similar, but distinct domains, and they have drawn an increasingly broad range of interest from diverse sectors of academia and industry. This study systematically analyzes and compares the intellectual landscapes of the two domains between 2000 and 2014. The present study is based on bibliographic records retrieved from the Web of Science. Using a topic search and a citation expansion, we collected two sets of data in each domain. Then, we identified emerging trends and recent developments in information visualization and data visualization, captivated in intellectual landscapes, landmark articles, bursting keywords, and citation trends of the domains. We found out that both domains have computer engineering and applications as their shared grounds. Our study reveals that information visualization and data visualization have scrutinized algorithmic concepts underlying the domains in their early years. Successive literature citing the datasets focuses on applying information and data visualization techniques to biomedical research. Recent thematic trends in the fields reflect that they are also diverging from each other. In data visualization, emerging topics and new developments cover dimensionality reduction and applications of visual techniques to genomics. Information visualization research is scrutinizing cognitive and theoretical aspects. In conclusion, information visualization and data visualization have co-evolved. At the same time, both fields are distinctively developing with their own scientific interests.