Collaborative mining and interpretation of large-scale data for biomedical research insights

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Tsiliki, Georgia ^a   Karacapilidis, Nikos ^b   Christodoulou, Spyros ^b   Tzagarakis, Manolis ^b  

^a NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

^b University of Patras and Computer Technology Institute   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DATA ANALYSIS; DATA MINING; INFORMATION PROCESSING; INFORMATION SERVICE; INTERNET; MEDICAL RESEARCH; COMPUTER PROGRAM; COOPERATION; HUMAN; INFORMATION DISSEMINATION; ORGANIZATION AND MANAGEMENT; PROCEDURES;

ALGORITHMS; BIOMEDICAL RESEARCH; COOPERATIVE BEHAVIOR; DATA MINING; HUMANS; INFORMATION DISSEMINATION; SOFTWARE;

EID: 84907486467     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0108600     Document Type: Article

References (43)

1. Sullivan DE, Gabbard G, Shukla M, Sobral B (2010) Data integration for dynamic and sustainable systems biology resources: Challenges and lessons learned. Chem Biodivers 7: 1124-1141.
2. Quail A, Smith M, Coupland P, Otto T, Harris S, et al. (2012) A tale of three generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genom 13: 431.
3. (2011) Advancing discovery in science and engineering, white paper. Technical report, Computing Community Consortium. URL http://www.cra.org/ccc/ docs/web/data/spring.pdf.
4. Brazas M, Yamada JTT, Ouellette BE (2009) Evolution in bioinformatic resources: 2009 update on the bioinformatics links directory. Nucleic acids research 37: W3-5.
5. Lee ES (2007) Facilitating collaborative biomedical research. Technical report, NY, USA.
6. Costa F (2014) Big data in Biomedicine. Drug Discov Today 19: 433 -440.
7. Sun Y, Han J (2013) Mining heterogeneous information networks: a structural analysis approach. SIGKDD Explor Newsl 14: 20-28.
8. Foreman J (2013) Data Smart: Using Data Science to Transform Information into Insight. John Wiley & Sons, Hoboken, NJ, USA.
9. Karacapilidis N, Rüping S, Tzagarakis M, Poignè A, Christodoulou S (2011) Building on the synergy of machine and human reasoning to tackle dataintensive collaboration and decision making. In: Watada J, Philips-Wren G, Jain L, Hewlett R, editors, Proceedings of the 3rd International Conference on Inteligent Decision Technologies (IDT2011), Piraeus, Greece. Srienger, Berlin, Germany, Smart Innovation Systems and Technologies, pp. 113-122.
10. (2012) Challenges and opportunities with big data, white paper. Technical report, Computing Community Consortium. URL http://cra.org/ccc/docs/init/bigdatawhitepaper.pdf.
11. Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, et al. (2008) Integrating Global Gene Expression and Radiation Survival Parameters across the 60 Cell Lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res 68: 415-424.
12. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) Biogrid: a general repository for interaction datasets. Nucleic Acids Research 34: D535-D539.
13. Birkl A, Yona G (2006) Biozon: a hub of heterogeneous biological data. Nucleic Acids Research 34: D235-D242.
14. GubermanJM, Ai J, Arnaiz O, Baran J, Blake A, et al. (2011) Biomart central portal: an open database network for the biological community. Database: bar041.
15. Rhodes D, Yu J, Shanker K, Deshpande N, Varambally R, et al. (2004) Oncomine: A cancer microarray database and integrated data-mining platform. Neoplasia 6: 1-6.
16. Hoshida Y, Brunet J, Tamayo P, Golub T, MesirovJ (2007) Subclass mapping: identifying common subtypes in independent disease data sets. PLoS ONE 2: el 195.
17. Goble C, Bhagat J, Don Cruickshank SA, Michaelides D, Newman D, et al. (2010) myexperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Research 38: W677-W682.
18. Karacapilidis N, editor (2014) Mastering Data-intensive Collaboration and Decision-Making: Cutting edge research and practical applications in the Dicode project. Studies in Big Data (vol. 5). Springer, Berlin, Germany.
19. Swick R, Ackerman M (1988) The x toolkit: more bricks for building user interfaces, or widgets for hire. In: Proceedings of Usenix Winter 1988 Conf. pp. 221-228.
20. Hall M, editor (2001) More Servlets and JavaServer Pages. Prentice Hall PTR, Englewood Cliffs.
21. Hanson R, Tacy A, editors (2007) GWT in Action: Easy Ajax with the Google Web Toolkit. Manning Publications Co., Greenwich, UK.
22. Pautasso C, Zimmermann O, Leymann F (2008) Restful web services vs. big web services: making the right architectural decision. In: Proceedings of the 17th international conference on World Wide Web. ACM, NY, USA, WWW 08, pp. 805-814. doi:DOI:http://dx.doi.org/10.1145/1367497.1367606.
23. Thakker D, Yang-Turner F, Lau L, Dimitrova V (2011) Socio-technical ontology development for modelling sensemaking in heterogeneous domains. In: Proceedings of OCAS 2011 Workshop at the 10th International Semantic Web Conference. Bonn, Germany, pp. 60 -71.
24. Snir M, Otto SW, Walker DW, Dongarra J, Huss-Lederman S (1995) MPI: The Complete Reference. MIT Press, Cambridge, MA, USA.
25. de la Calle G, Alonso-Martinez E, Tzagarakis M, Karacapilidis N (2012) The dicode workbench: A flexible framework for the integration of information and web services. In: Taniar D, Pardede E, Steinbauer M, Khalil I, editors, Proceedings of the 14th International Conference on Information Integration and Web-based Applications & Services (iiWAS2012). Bali, Indonesia, pp. 16 -25.
26. de la Calle G, Alonso-Martnez E, Rojas-Vera M, Garciá-Remesal M (2014) Integrating Dicode Services: The Dicode Workbench, In [18]. 141-164 pp.
27. Shipman F, McCal R (1994) Supporting knowledge-base evolution with incremental formalization. In: Proceedings CHI 94 Conference, pp. 285-291.
28. Karacapilidis N, Tzagarakis M (2012) Towards a seamless integration of human and machine reasoning in data-intensive collaborative decision making settings: The dicode approach. In: Proceedings of the 16th IFIP WG8.3 International Conference on Decision Support Systems. IOS Press, Amsterdam, DSS 2012, pp. 223-228.
29. Marshall C, Shipman F (1997) Spatial hypertext and the practice of information triage. In: Proceedings of the 8th ACM Conference on Hypertext. Southampton, UK, pp. 124-133.
30. Haendel M, Vasilevsky N, Wirz J (2012) Dealing with data: A case study on information and data management literacy. PLoS Biol 10: e1001339.
31. Kahn S (2011) On the future of genomic data. Science 331: 728.
32. Tsiliki G, Kossida S (2014) Clinico-Genomic Research Assimilator: A Dicode Use Case, In [18]. 165-180 pp.
33. Tzagarakis M, Karacapilidis N, Christodoulou S, Yang-Turner F, Lau L (2014) The Dicode Collaboration and Decision Making Support Services, In [18]. 119139 pp.
34. Tsiliki G, Kossida S, Friesen N, Ruepping S, Tzagarakis M, et al. (2014) A data mining based approach for collaborative analysis of biomedical data. Int J Artif In tell T 23: 1460010.
35. Friesen N, Jakob M, Kindermann J, Maassen D, Poigné A, et al. (2014) The Dicode Data Mining Services, In [18]. 89-118 pp.
36. Huber-Keener K, Liu X, Wang Z, Freeman W, Wu S, et al. (2012) Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of rna-seq data. PLoS ONE 7: e41333.
37. Atzmueller M, Puppe F, Buscher H (2005) Exploiting background knowledge for knowledge-intensive subgroup discovery. In: Proceedings of IJCAI05. pp. 647 -652.
38. Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102: 15545-15550.
39. Sass S, Buettner F, Mueller N, Theis F (2014) A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res 41: 9622-9633.
40. Kaever A, Landesfeind M, Feussner K, Morgenstern B, Feussner I, et al. (2014) Meta-analysis of pathway enrichment: Combining independent and dependent omics data sets. PLoS ONE 9: e89297.
41. Jacobs MR (2014) Institutional review boards and independent ethics committees, white paper. Technical report. URL http://www.pharmapress. com/files/docs/principlesclinpractsample.pdf.
42. Nielsen J (1999) Designing Web Usability: The Practice of Simplicity. New Riders Publishing, Indianapolis, USA.
43. Norman D, The MIT Press U (1998) The Design of Everyday Things. The MIT Press, USA.