[1] | Coopers PW (2008) Research rewired. 48 p.
|
[2] | Casey K, Elwell K, Friedman J, Gibbons D, Goggin M, et al.. (2008) A broken pipeline? Flat funding of the NIH puts a generation of science at risk. 24 p.
|
[3] | Payne PR, Johnson SB, Starren JB, Tilson HH, Dowdy D (2005) Breaking the translational barriers: the value of integrating biomedical informatics and translational research. J Investig Med 53: 192–200. doi: 10.2310/6650.2005.00402
|
[4] | Research NDsPoC (1997) NIH director's panel on clinical research report. Bethesda, MD: National Institutes of Health.
|
[5] | Sung NS, Crowley WF Jr, Genel M, Salber P, Sandy L, et al. (2003) Central challenges facing the national clinical research enterprise. JAMA 289: 1278–1287. doi: 10.1001/jama.289.10.1278
|
[6] | Butte AJ (2008) Medicine. The ultimate model organism. Science 320: 325–327. doi: 10.1126/science.1158343
|
[7] | Chung TK, Kukafka R, Johnson SB (2006) Reengineering clinical research with informatics. J Investig Med 54: 327–333. doi: 10.2310/6650.2006.06014
|
[8] | Kaiser J (2008) U.S. budget 2009. NIH hopes for more mileage from roadmap. Science 319: 716. doi: 10.1126/science.319.5864.716b
|
[9] | Kush RD, Helton E, Rockhold FW, Hardison CD (2008) Electronic health records, medical research, and the Tower of Babel. N Engl J Med 358: 1738–1740. doi: 10.1056/nejmsb0800209
|
[10] | Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, et al. (2007) Advancing translational research with the Semantic Web. BMC Bioinformatics 8 Suppl 3: S2. doi: 10.1186/1471-2105-8-s3-s2
|
[11] | Fridsma DB, Evans J, Hastak S, Mead CN (2008) The BRIDG project: a technical report. J Am Med Inform Assoc 15: 130–137. doi: 10.1197/jamia.m2556
|
[12] | Maojo V, García-Remesal M, Billhardt H, Alonso-Calvo R, Pérez-Rey D, et al. (2006) Designing new methodologies for integrating biomedical information in clinical trials. Methods Inf Med 45: 180–185.
|
[13] | Ash JS, Anderson NR, Tarczy-Hornoch P (2008) People and organizational issues in research systems implementation. J Am Med Inform Assoc 15: 283–289. doi: 10.1197/jamia.m2582
|
[14] | Payne PR, Mendonca EA, Johnson SB, Starren JB (2007) Conceptual knowledge acquisition in biomedicine: a methodological review. J Biomed Inform 40: 582–602. doi: 10.1016/j.jbi.2007.03.005
|
[15] | Richesson RL, Krischer J (2007) Data standards in clinical research: gaps, overlaps, challenges and future directions. J Am Med Inform Assoc 14: 687–696. doi: 10.1197/jamia.m2470
|
[16] | Erickson J (2008) A decade and more of UML: an overview of UML semantic and structural issues and UML field use. Journal of Database Management 19: I–Vii.
|
[17] | van Bemmel JH, van Mulligen EM, Mons B, van Wijk M, Kors JA, et al. (2006) Databases for knowledge discovery. Examples from biomedicine and health care. Int J Med Inform 75: 257–267. doi: 10.1016/j.ijmedinf.2005.08.012
|
[18] | Oster S, Langella S, Hastings S, Ervin D, Madduri R, et al. (2008) caGrid 1.0: an enterprise grid infrastructure for biomedical research. J Am Med Inform Assoc 15: 138–149. doi: 10.1197/jamia.m2522
|
[19] | Kukafka R, Johnson SB, Linfante A, Allegrante JP (2003) Grounding a new information technology implementation framework in behavioral science: a systematic analysis of the literature on IT use. J Biomed Inform 36: 218–227. doi: 10.1016/j.jbi.2003.09.002
|
[20] | Zerhouni EA (2005) Translational and clinical science–time for a new vision. N Engl J Med 353: 1621–1623. doi: 10.1056/nejmsb053723
|
[21] | Sim I (2008) Trial registration for public trust: making the case for medical devices. J Gen Intern Med 23 Suppl 1: 64–68. doi: 10.1007/s11606-007-0300-7
|
[22] | Preece A (2001) Evaluating verification and validation methods in knowledge engineering. Micro-Level Knowledge Management: 123–145.
|
[23] | Brachman RJ, McGuinness DL (1988) Knowledge representation, connectionism and conceptual retrieval. Proceedings of the 11th annual international ACM SIGIR conference on research and development in information retrieval. Grenoble, France: ACM Press.
|
[24] | Compton P, Jansen R (1990) A philosophical basis for knowledge acquisition. Knowledge Acquisition 2: 241–257. doi: 10.1016/s1042-8143(05)80017-2
|
[25] | Gaines BR (1989) Social and cognitive processes in knowledge acquisition. Knowledge Acquisition 1: 39–58. doi: 10.1016/s1042-8143(89)80004-4
|
[26] | Gaines BR, Shaw MLG (1993) Knowledge acquisition tools based on personal construct psychology.
|
[27] | Liou YI (1990) Knowledge acquisition: issues, techniques, and methodology. Orlando, Florida, United States: ACM Press. pp. 212–236.
|
[28] | Yihwa Irene L (1990) Knowledge acquisition: issues, techniques, and methodology. Proceedings of the 1990 ACM SIGBDP conference on trends and directions in expert systems. Orlando, Florida, United States: ACM Press.
|
[29] | Glaser R (1984) Education and thinking: the role of knowledge. American Psychologist 39: 93–104. doi: 10.1037/0003-066x.39.2.93
|
[30] | Hiebert J (1986) Procedural and conceptual knowledge: the case of mathematics. London: Lawrence Erlbaum Associates.
|
[31] | McCormick R (1997) Conceptual and procedural Knowledge. International Journal of Technology and Design Education 7: 141–159. doi: 10.1023/a:1008819912213
|
[32] | Scribner S (1985) Knowledge at work. Anthropology & Education Quarterly 16: 199–206. doi: 10.1525/aeq.1985.16.3.05x1486d
|
[33] | Barsalow LW, Simmons WK, Barbey AK, Wilson CD (2003) Grounding conceptual knowledge in modaltiy-specific systems. Trends Cogn Sci 7: 84–91. doi: 10.1016/s1364-6613(02)00029-3
|
[34] | Borlawsky T, Li J, Jalan S, Stern E, Williams R, et al. (2005) Partitioning knowledge bases between advanced notification and clinical decision support systems. AMIA Annu Symp Proc 901. doi: 10.1016/j.dss.2006.02.006
|
[35] | Newell A, Simon HA (1981) Computer science as empirical inquiry: symbols and search. In: Haugeland J, editor. Mind design. Cambridge: MIT Press/Bradfor Books. pp. 35–66.
|
[36] | Newell A, Simon HA (1975) Computer science as empirical inquiry: symbols and search. Minneapolis.
|
[37] | Kelly GA (1955) The psychology of personal constructs. New York: Norton. 2 v. (1218).
|
[38] | Hawkins D (1983) An analysis of expert thinking. Int J Man-Mach Stud 18: 1–47. doi: 10.1016/s0020-7373(83)80002-9
|
[39] | Zhang J (2002) Representations of health concepts: a cognitive perspective. J Biomed Inform 35: 17–24. doi: 10.1016/s1532-0464(02)00003-5
|
[40] | Horsky J, Kaufman DR, Oppenheim MI, Patel VL (2003) A framework for analyzing the cognitive complexity of computer-assisted clinical ordering. J Biomed Inform 36: 4–22. doi: 10.1016/s1532-0464(03)00062-5
|
[41] | Horsky J, Kaufman DR, Patel VL (2003) The cognitive complexity of a provider order entry interface. AMIA Annu Symp Proc 294–298.
|
[42] | Horsky J, Kaufman DR, Patel VL (2004) Computer-based drug ordering: evaluation of interaction with a decision-support system. Medinfo 11: 1063–1067.
|
[43] | Horsky J, Kuperman GJ, Patel VL (2005) Comprehensive analysis of a medication dosing error related to CPOE. J Am Med Inform Assoc 12: 377–382. doi: 10.1197/jamia.m1740
|
[44] | Horsky J, Zhang J, Patel VL (2005) To err is not entirely human: complex technology and user cognition. J Biomed Inform 38: 264–266. doi: 10.1016/j.jbi.2005.05.002
|
[45] | Patel VL, Arocha JF, Diermeier M, Greenes RA, Shortliffe EH (2001) Methods of cognitive analysis to support the design and evaluation of biomedical systems: the case of clinical practice guidelines. J Biomed Inform 34: 52–66. doi: 10.1006/jbin.2001.1002
|
[46] | Patel VL, Arocha JF, Kaufman DR (2001) A primer on aspects of cognition for medical informatics. J Am Med Inform Assoc 8: 324–343. doi: 10.1136/jamia.2001.0080324
|
[47] | Wikipedia (2006) Semiotics. Wikipedia.
|
[48] | Campbell KE, Oliver DE, Spackman KA, Shortliffe EH (1998) Representing thoughts, words, and things in the UMLS. J Am Med Inform Assoc 5: 421–431. doi: 10.1136/jamia.1998.0050421
|
[49] | Harris Z (1976) On a theory of language. The Journal of Philosophy 73: 253–276.
|
[50] | Friedman C, Kra P, Rzhetsky A (2002) Two biomedical sublanguages: a description based on the theories of Zellig Harris. J Biomed Inform 35: 222–235. doi: 10.1016/s1532-0464(03)00012-1
|
[51] | Grishman R, Kittredge R (1986) Analyzing language in restricted domains: sublangauge description and processing. Hillsdale, NJ.: Lawrence Erlbaum.
|
[52] | Starren J (1997) From multimodal sublanguages to medical data presentations. New York: Columbia University.
|
[53] | Alan LR, Chris W, Jeremy R, Angus R (2001) Untangling taxonomies and relationships: personal and practical problems in loosely coupled development of large ontologies. Proceedings of the international conference on knowledge capture. Victoria, British Columbia, Canada: ACM Press.
|
[54] | Canas AJ, Leake DB, Wilson DC (1999) Managing, mapping, and manipulating conceptual knowledge. Menlo Park: AAAI Press. pp. 10–14.
|
[55] | Ian N, Adam P (2001) Towards a standard upper ontology. Proceedings of the international conference on formal ontology in information systems - volume 2001. Ogunquit, Maine, United States: ACM Press.
|
[56] | Joachim H, Gerd S, Rudolf W, Uta W (2000) Conceptual knowledge discovery and data analysis. Springer-Verlag. pp. 421–437.
|
[57] | Tayar N (1993) A model for developing large shared knowledge bases. Washington, (D.C.): ACM Press. pp. 717–719.
|
[58] | Boy GA (1997) The group elicitation method for participatory design and usability testing. interactions 4: 27–33. doi: 10.1145/245129.245132
|
[59] | Morgan MS, Martz Jr WB (2004) Group consensus: do we know it when we see it? Proceedings of the 37th annual Hawaii international conference on system sciences (HICSS'04) - track 1 - volume 1: IEEE Computer Society.
|
[60] | Wood WC, Roth RM (1990) A workshop approach to acquiring knowledge from single and multiple experts. Orlando, Florida, United States: ACM Press. pp. 275–300.
|
[61] | Adria HL, William AS, Stephen DK (2003) GMS: preserving multiple expert voices in scientific knowledge management. San Francisco, California: ACM Press. pp. 1–4.
|
[62] | John H, Val K, Tom R, Hans A (1995) The role of ethnography in interactive systems design. interactions 2: 56–65. doi: 10.1145/205350.205358
|
[63] | Wickstrom G, Bendix T (2000) The “Hawthorne effect”–what did the original Hawthorne studies actually show? Scand J Work Environ Health 26: 363–367.
|
[64] | Rahat I, Richard G, Anne J (2005) A general approach to ethnographic analysis for systems design. Coventry, United Kingdom: ACM Press. pp. 34–40.
|
[65] | Rugg G, McGeorge P (1997) The sorting techniques: a tutorial paper on card sorts, picture sorts and item sorts. Expert Systems 14: 80–93. doi: 10.1111/1468-0394.00045
|
[66] | Cimiano P, Hotho A, Stumme G, Tane J (2004) Conceptual knowledge processing with formal concept analysis and ontologies. 189 p.
|
[67] | Cole R, Becker P (2004) Agreement contexts in formal concept analysis. 172 p.
|
[68] | Sowa JF (1980) A conceptual schema for knowledge-based systems. Pingree Park, Colorado: ACM Press. pp. 193–195.
|
[69] | Salomons OW, van Houten FJAM, Kals HJJ (1995) Conceptual graphs in constraint based re-design. Proceedings of the third ACM symposium on solid modeling and applications. Salt Lake City, Utah, United States: ACM Press.
|
[70] | Yang G, Oh J (1993) Knowledge acquisition and retrieval based on conceptual graphs. Proceedings of the 1993 ACM/SIGAPP symposium on applied computing: states of the art and practice. Indianapolis, Indiana, United States: ACM Press.
|
[71] | Campbell JR, Carpenter P, Sneiderman C, Cohn S, Chute CG, et al. (1997) Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures. J Am Med Inform Assoc 4: 238–251. doi: 10.1136/jamia.1997.0040238
|
[72] | Campbell KE, Oliver DE, Shortliffe EH (1998) The Unified Medical Language System: toward a collaborative approach for solving terminologic problems. J Am Med Inform Assoc 5: 12–16. doi: 10.1136/jamia.1998.0050012
|
[73] | Cimino JJ (2000) From data to knowledge through concept-oriented terminologies: experience with the Medical Entities Dictionary. J Am Med Inform Assoc 7: 288–297. doi: 10.1136/jamia.2000.0070288
|
[74] | TOCKIT (2006) Tupleware. 0.1 ed: Technische Universitaet Darmstadt and University of Queensland.
|
[75] | Hereth J, Stumme G, Wille R, Wille U (2000) Conceptual knowledge discovery and data analysis. Springer-Verlag. pp. 421–437.
|
[76] | Priss U (2006) Formal concept analysis in information science. In: Blaise C, editor. Annual review of information science and technology. Medford, NJ: Information Today, Inc.
|
[77] | Polson PG (1987) A quantitative theory of human-computer interaction. Interfacing thought: cognitive aspects of human-computer interaction. MIT Press. pp. 184–235.
|
[78] | Polson PG, Lewis C, Rieman J, Wharton C (1992) Cognitive walkthroughs: a method for theory-based evaluation of user interfaces. Int J Man-Mach Stud 36: 741–773. doi: 10.1016/0020-7373(92)90039-n
|
[79] | Alvarez R (2002) Discourse analysis of requirements and knowledge elicitation interviews. IEEE Computer Society. 255 p.
|
[80] | Davidson JE (1977) Topics in discourse analysis. University of British Columbia.
|
[81] | Friedman C, Alderson PO, Austin JH, Cimino JJ, Johnson SB (1994) A general natural-language text processor for clinical radiology. J Am Med Inform Assoc 1: 161–174. doi: 10.1136/jamia.1994.95236146
|
[82] | Friedman C, Hripcsak G (1998) Evaluating natural language processors in the clinical domain. Methods Inf Med 37: 334–344.
|
[83] | Friedman C, Hripcsak G (1999) Natural language processing and its future in medicine. Acad Med 74: 890–895. doi: 10.1097/00001888-199908000-00012
|
[84] | Friedman C, Hripcsak G, Shablinsky I (1998) An evaluation of natural language processing methodologies. Proc AMIA Symp: 855–859.
|
[85] | Hripcsak G, Friedman C, Alderson PO, DuMouchel W, Johnson SB, et al. (1995) Unlocking clinical data from narrative reports: a study of natural language processing. Ann Intern Med 122: 681–688. doi: 10.7326/0003-4819-122-9-199505010-00007
|
[86] | Corbridge C, Rugg G, Major NO, Shadbolt NR, Burton AM (1994) Laddering: technique and tool use in knowledge acquisition. Knowledge Acquisition 6: 315–341. doi: 10.1006/knac.1994.1016
|
[87] | Agostini A, Albolino S, Boselli R, De Michelis G, De Paoli F, et al.. (2003) Stimulating knowledge discovery and sharing; 2003; Sanibel Island, Florida, United States: ACM Press. pp. 248–257.
|
[88] | Roth RM, Wood WC (1990) A Delphi approach to acquiring knowledge from single and multiple experts; 1990; Orlando, Florida, United States: ACM Press. pp. 301–324.
|
[89] | Embi PJ, Payne PR (2009) Clinical research informatics: challenges, opportunities and definition for an emerging domain. J Am Med Inform Assoc 16: 316–327. doi: 10.1197/jamia.m3005
|
[90] | Crabtree BF, Miller WL (1992) Doing qualitative research. Newbury Park, CA: Sage.
|
[91] | Glaser B, Strauss A (1967) The discovery of grounded theory: strategies for qualitative research. Piscataway, NJ: Aldine Transaction. 271 p.
|
[92] | Patton MQ (2001) Qualitative research & evaluation methods. New York: Sage Publications. 688 p.
|
[93] | Khan SA, Kukafka R, Payne PR, Bigger JT, Johnson SB (2007) A day in the life of a clinical research coordinator: observations from community practice settings. Medinfo 12: 247–251.
|
[94] | Khan SA, Payne PR, Johnson SB, Bigger JT, Kukafka R (2006) Modeling clinical trials workflow in community practice settings. AMIA Annual Symposium proceedings/AMIA Symposium 419–423.
|
[95] | Rayhupathi W, Umar A (2008) Exploring a model-driven architecture (MDA) approach to health care information systems development. Int J Med Inform 77: 305–314. doi: 10.1016/j.ijmedinf.2007.04.009
|
[96] | Aksit M, Kurtev I (2008) Elsevier special issue on foundations and applications of model driven architecture. Science of Computer Programming 73: 1–2. doi: 10.1016/j.scico.2008.05.001
|
[97] | Shurville S (2007) Model driven architecture and ontology development. Interactive Learning Environments 15: 96–99.
|
[98] | Uhl A (2003) Model driven architecture is ready for prime time. IEEE Software 20: 70-+. doi: 10.1109/ms.2003.1231155
|
[99] | Soley RM (2003) Model driven architecture: the evolution of object-oriented systems? Object-Oriented Information Systems 2817: 2–2. doi: 10.1007/978-3-540-45242-3_2
|
[100] | Vanderperren Y, Mueller W, Dehaene W (2008) UML for electronic systems design: a comprehensive overview. Design Automation for Embedded Systems 12: 261–292. doi: 10.1007/s10617-008-9028-9
|
[101] | Dobing B, Parsons J (2008) Dimensions of UML diagram use: a survey of practitioners. Journal of Database Management 19: 1–18. doi: 10.4018/jdm.2008010101
|
[102] | Batra D (2008) Unified modeling language (UML) topics: the past, the problems, and the prospects. Journal of Database Management 19: I–Vii.
|
[103] | Komatsoulis GA, Warzel DB, Hartel FW, Shanbhag K, Chilukuri R, et al. (2008) caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. J Biomed Inform 41: 106–123. doi: 10.1016/j.jbi.2007.03.009
|
[104] | Kunz I, Lin MC, Frey L (2009) Metadata mapping and reuse in caBIG. BMC Bioinformatics 10 Suppl 2: S4. doi: 10.1186/1471-2105-10-s2-s4
|
[105] | Chakravarthy S, Whang WK, Navathe SB (1994) A logic-based approach to query-processing in federated databases. Information Sciences 79: 1–28. doi: 10.1016/0020-0255(94)90037-x
|
[106] | Ariyachandra T, Watson HJ (2008) Which data warehouse architecture is best? Communications of the ACM 51: 146–147. doi: 10.1145/1400181.1400213
|
[107] | DeWitt JG, Hampton PM (2005) Development of a data warehouse at an academic health system: knowing a place for the first time. Acad Med 80: 1019–1025. doi: 10.1097/00001888-200511000-00009
|
[108] | Braa J (2005) A data warehouse approach can manage multiple data sets. Bull World Health Organ 83: 638–639.
|
[109] | Yu J, Benatallah B, Casati F, Daniel F (2008) Understanding mashup development. IEEE Internet Computing 12: 44–52. doi: 10.1109/mic.2008.114
|
[110] | Scotch M, Yip KY, Cheung KH (2008) Development of grid-like applications for public health using web 2.0 mashup techniques. J Am Med Inform Assoc 15: 783–786. doi: 10.1197/jamia.m2731
|
[111] | Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP (2008) An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence. J Biomed Inform 41: 752–765. doi: 10.1016/j.jbi.2008.02.006
|
[112] | Cheung KH, Yip KY, Townsend JP, Scotch M (2008) HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. J Biomed Inform 41: 694–705. doi: 10.1016/j.jbi.2008.04.001
|
[113] | Cheung KH, Kashyap V, Luciano JS, Chen HJ, Wang YM, et al. (2008) Semantic mashup of biomedical data. J Biomed Inform s 41: 683–686. doi: 10.1016/j.jbi.2008.08.003
|
[114] | Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J (2008) Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 41: 706–716. doi: 10.1016/j.jbi.2008.03.004
|
[115] | Marks P (2006) ‘Mashup’ websites are a dream come true for hackers. New Scientist 190: 28–29.
|
[116] | Payne PR, Borlawsky T, Kwok A, Greaves A (2008) Supporting the design of translational clinical studies through the generation and verification of conceptual knowledge-anchored hypotheses. AMIA Annu Symp Proc 566–570.
|
[117] | Mansmann U (2005) Genomic profiling - interplay between clinical epidemiology, bioinformatics and biostatistics. Methods Inf Med 44: 454–460.
|
[118] | Xu R, Wunsch D (2005) Survey of clustering algorithms. IEEE Transactions on Neural Networks 16: 645–678. doi: 10.1109/tnn.2005.845141
|
[119] | Ardekani AM, Akhondi MM, Sadeghi MR (2008) Application of genomic and proteomic technologies to early detection of cancer. Archives of Iranian Medicine 11: 427–434.
|
[120] | De Fonzo V, Aluffi-Pentini F, Parisi V (2007) Hidden Markov models in bioinformatics. Curr Bioinform 2: 49–61. doi: 10.2174/157489307779314348
|
[121] | Feng J, Naiman DQ, Cooper B (2007) Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies. Bioinformatics 23: 2210–2217. doi: 10.1093/bioinformatics/btm267
|
[122] | Oehmen CS, Straatsma TP, Anderson GA, Orr G, Webb-Robertson BJM, et al. (2006) New challenges facing integrative biological science in the post-genomic era. Journal of Biological Systems 14: 275–293. doi: 10.1142/s0218339006001805
|
[123] | Way JC, Silver PA (2007) Systems engineering without an engineer: why we need systems biology. Complexity 13: 22–29. doi: 10.1002/cplx.20198
|
[124] | Knaup P, Ammenwerth E, Brandner R, Brigl B, Fischer G, et al. (2004) Towards clinical bioinformatics: advancing genomic medicine with informatics methods and tools. Methods Inf Med 43: 302–307.
|
[125] | Levy D, Dondero R, Veronneau P (2008) Research rewired. Price Waterhouse Coopers. 48 p.
|
[126] | Webb CP, Pass HI (2004) Translation research: from accurate diagnosis to appropriate treatment. J Transl Med 2: 35.
|
[127] | (2012) Merriam Webster online dictionary. Merriam Webster.
|
[128] | (2012) Wordnet. Princeton University.
|