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Lecture 4 Biomedical Databases: Acquisition, Storage, Information Retrieval, and Use

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References

  • Aronson A, Rindflesch T, Browne A (1994) Exploiting a large thesaurus for information retrieval RIAO Recherche d’Information assistee par Ordinateur—Computer-aided information retrieval, pp 197–216

    Google Scholar 

  • Baeza-Yates R, Ribeiro-Neto B (2011) Modern information retrieval: the concepts and technology behind search. Pearson, Harlow

    Google Scholar 

  • Bastiao-Silva LA, Costa C, Silva A, Oliveira JL (2011) A PACS gateway to the cloud. 6th Iberian conference on information systems and technologies (CISTI), pp 1–6

    Google Scholar 

  • Bemmel JHV, Musen MA (1997) Handbook of medical informatics. Springer, Heidelberg

    Google Scholar 

  • Berman JJ (2013a) Chapter 2—Identification, deidentification, and reidentification. In: Berman JJ (ed) Principles of big data. Morgan Kaufmann, Boston, pp 15–33

    Chapter  Google Scholar 

  • Berman JJ (2013b) Chapter 4—Introspection. In: Berman JJ (ed) Principles of big data. Morgan Kaufmann, Boston, pp 49–61

    Chapter  Google Scholar 

  • Bleiholder J, Naumann F (2008) Data fusion. ACM Comput Surv 41(1):1

    Article  Google Scholar 

  • Blum RL, Wiederhold GC (1985) Studying hypotheses on a time-oriented clinical database: an overview of the RX project. Computer-assisted medical decision making. Springer, New York, NY, pp 242–253

    Google Scholar 

  • Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)[mdash]toward standards for microarray data. Nat Genet 29(4):365–371

    Article  Google Scholar 

  • Campbell M, Hoane AJ, Hsu F-H (2002) Deep blue. Artif Intell 134(1):57–83

    Article  MATH  Google Scholar 

  • Canfora G, Cerulo L (2004) A taxonomy of information retrieval models and tools. J Comput Inf Technol 12(3):175–194

    Google Scholar 

  • Chute CG, Beck SA, Fisk TB, Mohr DN (2010) The Enterprise Data Trust at Mayo Clinic: a semantically integrated warehouse of biomedical data. J Am Med Inform Assoc 17(2):131–135

    Article  Google Scholar 

  • Doan A, Halevy A, Ives Z (2012) 19—The future of data integration. In: Doan A, Halevy A, Ives Z (eds) Principles of data integration. Morgan Kaufmann, Boston, pp 453–457

    Chapter  Google Scholar 

  • Efthimiadis E (1996) Query expansion. In: Williams ME (ed) Annual review of information systems and technology (ARIST), Vol 31, pp 121–187

    Google Scholar 

  • Fayyad U, Piatetsky-Shapiro G, Smyth P (1996) The KDD process for extracting useful knowledge from volumes of data. Commun ACM 39(11):27–34

    Article  Google Scholar 

  • Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, Mclaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM (2011) Ensembl 2011. Nucleic Acids Res 39(Database issue):D800–D806

    Article  Google Scholar 

  • Gardner RM, Pryor TA, Warner HR (1999) The HELP hospital information system: update 1998. Int J Med Inform 54(3):169–182

    Article  Google Scholar 

  • Gigerenzer G, Gaissmaier W (2011) Heuristic decision making. In: Fiske ST, Schacter DL, Taylor SE (eds) Annual review of psychology, vol 62. Palo Alto, Annual Reviews, pp 451–482

    Google Scholar 

  • Gschwandtner T, Gärtner J, Aigner W, Miksch S (2012) A taxonomy of dirty time-oriented data. In: Quirchmayr G, Basl J, You I, Xu L, Weippl E (eds) Multidisciplinary research and practice for information systems. Springer, Berlin, pp 58–72

    Chapter  Google Scholar 

  • Hastie T, Tibshirani R, Friedman J (2009) The elements of statistical learning: data mining, inference, and prediction, 2nd edn. Springer, New York

    Book  Google Scholar 

  • Haux R (2006) Health information systems-past, present, future. Int J Med Inform 75(3–4):268–281

    Article  Google Scholar 

  • Haux R, Lagemann A, Knaup P, Schmücker P, Winter A (1998) Management von Informationssystemen: Analyse, Bewertung, Auswahl, Bereitstellung und Einführung von Informationssystemkomponenten am Beispiel von Krankenhausinformationssystemen. Teubner, Stuttgart

    Book  MATH  Google Scholar 

  • Hawkins RC (2005) The evidence based medicine approach to diagnostic testing: practicalities and limitations. Clin Biochem Rev 26(2):7

    Google Scholar 

  • Hearst MA (1999) Untangling text data mining. Proceedings of the 37th annual meeting of the Association for Computational Linguistics on computational linguistics. Association for Computational Linguistics, pp 3–10

    Google Scholar 

  • Hermjakob H, Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32(Suppl 1):D452–D455

    Article  Google Scholar 

  • Holzinger A (2003) Experiences with User Centered Development (UCD) for the Front End of the Virtual Medical Campus Graz. In: Jacko JA, Stephanidis C (eds) Human-computer interaction, theory and practice. Lawrence Erlbaum, Mahwah, NJ, pp 123–127

    Google Scholar 

  • Holzinger A (2013) Human–computer interaction & knowledge discovery (HCI-KDD): what is the benefit of bringing those two fields to work together? In: Alfredo Cuzzocrea C, Simos DE, Weippl E, Xu L (eds) Multidisciplinary research and practice for information systems, vol 8127, Lecture notes in computer science (LNCS). Springer, Heidelberg, pp 319–328

    Google Scholar 

  • Holzinger A, Baernthaler M, Pammer W, Katz H, Bjelic-Radisic V, Ziefle M (2011) Investigating paper vs. screen in real-life hospital workflows: performance contradicts perceived superiority of paper in the user experience. Int J Hum Comput Stud 69(9):563–570

    Article  Google Scholar 

  • Holzinger A, Geierhofer R, Ackerl S, Searle G (2005) CARDIAC@VIEW: the user centered development of a new medical image viewer. In: Zara J, Sloup J (eds) Central European multimedia and virtual reality conference (available in Eurographics Library). Czech Technical University (CTU), Prague, pp 63–68

    Google Scholar 

  • Holzinger A, Geierhofer R, Errath M (2007) Semantische Informationsextraktion in medizinischen Informationssystemen. Informatik Spektrum 30(2):69–78

    Article  Google Scholar 

  • Holzinger A, Simonic K-M (eds) (2011) Information quality in e-Health, vol 7058, Lecture notes in computer science (LNCS). Springer, Heidelberg

    Google Scholar 

  • Hotho A, Nürnberger A, Paaß G (2005) A brief survey of text mining. GLDV J Comput Linguist Lang Technol 20(1):19–62

    Google Scholar 

  • Johnston T, Weis R (2010) Managing time in relational databases: how to design, update and query temporal data. Morgan Kaufmann, San Francisco

    Google Scholar 

  • Kampen AV (2013) Medical bioinformatics and e-bioscience [Online]. http://www.bioinformaticslaboratory.nl/twiki/bin/view/BioLab/EducationMIK1-2. Accessed 22 Apr 2013

  • Kell DB (2007) The virtual human: towards a global systems biology of multiscale, distributed biochemical network models. IUBMB Life 59(11):689–695

    Article  Google Scholar 

  • Kingsland LC, Harbourt AM, Syed EJ, Schuyler PL (1993) Coach: applying UMLS knowledge sources in an expert searcher environment. Bull Med Libr Assoc 81:178–183

    Google Scholar 

  • Kreuzthaler M, Bloice MD, Faulstich L, Simonic KM, Holzinger A (2011) A comparison of different retrieval strategies working on medical free texts. J Univ Computer Sci 17(7):1109–1133

    Google Scholar 

  • Lenz R, Reichert M (2007) IT support for healthcare processes-premises, challenges, perspectives. Data Knowl Eng 61(1):39–58

    Article  Google Scholar 

  • Lenzerini M (2002) Data integration: a theoretical perspective. Proceedings of the twenty-first ACM SIGMOD-SIGACT-SIGART symposium on principles of database systems. ACM, pp 233–246

    Google Scholar 

  • Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C (2010) BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92

    Article  Google Scholar 

  • Louie B, Mork P, Martin-Sanchez F, Halevy A, Tarczy-Hornoch P (2007) Data integration and genomic medicine. J Biomed Inform 40(1):5–16

    Article  Google Scholar 

  • Maimon O, Rokach L (eds) (2010) Data mining and knowledge discovery handbook, 2nd edn. Springer, New York

    MATH  Google Scholar 

  • Masic I, Milinovic K (2012) On-line biomedical databases–the best source for quick search of the scientific information in the biomedicine. Acta Inform Med 20(2):72

    Article  Google Scholar 

  • Page L, Brin S, Motwani R, Winograd T (1999) The PageRank citation ranking: bringing order to the web. Technical Report Stanford InfoLab

    Google Scholar 

  • Piatetsky-Shapiro G (2000) Knowledge discovery in databases: 10 years after. ACM SIGKDD Explor Newslett 1(2):59–61

    Article  Google Scholar 

  • Plattner H (2013) A course in in-memory data management: the inner mechanics of in-memory databases. Springer, Heidelberg

    Book  Google Scholar 

  • Reichertz PL (2006) Hospital information systems—past, present, future. Int J Med Inform 75(3–4):282–299

    Article  Google Scholar 

  • Robinson I, Webber J, Eifrem E (2013) Graph databases. O’Reilly Media, Sebastopol

    Google Scholar 

  • Roden DM, Pulley JM, Basford MA, Bernard GR, Clayton EW, Balser JR, Masys DR (2008) Development of a large-scale de-identified DNA biobank to enable personalized medicine. Clin Pharmacol Therapeut 84(3):362–369

    Article  Google Scholar 

  • Salton G, Buckley C (1988) Term-weighting approaches in automatic text retrieval. Inf Process Manag 24(5):513–523

    Article  Google Scholar 

  • Salton G, Fox EA, Wu H (1983) Extended Boolean information retrieval. Commun ACM 26(11):1022–1036

    Article  MATH  MathSciNet  Google Scholar 

  • Salton G, Wong A, Yang CS (1975) A vector space model for automatic indexing. Commun ACM 18(11):613–620

    Article  MATH  Google Scholar 

  • Shortliffe EH, Perrault LE, Wiederhold G, Fagan LM (2001) Medical informatics: computer applications in health care and biomedicine, 2nd edn. Springer, New York

    Book  Google Scholar 

  • Silberschatz A, Korth HF, Sudarshan S (2010) Database system concepts, 6th edn. McGraw-Hill Hightstown, New York

    Google Scholar 

  • Simonic K-M, Holzinger A (2010) Zur Bedeutung von Information in der Medizin. OCG J 35(1):8

    Google Scholar 

  • Sreenivasaiah PK (2010) Current trends and new challenges of databases and web applications for systems driven biological research. Front Physiol 1:147

    Article  Google Scholar 

  • Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11(5)

    Google Scholar 

  • Tata S, Patel JM (2007) Estimating the selectivity of tf-idf based cosine similarity predicates. ACM SIGMOD Rec 36(2):7–12

    Article  Google Scholar 

  • Vallet D, Fernández M, Castells P (2005) An ontology-based information retrieval model. In: Gómez-Pérez A, Euzenat J (eds) The semantic web: research and applications. Springer, Berlin, pp 103–110

    Google Scholar 

  • Van Rijsbergen CJ (1979) Information retrieval, 2nd edn. Butterworths, London

    Google Scholar 

  • Waterson P, Glenn Y, Eason K (2012) Preparing the ground for the ‘paperless hospital’: a case study of medical records management in a UK outpatient services department. Int J Med Inform 81(2):114–129

    Article  Google Scholar 

  • Wiltgen M, Holzinger A (2005) Visualization in bioinformatics: protein structures with physicochemical and biological annotations. In: Zara J, Sloup J (eds) Central European multimedia and virtual reality conference (available in EG Eurographics Library). Czech Technical University (CTU), Prague, pp 69–74

    Google Scholar 

  • Wiltgen M, Holzinger A, Tilz GP (2007) Interactive analysis and visualization of macromolecular interfaces between proteins. In: Holzinger A (ed) HCI and usability for medicine and health care, vol 4799, Lecture notes in computer science (LNCS). Springer, Berlin, pp 199–212

    Chapter  Google Scholar 

  • Witten IH, Frank E, Hall MA (2011) Data mining: practical machine learning tools and techniques. Morgan Kaufmann, San Francisco

    Google Scholar 

  • Zhang M, Zhang H, Tjandra D, Wong STC (2004) DBMap: a space-conscious data visualization and knowledge discovery framework for biomedical data warehouse. IEEE Trans Inf Technol Biomed 8(3):343–353

    Article  Google Scholar 

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  1. Medical University Graz and Graz University of Technology, Graz, Austria

    Andreas Holzinger

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Holzinger, A. (2014). Lecture 4 Biomedical Databases: Acquisition, Storage, Information Retrieval, and Use. In: Biomedical Informatics. Springer, Cham. https://doi.org/10.1007/978-3-319-04528-3_4

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  • DOI: https://doi.org/10.1007/978-3-319-04528-3_4

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