Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care

In this paper, we review the results of BIOINFOMED, a study funded by the European Commission (EC) with the purpose to analyse the different issues and challenges in the area where Medical Informatics and Bioinformatics meet. Traditionally, Medical Informatics has been focused on the intersection between computer science and clinical medicine, whereas Bioinformatics have been predominantly centered on the intersection between computer science and biological research. Although researchers from both areas have occasionally collaborated, their training, objectives and interests have been quite different. The results of the Human Genome and related projects have attracted the interest of many professionals, and introduced new challenges that will transform biomedical research and health care. A characteristic of the 'post genomic' era will be to correlate essential genotypic information with expressed phenotypic information. In this context, Biomedical Informatics (BMI) has emerged to describe the technology that brings both disciplines (BI and MI) together to support genomic medicine. In recognition of the dynamic nature of BMI, institutions such as the EC have launched several initiatives in support of a research agenda, including the BIOINFOMED study.

[1]  K.J. Cios,et al.  From the guest editor medical data mining and knowledge discovery , 2000, IEEE Engineering in Medicine and Biology Magazine.

[2]  Marti A. Hearst.  Untangling Text Data Mining , 1999, ACL.

[3]  Witold Pedrycz,et al.  Data Mining Methods for Knowledge Discovery , 1998, IEEE Trans. Neural Networks.

[4]  Marius Fieschi,et al.  An Adaptive Medical E-Learning Environment: The MEDIDACTE Project , 2001, MedInfo.

[5]  Ralph Wayne Mullins.  Connectivity Industry Consortium Point-of-Care Communications in the Past, Present, and Future , 2002 .

[6]  W J Schaller,et al.  Applying World Wide Web Technology to the Study of Patients with Rare Diseases , 1998, Annals of Internal Medicine.

[7]  Walter V. Sujansky,et al.  Heterogeneous Database Integration in Biomedicine , 2001, J. Biomed. Informatics.

[8]  Isaac S. Kohane,et al.  Bioinformatics and Clinical Informatics: The Imperative to Collaborate , 2000, J. Am. Medical Informatics Assoc..

[9]  Stephen H. Friend,et al.  Toxicogenomics and drug discovery: will new technologies help us produce better drugs? , 2002, Nature Reviews Drug Discovery.

[10]  A. Roses,et al.  Pharmacogenetics and future drug development and delivery , 2000, The Lancet.

[11]  K. Cios.  Medical data mining and knowledge discovery. , 2000, IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society.

[12]  Michael Fung Kee Fung.  Keynotes: KOALA:An internet-based learning and knowledge management system , 2002 .

[13]  Astrid M. van Ginneken,et al.  Research Paper: Evaluation of Reporting Based on Descriptional Knowledge , 1995, J. Am. Medical Informatics Assoc..

[14]  Marc Broudo,et al.  MEDICOL: online learning in medicine and dentistry. , 2002, Academic medicine : journal of the Association of American Medical Colleges.

[15]  Russ B. Altman.  Viewpoint: The Interactions Between Clinical Informatics and Bioinformatics: A Case Study , 2000, J. Am. Medical Informatics Assoc..

[16]  C. Sabatti,et al.  The Human Phenome Project , 2003, Nature Genetics.

[17]  Vimla L. Patel,et al.  Research Paper: Representing Clinical Guidelines in GLIF: Individual and Collaborative Expertise , 1998, J. Am. Medical Informatics Assoc..

[18]  Russ B. Altman,et al.  Bioinformatics in support of molecular medicine , 1998, AMIA.

[19]  P. Tang,et al.  Medical Computer Applications in Health Care and Biomedicine , 2002 .

[20]  S. Friend,et al.  How DNA microarrays and expression profiling will affect clinical practice , 1999, BMJ.

[21]  Ellen Murphy,et al.  Genomics in anti-infective drug discovery--getting to endgame. , 2002, Current pharmaceutical design.

[22]  G. Ginsburg,et al.  Personalized medicine: revolutionizing drug discovery and patient care. , 2001, Trends in biotechnology.

[23]  Bart Preneel,et al.  Towards Measuring Anonymity , 2002, Privacy Enhancing Technologies.

[24]  B. Rannala.  Bioinformatics: The Machine Learning Approach.Second Edition. Adaptive Computation and Machine Learning. ByPierre Baldiand, Sørenv Brunak.A Bradford Book. Cambridge (Massachusetts): MIT Press. $49.95. xxiii + 452 p; ill.; index. ISBN: 0–262–02506‐X. 2001. , 2002 .

[25]  Thomas G. Dietterich,et al.  Bioinformatics The Machine Learning Approach 2nd ed. , 2001 .

[26]  Charles P. Friedman,et al.  Viewpoint: Toward a New Culture for Biomedical Informatics: Report of the 2001 ACMI Symposium , 2001, J. Am. Medical Informatics Assoc..

[27]  J. Claibornestephens,et al.  Single-nucleotide polymorphisms, haplotypes, and their relevance to pharmacogenetics , 1999 .

[28]  R. Wootton,et al.  Telemedicine and clinical genetics: Establishing a successful service , 2001, Journal of telemedicine and telecare.

[29]  Manolis Tsiknakis,et al.  An open, component-based information infrastructure for integrated health information networks , 2002, Int. J. Medical Informatics.

[30]  Ash A. Alizadeh,et al.  Towards a novel classification of human malignancies based on gene expression patterns , 2001, The Journal of pathology.

[31]  Schlag,et al.  On the Way to New Horizons: Telemedicine in Oncology. , 1997, The oncologist.

[32]  Jeanne M Meck,et al.  Cytogenetic analysis using telemedicine consultation: An improved means of providing expert cross‐coverage , 1999, Genetics in Medicine.

[33]  Russ B. Altman,et al.  Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models , 2002, ISMB.

[34]  Richard Wise,et al.  Science, medicine, and the future , 1998 .

[35]  J. Stephens,et al.  Single-nucleotide polymorphisms, haplotypes, and their relevance to pharmacogenetics. , 1999, Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology.

[36]  F. Collins,et al.  Shattuck lecture--medical and societal consequences of the Human Genome Project. , 1999, The New England journal of medicine.

[37]  Ardeshir Bayat,et al.  Science, medicine, and the future: Bioinformatics. , 2002, BMJ.

[38]  Jeffrey Augen,et al.  The evolving role of information technology in the drug discovery process. , 2002, Drug discovery today.

[39]  K Engel,et al.  Secure interoperability of patient data cards in health networks. , 2000, Studies in health technology and informatics.

[40]  G Dutton.  Computational genomics: the medicine of the future? , 1999, Annals of internal medicine.

[41]  V. Maojo,et al.  Integrating Genomics into Health Information Systems , 2002, Methods of Information in Medicine.

[42]  José Manuel Gutiérrez,et al.  Expert Systems and Probabiistic Network Models , 1996 .

[43]  Thomas D Pollard.  The future of biomedical research: from the inventory of genes to understanding physiology and the molecular basis of disease. , 2002, JAMA.

[44]  Lawrence M. Fagan,et al.  Medical informatics: computer applications in health care and biomedicine (Health informatics) , 2003 .

[45]  Francis S. Collins,et al.  Genomic medicine--a primer. , 2002, The New England journal of medicine.

[46]  Lawrence M. Fagan,et al.  Medical Informatics: Computer Applications in Health Care , 1991 .

[47]  James C. Schaff,et al.  The Virtual Cell , 2002, Annals of the New York Academy of Sciences.

[48]  Douglas L. Brutlag,et al.  Viewpoint: Directions for Clinical Research and Genomic Research into the Next Decade: Implications for Informatics , 1998, J. Am. Medical Informatics Assoc..

[49]  R Haux,et al.  Aims and tasks of medical informatics. , 1997, International journal of medical informatics.

[50]  R. Eils,et al.  Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Jaques Reifman,et al.  White Paper: Military Research Needs in Biomedical Informatics , 2002, J. Am. Medical Informatics Assoc..

[52]  Yuval Shahar,et al.  Synthesis of Research: EON: A Component-Based Approach to Automation of Protocol-Directed Therapy , 1996, J. Am. Medical Informatics Assoc..

[53]  Manolis Tsiknakis,et al.  An Infrastructure for Integrated Electronic Health Record Services: The Role of XML (Extensible Markup Language) , 2000, Journal of medical Internet research.

[54]  Joshua M. Stuart,et al.  Integrating genotype and phenotype information: an overview of the PharmGKB project , 2001, The Pharmacogenomics Journal.

[55]  P Goettner,et al.  Effective e-learning for healthcare. , 2000, Health management technology.

[56]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[57]  Y N Cheah,et al.  Healthcare knowledge acquisition: an ontology-based approach using the extensible markup language (XML). , 2000, Studies in health technology and informatics.

[58]  N M Luscombe,et al.  What is Bioinformatics? A Proposed Definition and Overview of the Field , 2001, Methods of Information in Medicine.

[59]  G. D. de Moor,et al.  Privacy Enhancing Techniques , 2003, Methods of Information in Medicine.

[60]  James H Ford,et al.  Information requirements of genomics researchers from the patient clinical record. , 2002, Journal of healthcare information management : JHIM.

[61]  Perry L. Miller,et al.  Viewpoint: Opportunities at the Intersection of Bioinformatics and Health Informatics: A Case Study , 2000, J. Am. Medical Informatics Assoc..

[62]  Leslie M Loew,et al.  The virtual cell: an integrated modeling environment for experimental and computational cell biology. , 2002, Annals of the New York Academy of Sciences.

[63]  C. Kulikowski.  The Micro-Macro Spectrum of Medical Informatics Challenges: From Molecular Medicine to Transforming Health Care in a Globalizing Society , 2002, Methods of Information in Medicine.

[64]  A. Bayat,et al.  Science, medicine, and the future: Bioinformatics. , 2002, BMJ.

[65]  A. Roses,et al.  Pharmacogenetics place in modern medical science and practice. , 2002, Life sciences.

[66]  Enrique F. Castillo,et al.  Expert Systems and Probabilistic Network Models , 1996, Monographs in Computer Science.

[67]  A. Karim Qayumi,et al.  Computer-assisted learning: cyberPatient--a step in the future of surgical education. , 1999, Journal of investigative surgery : the official journal of the Academy of Surgical Research.

[68]  Ami Marowka,et al.  The GRID: Blueprint for a New Computing Infrastructure , 2000, Parallel Distributed Comput. Pract..

[69]  V Maojo,et al.  Establishing an agenda for biomedical informatics. , 2003, Methods of information in medicine.

[70]  G Hughes,et al.  Managing acute anaphylaxis , 1999 .

[71]  K. Brain,et al.  A pilot study of telegenetics , 2000, Journal of telemedicine and telecare.

[72]  Bernd Blobel,et al.  Securing interoperability between chip card based medical information systems and health networks , 2001, Int. J. Medical Informatics.

[73]  Julie J. McGowan,et al.  The Senior Assessment Coupler: point-of-care decision support and data acquisition tool , 1999, AMIA.

[74]  Hongfang Liu,et al.  Representing information in patient reports using natural language processing and the extensible markup language. , 1999, Journal of the American Medical Informatics Association : JAMIA.

[75]  Victor Maojo,et al.  A New Method for Unifying Heterogeneous Databases , 2001, ISMDA.

[76]  Ian Foster,et al.  The Grid 2 - Blueprint for a New Computing Infrastructure, Second Edition , 1998, The Grid 2, 2nd Edition.

[77]  Ian T. Foster,et al.  The anatomy of the grid: enabling scalable virtual organizations , 2001, Proceedings First IEEE/ACM International Symposium on Cluster Computing and the Grid.

[78]  V Breton,et al.  DataGrid, prototype of a biomedical grid. , 2003, Methods of information in medicine.

[79]  G. Forgacs,et al.  Mechanotransduction through the cytoskeleton. , 2002, American journal of physiology. Cell physiology.

[80]  T. Poggio,et al.  Prediction of central nervous system embryonal tumour outcome based on gene expression , 2002, Nature.

[81]  Victor Maojo,et al.  Medical Informatics and Bioinformatics: European Efforts to Facilitate Synergy , 2001, J. Biomed. Informatics.

[82]  C. Tang,et al.  The impact of microbial genomics on antimicrobial drug development. , 2001, Annual review of genomics and human genetics.

[83]  Pierre Baldi,et al.  Bioinformatics - the machine learning approach (2. ed.) , 2000 .

[84]  Jocelyn Kaiser,et al.  Population Databases Boom, From Iceland to the U.S. , 2002, Science.

[85]  Thomas G. Dietterich.  Adaptive computation and machine learning , 1998 .

[86]  M. Simmons,et al.  Combining Medical Informatics and Bioinformatics toward Tools for Personalized Medicine , 2003, Methods of Information in Medicine.

[87]  Simon Parsons,et al.  Bioinformatics: The Machine Learning Approach by P. Baldi and S. Brunak, 2nd edn, MIT Press, 452 pp., $60.00, ISBN 0-262-02506-X , 2004, The Knowledge Engineering Review.

[88]  F. Collins,et al.  Implications of the Human Genome Project for medical science. , 2001, JAMA.

[89]  Gregory Piatetsky-Shapiro,et al.  Advances in Knowledge Discovery and Data Mining , 2004, Lecture Notes in Computer Science.

[90]  E. Shortliffe,et al.  Medical informatics. An emerging academic discipline and institutional priority. , 1990, JAMA.

[91]  J. Craig Venter,et al.  Microbial Disease in Humans: A Genomic Perspective , 2012, Molecular Diagnosis.