School of Industrial and Information Engineering Master of Science in Information Engineering Master of Science in Biomedical Engineering

Transcription

1 School of Industrial and Information Engineering Master of Science in Information Engineering Master of Science in Biomedical Engineering Dipartimento di Elettronica, Informazione e Bioingegneria ICT for Health Care Marco Masseroli, PhD marco.masseroli@polimi.it

2 School of Industrial and Information Engineering Master of Science in Information Engineering Master of Science in Biomedical Engineering Dipartimento di Elettronica, Informazione e Bioingegneria Specialization path: Bioinformatics & e-health Marco Masseroli, PhD marco.masseroli@polimi.it

3 Master of Science in Information Engineering ( Marco Masseroli, PhD 3

4 Master of Science in Information Engineering ( Marco Masseroli, PhD 4

5 Master of Science in Information Engineering ( Marco Masseroli, PhD 5

6 Bioinformatics & e-health Educational and training goals Information and Communication Technology (ICT) pervasiveness in modern life science and health care is continuously increasing: from biomolecular to clinicalhealthcare domain, till informatics technologies supporting people with special needs (elder and disable) Relevant computer science technologies cover a wide range from sensor networks to wearable computing, nano-technology instruments for experimental data production, to robotic systems, augmented reality systems,. Marco Masseroli, PhD 6

7 Bioinformatics & e-health Educational and training goals Simultaneously, ICT also strongly contributes to Bioinformatics and e-health, through the collection, access and use of data - biomedical but not only needed, in biological and medical research, to the advancement of the bio-medical knowledge and, in the clinical-healthcare areas, to the diagnosis, therapy and assistance, through techniques, methods and models for the analysis and management of such data Marco Masseroli, PhD 7

8 Bioinformatics & e-health Educational and training goals Goal of Bioinformatics & e-health specialization path is provide advanced notions and insights of ICT technologies and methods together with base competences in biology, molecular biology, physiology, biological signals and data, advanced technologies of bio-medical-molecular data production, and clinical-healthcare processes of diagnosis and care, besides expertise in technological standards that enable interoperability of bio-medical-healthcare data and systems The base bio-medical notions are integrated with practical examples of effective application of ICT methods and technologies in some specific life science and health areas, as bioinformatics, robotics for health, telemedicine, e-health, etc. Marco Masseroli, PhD 8

9 Bioinformatics & e-health Educational and training goals Thus, the Bioinformatics & e-health path give strong training in methods and technologies of computer science engineering applied to medical and biological issues, training professionals able to effectively face the complex biomedical issues, which require a significant modeling and abstraction ability, also using formal tools, as well as the integration of different and sophisticated expertise and technologies Marco Masseroli, PhD 9

10 Bioinformatics & e-health Educational and training goals Depending on specific informatics courses chosen, the Bioinformatics & e-health specialization path trains a professional profile of ICT expert with applied knowledge in the bio-medical-healthcare domain; in particular to the: Development and management of bio-medical-healthcare information systems and biomedical decision support systems (ICT management) Software development for collection and analysis of biomedical data and information, and for management of clinical-healthcare processes (Software methods) Development of integrated hardware and software architectures supporting bio-medical-healthcare activities (ICT Architectures) Marco Masseroli, PhD 10

11 Bioinformatics & e-health Educational and training goals Such specialization path aims at training leaders in Computer Science Engineering applied to Biology and Medicine, who, besides having a good technological competences in ICT, also knows the complex and specific issues of life sciences and health and are able to rapidly interact with other professionals with a different training (medical, biomedical, biological, chemical, ) and to easily and profitably fit, bringing their own ICT expertise, in interdisciplinary groups, which are currently essential to play a relevant role in life sciences and health Marco Masseroli, PhD 11

12 Master of Science in Information Engineering ( Marco Masseroli, PhD 12

13 Master of Science in Information Engineering Bioinformatics & e-health Marco Masseroli, PhD 13

14 Bioinformatics & e-health Main interdisciplinary courses ICT for Health Care Bioinformatics and Computational Biology Marco Masseroli, PhD 14

15 ICT for Health Care Introduction Course organization Marco Masseroli, PhD 15

16 Index Course organization Lecturers and contacts Background and goals Syllabus of lessons and practices Bibliography Logistics Evaluation procedure Projects and Theses Marco Masseroli, PhD 16

17 Course organization Lecturers and contacts Marco Masseroli Floor 1, DEIB building 20, Leonardo, office 055 tel.: Emanuele Della Valle Arif Canakoglu All on [people/alphabetic list/ ] Marco Masseroli, PhD 17

18 Course organization Background and goals Information and communication technologies (ICT) have been having a tremendous impact both on life sciences and health care research and clinical practice, and on how health is supported through the healthcare systems The course presents computer science principles, technologies, methods and instruments for the structured collection, integration, sharing and computational analysis of clinical information and biomedical knowledge, described both at macroscopic and biomolecular level Marco Masseroli, PhD 18

19 Course organization Background and goals The course will point out as information and knowledge engineering in particular the areas regarding knowledge description, data bases, semantic web, workflows, web services and service oriented architectures can profitably support the effective management of medical, clinical and biomolecular data, and contribute to extract their valuable information content toward improving biomedical knowledge and health care Marco Masseroli, PhD 19

20 Course organization Background and goals During the course, students will build knowledge on issues related to bio-medical-molecular data and clinical information, will develop skills on ICT instruments enabling the development of applications to manage and process such data and information, and will learn how to effectively use the ICT to efficiently tackle the mentioned issues in an adequate and sustainable way for the biomedical domain After the course, students will be able to leverage the acquired competences to take advantage of the opportunities offered by the increasing ICT development and relevance in the life sciences and healthcare Marco Masseroli, PhD 20

21 Course organization Background and goals Prerequisite: None; biomedical concepts required to understand motivations and aims of the presented methods and technological applications will be introduced during the course Marco Masseroli, PhD 21

22 Course organization Syllabus Introduction: Definitions, methodologies and motivations Medical information and medical record standards for interoperability and sharing: Taxonomy of medical information and examples of medical records Concepts of biomedical data security and privacy Standards for biomedical information structuring, interoperability and sharing Biomedical terminologies and ontologies: Controlled vocabularies for digital medical records Interoperability of biomedical nomenclature systems Marco Masseroli, PhD 22

23 Course organization Syllabus Databanks of bio-medical-molecular information: Bio-medical-molecular databanks and web applications to use them Integration and analysis of the provided information Semantic web for health care and life sciences: Introduction and main technological features Biomedical data in RDF SPARQL for data integration and querying Biomedical ontologies in RDF-S/OWL Automatic reasoning and its requirements Marco Masseroli, PhD 23

24 Course organization Syllabus Biomedical web services and workflows: Hints of Service Oriented Architectures Technologies for programmatic access to biomedical distributed resources Web service composition and orchestration Workflow execution and sharing Examples of some available software tools for healthcare and biomedicine: Software tools available as: - Web applications - Web services - Freeware and open source programs Suggestion: Interact in class with the lecturer: ask questions! Marco Masseroli, PhD 24

25 Course organization Bibliography Suggested readings: T. Benson. Principles of health interoperability HL7 and SNOMED. Springer, New York, NJ (Health informatics). C.J.O. Baker, K-H. Cheung, editors. Semantic web. Revolutionizing knowledge discovery in the life sciences. ISBN: Springer, New York, NJ F. Pinciroli, M. Masseroli, curatori. Elementi di informatica biomedica. Polipress, Milano, IT E. Della Valle, I. Celino, D. Cerizza. Semantic web. Dai fondamenti alla realizzazione di un'applicazione. Pearson Education Italia, Torino, IT Handouts and other teaching material (Website): Politecnico di Milano BeeP (Be e-poli) ( Your matricola and password (same as webpoliself) ICT for Health Care (Masseroli) Marco Masseroli, PhD 25

26 Course organization Logistics Lessons: Wednesday, 12,15-14,15 room L Lessons and practices in informatics room: Thursday, 16,15-18,15 room E.G.7 Laboratory activity During course practices, all in an informatics room, several information and communication technologies, data banks and public available tools will be illustrated and used in the health care and life science context Marco Masseroli, PhD 26

27 Course organization Evaluation procedure Written test: Some questions about any of the course subjects, to be answered in free text (more details in Examination procedure on course web site) Final evaluation will be in English; yet, the student who prefers to answer in Italian the English questions of the written test can do so Marco Masseroli, PhD 27

28 Course organization Projects and Theses Theses: Integration, visualization and web browsing of biomedicalmolecular data Analysis and mining of biomedical-molecular information Big data analytics and machine learning in health care at the Vimercate Hospital: - Some on course web site - For others, ask directly to M. Masseroli Marco Masseroli, PhD 28

29 Definitions, motivations and methods Marco Masseroli, PhD 29

30 Index Definitions and Motivations Biomedical Informatics, Translational Bioinformatics, Clinical Informatics, Health Informatics, Health Care and Life Sciences Interest Group - What they are and why they are important Methods Information and Communication Technologies (ICT) role - Data, information, algorithms, tools and services Interdisciplinarity Marco Masseroli, PhD 30

31 Definitions Biomedical Informatics The increasing convergence of biology, medicine and genetics provides the opportunity to leverage synergies between the three areas for the benefit of health. Biology and genetics are emerging as information sciences while medicine is increasingly adopting information systems and informatics approaches to support healthcare delivery Biomedical Informatics is viewed as the discipline that aims to bring together the domains of bioinformatics and medical/health informatics to further the discovery of novel diagnostic and therapeutic methods Marco Masseroli, PhD 31

32 Definitions Translational Bioinformatics AMIA refers to translational bioinformatics as the development of storage, analytic, and interpretative methods to optimize the transformation of increasingly voluminous biomedical data into proactive, predictive, preventative, and participatory health Translational bioinformatics includes research on the development of novel techniques for the integration of biological and clinical data and the evolution of clinical informatics methodology to encompass biological observations. The end product of translational bioinformatics is newly found knowledge from these integrative efforts [ Special Issue Journal Biomedical Informatics, June 2010 Marco Masseroli, PhD 32

33 Definitions Clinical Informatics Clinical Informatics is the scientific discipline that seeks to enhance human health by implementing novel information technology, computer science and knowledge management methodologies to prevent disease, deliver more efficient and safer patient care, increase the effectiveness of translational research, and improve biomedical knowledge access "Clinical informaticians transform health care by analyzing, designing, implementing, and evaluating information and communication systems that enhance individual and population health outcomes, improve patient care, and strengthen the clinician-patient relationship" Gardner RM et al. Core content for the subspecialty of clinical informatics J Am Med Inform Assoc Mar-Apr;16(2): Marco Masseroli, PhD 33

34 Definitions Clinical Informatics Clinical Informatics is the application of informatics and information technology to deliver healthcare services Despite acknowledged variations, AMIA considers informatics when used for healthcare delivery to be the same regardless of the health professional group involved (whether dentist, pharmacist, physician, nurse, or other health professional) Clinical Informatics is concerned with information use in health care by clinicians. It includes a wide range of topics ranging from clinical decision support to visual images (e.g. radiological, pathological, dermatological, ophthalmological, ); from clinical documentation to provider order entry systems; and from system design to system implementation and adoption issues Marco Masseroli, PhD 34

35 Definitions Health Informatics Health informatics (also specified as health care informatics, healthcare informatics, medical informatics, nursing informatics, clinical informatics, or biomedical informatics) is a discipline at the intersection of information science, computer science, and health care It deals with the resources, devices, and methods required to optimize the acquisition, storage, retrieval, and use of information in health and biomedicine. Health informatics tools include not only computers but also clinical guidelines, formal medical terminologies, and information and communication systems. It is applied to the areas of nursing, clinical care, dentistry, pharmacy, public health, occupational therapy, and (bio)medical research Marco Masseroli, PhD 35

36 Definitions HCLS Interest Group Semantic Web Health Care and Life Sciences (HCLS) Interest Group ( The mission of the Semantic Web Health Care and Life Sciences Interest Group (HCLS IG) is to develop, advocate for, and support the use of Semantic Web technologies across health care, life sciences, clinical research and translational medicine. These domains stand to gain tremendous benefit from intra- and inter-domain application of Semantic Web technologies as they depend on the interoperability of information from many disciplines Motivations ( Marco Masseroli, PhD 36

37 Definitions HCLS Interest Group. Marco Masseroli, PhD 37

38 Definitions HCLS Interest Group Marco Masseroli, PhD 38

39 Definitions HCLS Interest Group itunes Anatomy Atlas Marco Masseroli, PhD 39

40 Definitions HCLS Interest Group itunes Anatomy Lite Marco Masseroli, PhD 40

41 Definitions HCLS Interest Group itunes Anatomy Atlas Marco Masseroli, PhD 41

42 Definitions HCLS Interest Group ZygoteBody 3D Anatomy Viewer /12/google-bodybrowser.html Marco Masseroli, PhD 42

43 Definitions HCLS Interest Group ZygoteBody 3D Anatomy Viewer /12/google-bodybrowser.html Marco Masseroli, PhD 43

44 Methods Information technology role From the definitions, it is clear the important role of the Information and Communication Technologies (ICT) in health care and life sciences to: Management (store, integrate, query, search, retrieve, ) and analysis of data and information (knowledge) Development of models and algorithms Implementation of instruments and services (infrastructures) Creation of visualization tools Computational and systemic approach Marco Masseroli, PhD 44

45 Methods Information technology role The relevant ICT contribution to health care and life sciences can appear only if based on a background (at least minimum) of biomedical knowledge, since the goal is not only the correct and efficient execution of ICT methods, but the answer to biomedical requirements On these bases, computer science shows all its relevance in contributing to the progress of the life science and health care knowledge Marco Masseroli, PhD 45

46 Methods Interdisciplinary Modern health care and life sciences are collaborative and interdisciplinary activities: Different background and expertise professionals working together (informatics, engineering, physical, chemical, medical, biological, social, ) Need of: Using a simple language, clear also to people with different expertise Acquiring base knowledge of other disciplines, to be able to productively collaborate with other expertise people Marco Masseroli, PhD 46