Bioinformatioc: Information Retrieval

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  • Bioinformatioc: Information Retrieval

    1. 1. not a biomedical expert...
    2. 2. Bioinformatics in Public Health <ul><ul><li>Information Retrieval </li></ul></ul><ul><ul><li>Rupak Chakravarty </li></ul></ul><ul><ul><li>Department of Library & Information Science </li></ul></ul><ul><ul><li>Panjab University, Chandigarh </li></ul></ul><ul><ul><li>rupak@pu.ac.in, rupak2811@ gmail.com </li></ul></ul><ul><ul><li>9217133380, 0172-2700459 </li></ul></ul>
    3. 3. Information Retrieval <ul><li>Data, information, knowledge and wisdom. </li></ul><ul><li>Value of information </li></ul><ul><li>Role of information </li></ul><ul><li>Information Retrieval </li></ul><ul><li>Challenges </li></ul><ul><li>Information Society </li></ul>
    4. 4. Information <ul><li>The word “information” is used to refer to a number of different phenomena. These phenomena have been classified into three groupings: </li></ul><ul><li>(1) Anything perceived as potentially signifying something (e.g. printed books); </li></ul><ul><li>(2) The process of informing; and </li></ul><ul><li>(3) That which is learned from some evidence or communication. </li></ul>
    5. 5. Information <ul><li>Information as process </li></ul><ul><li>Information as communication </li></ul><ul><li>Information as message transmission and reception communication. </li></ul>
    6. 6. Information <ul><li>Information is that which is conveyed, and possibly amenable to analysis and interpretation. </li></ul><ul><li>Knowledge is the general understanding and awareness garnered from accumulated information, tempered by experience, enabling new contexts to be envisaged. </li></ul>
    7. 7. Information <ul><li>Information represents a state of awareness (consciousness) and the physical manifestations they form. Information, as a phenomena, represents both a process and a product; </li></ul><ul><li>Information is resources useful or relevant or functional for information seekers. </li></ul>
    8. 8. Information <ul><li>Information is data that has been categorized, counted, and thus given meaning, relevance, or purpose. </li></ul><ul><li>Knowledge is information that has been given meaning and taken to a higher level.  </li></ul><ul><li>Knowledge emerges from analysis, reflection upon, and synthesis of information.  It is used to make a difference in an enterprise, learn a lesson, or solve a problem. </li></ul>
    9. 9. Data - Information - Knowledge <ul><li>What is Data? </li></ul><ul><li>Data is the raw material of information. It is the product of research and discovery. A single piece of data has no meaning unless the context is understood. Data needs to be transformed to information. </li></ul><ul><li>What is Information? </li></ul><ul><li>Information is a flow of messages. The patterns and relationship in the data is pointed out and discussed. The data is made informative and must be put into a context and linked like data. </li></ul>
    10. 10. DIKW
    11. 11. Information Hierarchy Data Information Knowledge Wisdom More refined and abstract
    12. 12. A (Facetious) Example <ul><li>Data </li></ul><ul><ul><li>98.6 º F, 99.5 º F, 100.3 º F, 101 º F, … </li></ul></ul><ul><li>Information </li></ul><ul><ul><li>Hourly body temperature: 98.6 º F, 99.5 º F, 100.3 º F, 101 º F, … </li></ul></ul><ul><li>Knowledge </li></ul><ul><ul><li>If you have a temperature above 100 º F, you most likely have a fever </li></ul></ul><ul><li>Wisdom </li></ul><ul><ul><li>If you don’t feel well, go see a doctor </li></ul></ul>
    13. 13. Information Retrieval <ul><ul><li>The meaning of the term information retrieval can be very broad. Just getting a credit card out of your wallet so that you can type in the card number is a form of information retrieval. However, as an academic field of study, information retrieval can be defined thus: </li></ul></ul><ul><ul><li>Information retrieval (IR) is finding material (usually documents) of an unstructured nature (usually text) that satisfies an information need from within large collections (usually stored on computers). </li></ul></ul>
    14. 14. Information Retrieval The user of an IR system is concerned more with retrieving information about a subject than with retrieving data which satisfies a given query A data retrieval language aims at retrieving all objects which satisfy clearly defined conditions such as those in a regular expression or in a relational algebra expression. Thus, for a data retrieval system, a single erroneous object among a thousand retrieved objects means total failure.
    15. 15. Information Retrieval <ul><ul><li>For an information retrieval system, however, the retrieved objects might be inaccurate and small errors are likely to go unnoticed. The main reason for this difference is that information retrieval usually deals with natural language text which is not always well structured and could be semantically ambiguous. </li></ul></ul><ul><ul><li>On the other hand, a data retrieval system (such as a relational database) deals with data that has a well defined structure and semantics. </li></ul></ul>
    16. 16. Information Retrieval <ul><ul><li>Data retrieval, while providing a solution to the user of a database system, does not solve the problem of retrieving information about a subject or topic. </li></ul></ul><ul><ul><li>To be effective in its attempt to satisfy the user information need, the IR system must somehow `interpret' the contents of the information items (documents) in a collection and rank them according to a degree of relevance to the user query. </li></ul></ul>
    17. 17. Information Retrieval <ul><ul><li>This `interpretation' of a document content involves extracting syntactic and semantic information from the document text and using this information to match the user information need. </li></ul></ul><ul><ul><li>The difficulty is not only knowing how to extract this information but also knowing how to use it to decide relevance. </li></ul></ul><ul><ul><li>Thus, the notion of relevance is at the center of information retrieval. In fact, the primary goal of an IR system is to retrieve all the documents which are relevant to a user query while retrieving as few non- relevant documents as possible. </li></ul></ul>
    18. 18. Information Retrieval at the Center of the Stage <ul><ul><li>In the past 20 years, the area of information retrieval has grown well beyond its primary goals of indexing text and searching for useful documents in a collection. Nowadays, research in IR includes modeling, document classification and categorization, systems architecture, user interfaces, data visualization, filtering, languages, etc. </li></ul></ul>
    19. 19. Information Retrieval at the Center of the Stage <ul><ul><li>The Web is becoming a universal repository of human knowledge and culture which has allowed unprecedented sharing of ideas and information in a scale never seen before. Its success is based on the conception of a standard user interface which is always the same no matter what computational environment is used to run the interface. </li></ul></ul>
    20. 20. IR at the Center of the Stage <ul><ul><li>Further, any user can create his own Web documents and make them point to any other Web documents without restrictions. This is a key aspect because it turns the Web into a new publishing medium accessible to everybody. As an immediate consequence, any Web user can push his personal agenda with little effort and almost at no cost. This universe without frontiers has attracted tremendous attention from millions of people everywhere since the very beginning. </li></ul></ul>
    21. 21. IR Issues <ul><ul><li>Furthermore, it is causing a revolution in the way people use computers and perform their daily tasks. For instance, home shopping and home banking are becoming very popular and have generated several hundred million dollars in revenues. </li></ul></ul><ul><ul><li>Despite so much success, the Web has introduced new problems of its own. Finding useful information on the Web is frequently a tedious and difficult task. </li></ul></ul>
    22. 22. IR Issues <ul><ul><li>For naive users, the problem becomes harder, which might entirely frustrate all their efforts. The main obstacle is the absence of a well defined underlying data model for the Web, which implies that information definition and structure is frequently of low quality. </li></ul></ul><ul><ul><li>These difficulties have attracted renewed interest in IR and its techniques as promising solutions. As a result, almost overnight, IR has gained a place with other technologies at the center of the stage. </li></ul></ul>
    23. 24. Information Overload
    24. 25. The Road to Information discovery...
    25. 26. From Diamond Mining to Data Mining
    26. 30. Informatics
    27. 32. Informatics <ul><li>Informatics is the science of information, the practice of information processing, and the engineering of information systems. Informatics studies the structure, algorithms, behaviour, and interactions of natural and artificial systems that store, process, access and communicate information. </li></ul>
    28. 33. Informatics <ul><li>It also develops its own conceptual and theoretical foundations and utilizes foundations developed in other fields. Since the advent of computers, individuals and organizations increasingly process information digitally. This has led to the study of informatics that has computational, cognitive and social aspects, including study of the social impact of information technologies. </li></ul>
    29. 34. Informatics <ul><li>Informatics is the science of information. It studies the representation , processing , and communication of information in natural and artificial systems. Since computers, individuals and organizations all process information, informatics has computational, cognitive and social aspects. </li></ul><ul><li>Used as a compound, in conjunction with the name of a discipline, as in medical informatics, bio-informatics, etc., it denotes the specialization of informatics to the management and processing of data, information and knowledge in the named discipline. </li></ul>
    30. 35. The scope of Informatics <ul><li>What these areas have in common is informatics: the focus on information and how it is represented in, processed by, and communicated between a variety of systems. </li></ul><ul><li>Representations include paper, analogue, and digital records of text, sounds and images, as well as, for instance, the information represented in a gene, and the memories of an individual or an organization. </li></ul>
    31. 36. The scope of Informatics <ul><li>Processing includes human reasoning, digital computation, and organizational processes. </li></ul><ul><li>Communication includes human communication and the human-computer interface - with speech and gesture, with text and diagram, as well as computer communications and networking, which may use radio, optical or electrical signals. </li></ul>
    32. 37. The scope of Informatics <ul><li>Informatics studies the interaction of information with individuals and organizations, as well as the fundamentals of computation and computability, and the hardware and software technologies used to store, process and communicate digitised information. </li></ul><ul><li>It includes the study of communication as a process that links people together, to affect the behaviour of individuals and organizations. </li></ul>
    33. 39. <ul><ul><li>Beijing has elaborated a risk identification and management system to deal with any major public health emergency during the 2008 Olympic Games. The system includes measures to deal with epidemic diseases and infectious micro-organisms, and to ensure food and drinking water safety. Prevention and control mechanisms have been set up, which has laid a sound foundation for the safety of the Olympics, Municipal Health Bureau director Jin Dapeng told a press conference at the Beijing Olympic Media Center. </li></ul></ul>
    34. 40. FOSS EHR
    35. 46. Google Health <ul><li>Google Health allows you to store and manage all of your health information in one central place. And it's completely free. </li></ul><ul><li>Google believes that you own your medical records and should have easy access to them. The way we see it, it's your information; why shouldn't you control it? </li></ul>
    36. 49. 1. Sign up for Google Health
    37. 50. 2. Start tracking a medical history and learn about your conditions
    38. 51. 3. Import your medical records
    39. 52. 4. View your medical history
    40. 53. 5. Find out how medications might interact
    41. 54. 6. Make your health information work for you
    42. 55. 7. Search for doctors and hospitals
    43. 59. Thank You for giving me this opportunity

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