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Biomedical Information Retrieval from Net

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The Presentation consists of over 90 Power Point PPT slides keeping in mind Bio-Medical Researchers. [Paid / Fee based services like Web of Science are not included in this presentation] …

The Presentation consists of over 90 Power Point PPT slides keeping in mind Bio-Medical Researchers. [Paid / Fee based services like Web of Science are not included in this presentation]
Presentation starts with an emphasis need for having a planned search strategy and evaluation of the retrieved results. The best tool and Internet resource to explore would depend upon the type of information being sought from the net. For general non-scholarly information Internet Search Engines, Meta Search Engines, Web Directories and Subject Guides would be the best way to start with. However there is need to evaluate all such information. Simple criteria - like the authority behind the information; the date of creation and modification and commercial interests if any - can be used to evaluate the authenticity of the information retrieved. Medical websites with "HONcode" logo could be easily evaluated and trusted.
For scholarly literature, researchers are advised to start with Bibliographic Databases. These databases provide references to high quality peer reviewed journals. PubMed and IndMED (For Indian Journals) are best known under this category. The presentation has some interesting pictures to explain the need for "Controlled Vocabulary" like MeSH. Other tools like Scirus can also be used for retrieving scholarly information. Google Scholar can be used to for limited "Cited By" information along with references.
Coming to Full Text of articles, looking for libraries' holdings would be a better strategy. "Union Catalogue" is useful tool to explore collection of neighborhood libraries. Many good journals are now coming out from Open Access Publishers like BioMed Central and PLoS. Some of the good Indian medical journals are also available for free through Internet. NIC's medIND project and MedKnow (an Indian Open Access Publisher) have been instrumental in putting most of them online. Directory of Open Access Journals is a useful tool to find out Open Access Journals in a subject domain. Other resources for finding full text articles are Institutional (like EPrints@IISc ) and Subject Repositories (like OpenMED@NIC). There are now about 1000 such registered and OAI-PMH compliant repositories all over the world. Tools like ROAR can used to find a relevant repository. These repositories can also be searched through search engine like Google and some special OAI-PMH search engines.
The presentation ends with some special type of resources like Cochrane Library (made freely accessible to Resident Indians through sponsorship by ICMR).


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  • 1. Bio-Medical Information Retrieval from Net By Sukhdev Singh
  • 2. PLAN
    • Problem of Plenty on Net.
    • Without a proper plan, you would lost in the sea of Information.
    • Therefore, have a PLAN
    • Choose the most appropriate place to look
    • Develop an effective search strategy
    • Carry out the search
    • Critically evaluate the results obtained
  • 3. Appropriate Place?
  • 4.
    • General Information
      • Web Search Engines / General Web Resources
    • Journal References
      • Databases like PubMed / IndMED etc) / Scholar Google
    • Full Text Articles
      • Free Open Access.
      • Fee Based – From Libraries .
    • Best Practices / Evidence Based Medicine
      • Cochrane Library
    Appropriate Place? Will depend on what you are looking for !!!
  • 5. General Information
  • 6. Best for Non-Scholarly Information
  • 7. General Information – Web Search Engines / Resources
    • Search Engines
    • Meta-Search Engines
    • Subject Directories
    • Subject Guides
  • 8.  
  • 9. Search Engines
        • Full-text of selected Web pages.
        • Search by keyword, trying to match exactly the words in the pages.
        • No browsing, no subject categories.
        • Databases compiled by "spiders" (computer-robot programs).
  • 10.  
  • 11.  
  • 12. Meta-Search Engines
        • Meta-Search Engines quickly and superficially search several individual search engines at once.
        • Return results compiled into a convenient format.
        • They only catch about 10% of search results in any of the search engines they visit.
  • 13.  
  • 14. Web Directories
        • Hand-selected sites. Organized into hierarchical subject categories.
        • Often annotated with descriptions (not in Yahoo!).
        • Browse subject categories or search using broad, general terms.
        • NO full-text of documents. Can search only the subject categories and descriptions.
  • 15.  
  • 16.  
  • 17.  
  • 18.  
  • 19.  
  • 20. Subject Guides
        • Web pages of collections of hypertext links on a subject.
        • Compiled by "expert" subject specialists, agencies, associations, and hobbyists.
  • 21.  
  • 22.  
  • 23.  
  • 24.  
  • 25. Evaluating Your Web Search Results
    • Each page should be examined and the following questions answered:
    • Who? Who is the authoring agency or individual?
    • What? What is the author's credentials?
    • Where? Where is the author's affiliation?
    • When? When was the page last updated
    • Why? Why is the page in existence? What is the author's purpose?
    • How? How does the page appear?
  • 26.  
  • 27.  
  • 28.  
  • 29.  
  • 30. Remember !!!
    • The Web just does not have it all. Even the best search engine will only search what is available. Remember that the Web is only the first tool in your arsenal of available resources.
    • Each search engine is different. Read the help before you proceed. Determine if you are using a Web directory or a search engine. See if there is an "advanced search" feature.
  • 31. So, What we have learned?
    • For General Information
    • (Non-Scholarly / Non Peer-Reviewed)
      • Search Engines
      • Meta Search Engines
      • Web Directories
      • Subject Guides
    • Evaluate Your Web Search Results
  • 32.
    • Scholarly Information
    • References
    • Bibliographic Databases
    • -PubMed
    • -IndMED
    • Search Engine
    • -Scholar Google
  • 33. Bibliographic Databases
        • Cover Peer Reviewed Literature. Journals are selected after quality checks.
        • References along with abstracts are available sometimes links to free full text of articles.
        • Require familiarization on searching.
        • Knowledge of Boolean Operators; Medical Subject Headings ( MeSH ) and Qualifiers are required for advanced searching.
  • 34.
        • http://pubmed.gov
        • Includes MEDLINE® (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine's® (NLM) premier bibliographic database that contains over 16 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature of MEDLINE is that the records are indexed with NLM's Medical Subject Headings (MeSH®).
  • 35.  
  • 36. Overview of Boolean Searching
  • 37.  
  • 38.  
  • 39.  
  • 40.  
  • 41. Is the life so Simple with Computers?
    • Let us say I want -
    • PITCH report of T20 World Cup Final between India and Pakistan
  • 42. PITCH
  • 43. Problem is with Natural Languages
    • Synonyms
      • (One Concept – different Words)
        • Female
        • Lady
        • Woman
    • Homonyms
      • (One Word – different Concepts)
    • Multiple Words (Phrase)
    • Punctuation
    • etc..
  • 44.  
  • 45.  
  • 46.  
  • 47.  
  • 48. All International Research !!! What about Indian Research?
  • 49. Coverage of Indian Journals
    • Only 25 – 32 Indian Medical Journals are covered in PubMed.
    • This means world Indian research does not get exposed adequately.
    • No credit for good work being done in the areas dealing with local medical problem.
  • 50. IndMED
    • IndMED Database
        • Bibliographic Database – indexes 77 Indian Biomedical Journals
  • 51.  
  • 52.  
  • 53.  
  • 54.  
  • 55. Google Scholar
    •   "Google Scholar uses Google search technology to search for scholarly materials such as: peer-reviewed papers, theses, books, abstracts and articles and more. Results come from academic publishers, professional societies, preprint repositories, universities and other scholarly organizations. Some of the literature will be freely found on the Web, while some links will offer the full-text of articles for payment."
    • http://scholar.google.com
  • 56.  
  • 57.  
  • 58.  
  • 59.  
  • 60.  
  • 61. So, for Scholarly Information
    • We start with Bibliographic Databases having references to journals and other scholarly literature
    • Different from Search Engines in respect to relying on Boolean Operators and Controlled Vocabularies.
    • PubMed, Scirus – International
    • IndMED – Indian
    • Scholar Google special in some aspects but scope not clearly defined.
  • 62.
    • Scholarly Information
    • Full text Journal Articles
    • Most expensive library resource
    • No Library can afford all the journals / Not even the core Journals of a subject
    • Things can improve with “Open Access” to scholarly literature
  • 63. Some Free Resources for Full Text Articles
    • From Open Access Publishers
    • Indian Journals online
    • From Institutional / Subject Repositories
  • 64.
    • http://uncat.nic.in
  • 65.  
  • 66.  
  • 67.  
  • 68.  
  • 69.  
  • 70.  
  • 71.  
  • 72.  
  • 73.  
  • 74.  
  • 75.  
  • 76. MedKnow
  • 77. OA Archives or Repositories
    • OA archives or repositories are free to access and allows uploading of articles and other scholarly materials by authors.
    • Archives may belong to institutions, such as universities and laboratories, or disciplines, such as physics and economics.
  • 78. http://archives.eprints.org/
  • 79.  
  • 80.  
  • 81. Some Other Examples http://dlist.sir.arizona.edu/ http://eprints.rclis.org/ http://eprints.iisc.ernet.in/index.html
  • 82.
    • Most of the Journals Requires High Subscription Fee – Libraries are find it difficult to afford even the core journals.
    • Some relief by Open Access Journals / Repositories
    • Use Directories like DOAJ and ROAR locate free resources
    Full Text Journal Articles
  • 83. Some Resources
  • 84. Cochrane Library
    • Paid Service
    • Made accessible to Indian Residents through Sponsorship by ICMR
    • Systematic Reviews
  • 85.  
  • 86.  
  • 87.  
  • 88.  
  • 89.  
  • 90.  
  • 91.  
  • 92. Was That Tooo Much?
  • 93.
    • Start with Google
    • Learn to Use PubMed
    • Use IndMED – http://indmed.nic.in
    • Take help from your Librarian.
  • 94. THANK YOU