Biology spring 2012_cell_biology


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Cell Biology

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Biology spring 2012_cell_biology

  1. 1. Finding Information in the Biological Sciences Bruce Slutsky Robert Van Houten Library
  2. 2. The Scientific Method <ul><li>The scientific method is the process by which scientists, collectively and over time, endeavor to construct an accurate representation of the world.  There are various thought processes that are used when the scientific method is employed </li></ul>
  3. 3. Information Retrieval <ul><li>Scientists, engineers and students must be able to find information at all levels from a multitude of information resources available to them. </li></ul>
  4. 4. Similarities between the Scientific Method and Information Retrieval <ul><li>Scientific Method </li></ul><ul><li>Know the subject </li></ul><ul><li>Require new knowledge </li></ul><ul><li>Propose an experiment to find new knowledge </li></ul><ul><li>Conduct the experiment </li></ul><ul><li>Observe and interpret the results </li></ul><ul><li>Revise the experiment </li></ul><ul><li>Interpret the final outcome of the experiment </li></ul><ul><li>Information Retrieval </li></ul><ul><li>Know the scope of and contents of databases in his/her field of endeavor </li></ul><ul><li>Require new knowledge </li></ul><ul><li>Devise an initial search strategy using relevant terminology in subject databases </li></ul><ul><li>Examine the initial answer set </li></ul><ul><li>Revise the strategy based on findings from the initial answer set </li></ul><ul><li>Explore alternative search options </li></ul><ul><li>Examine the final answer set </li></ul><ul><li>Find the relevant documents </li></ul><ul><li>Use the information found </li></ul>
  5. 5. Formats of the Scientific and Technical Literature <ul><li>Journal </li></ul><ul><li>Conference Proceeding </li></ul><ul><li>Magazine </li></ul><ul><li>Review Journal </li></ul><ul><li>Research Level Book (monograph) </li></ul><ul><li>Encyclopedia </li></ul>
  6. 6. What is a Journal? <ul><li>A journal is a publication issued periodically that reports original research. </li></ul><ul><li>Peer Review Process </li></ul><ul><li>Detailed articles with experimental procedures </li></ul><ul><li>Highly Specialized </li></ul>
  7. 7. Selected Cell Biology Journals (Available from the NJIT Library) <ul><li>Cell biology and toxicology   </li></ul><ul><li>Journal of cell biology   </li></ul><ul><li>Cell and tissue biology   </li></ul><ul><li>BMC cell biology   </li></ul><ul><li>DNA and cell biology   </li></ul>
  8. 8. What is a Conference Proceeding? <ul><li>Organized by professional societies such as the American Society for Cell Biology and the British Society for Cell Biology </li></ul><ul><li>Scientists and engineers report their research findings there </li></ul><ul><li>A conference proceedings is a permanent record of the presentation </li></ul>
  9. 9. Examples of Conference Proceedings <ul><li>European Society of Animal Cell Technology. General Meeting (9th : 1988 : Knokke-Heist, Belgium) </li></ul><ul><li>International School of Structural Biology and Magnetic Resonance 7th Course: Structure and Biophysics--New Technologies for Current Challenges in Biology and Beyond (2005 : Erice, Italy) </li></ul>
  10. 10. Review Journals <ul><li>Condensed version of a research journal </li></ul><ul><li>Summarizes research developments over a short time </li></ul><ul><li>Omits detailed experimental procedures </li></ul>
  11. 11. Examples of Review Journals <ul><li>Annual review of cell and developmental biology   </li></ul><ul><li>Quarterly review of biology     </li></ul>
  12. 12. Multidisciplinary Journals Covering Cell Biology <ul><li>Science </li></ul><ul><li>Nature </li></ul>
  13. 13. Magazines <ul><li>Scientific and technical articles are translated into a language suited for a more general audience </li></ul><ul><li>Written by journalists rather than researchers </li></ul>
  14. 14. Biology Magazines <ul><li>American Scientist </li></ul><ul><li>Discover </li></ul><ul><li>Scientific American </li></ul><ul><li>Smithsonian Magazine </li></ul>
  15. 15. Monographs <ul><li>Another name for a book </li></ul><ul><li>May be written at all levels </li></ul><ul><li>Reports research over a longer period of time </li></ul><ul><li>Brings the research to a much wider audience </li></ul>
  16. 16. Encyclopedias <ul><li>Encyclopedias introduce researchers to specialize fields of study.  </li></ul><ul><ul><li>Encyclopedia of Life Science </li></ul></ul><ul><ul><li>Encyclopedia of Human Biology </li></ul></ul><ul><ul><li>Encyclopedia of Molecular Biology </li></ul></ul><ul><ul><li>All of the above are available at the Dana Library </li></ul></ul>
  17. 17. Is Wikipedia Reliable? <ul><li>Can it be trusted as a source of information in the life sciences? </li></ul>
  18. 18. Advantages and Disadvantages of the Wikipedia <ul><li>Advantages : </li></ul><ul><li>Good for obtaining background knowledge on a topic </li></ul><ul><li>Articles can be revised and edited quickly. Information about recent events will appear there </li></ul><ul><li>Disadvantages : </li></ul><ul><li>Does not undergo the peer review process </li></ul><ul><li>Anyone can write or edit an article anonymously </li></ul><ul><li>Suggestion: Do not cite it in your bibliography </li></ul>
  19. 19. Flow of Scientific Information <ul><li>Scientists and engineers conceive ideas and perform experiments in the laboratory.  They want to make the results of their research public.  </li></ul><ul><li>The published information flows from the top of the chart (next slide)to the bottom.  Students needing information must start their research at the bottom of the chart.  Tertiary literature such as handbooks, encyclopedias, and textbooks should be consulted first </li></ul>
  20. 20. Flow of Scientific Information
  21. 21. Types of Databases <ul><li>Bibliographic - includes the elements needed to identify the document </li></ul><ul><ul><li>Author(s) </li></ul></ul><ul><ul><li>Title </li></ul></ul><ul><ul><li>Journal, Year, Volume, Issue Number, Pages </li></ul></ul><ul><li>Abstract - a one paragraph summary of the article to help the researcher decide if it is relevant to the research question </li></ul><ul><li>Full-Text - includes the entire article in electronic format </li></ul>
  22. 22. Database Formats <ul><li>Print </li></ul><ul><li>Very cumbersome and difficult to use </li></ul><ul><li>Online (1970s to the present) CD-ROM (1980s to the present) - Only so much information can fit on one disk </li></ul><ul><li>World Wide Web (1990s to the present ) </li></ul>
  23. 23. Limitations of Databases <ul><li>Subject coverage </li></ul><ul><li>Number of Publications </li></ul><ul><li>Dates of Publication </li></ul><ul><li>Types of Publication (i.e. journals only, patents only) </li></ul><ul><li>Not all databases provide full-text of the retrieved documents or links to them </li></ul>
  24. 24. NJIT Library Home Page http:// <ul><li>Catalog (Voyager) </li></ul><ul><ul><li>Database of the print holdings of NJIT Library </li></ul></ul><ul><li>Databases </li></ul><ul><li>Interlibrary Loan/Document Delivery Form </li></ul>
  25. 25. Voyager, the NJIT Library Catalog <ul><li>Books </li></ul><ul><li>Journals (print) </li></ul><ul><li>Technical Reports </li></ul><ul><li>Conference Proceedings </li></ul><ul><li>Theses and Dissertations (by NJIT students) </li></ul>
  26. 26. Databases with Biology Content from the NJIT Library <ul><li>BioMed Central </li></ul><ul><li>BioOne </li></ul><ul><li>Medline (PubMed) </li></ul><ul><li>Pubget </li></ul><ul><li>Scopus </li></ul><ul><li>Academic Search Premier </li></ul><ul><li>Scifinder Scholar (Chemical Abstracts) </li></ul>
  27. 27. BioMedCentral <ul><li>Publisher of 208 peer-reviewed open access journals </li></ul>
  28. 28. BioOne <ul><li>BioOne provides a unique aggregation of high-impact bioscience research journals, featuring timely content on a wide-array of today’s most pressing topics. </li></ul><ul><li>You may search this database for free, but will have to go to Rutgers to get the full-text of articles. </li></ul>
  29. 29. Medline <ul><li>MEDLINE is the NLM's (National Library of Medicine) premier bibliographic database covering the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and the preclinical sciences. MEDLINE contains bibliographic citations and author abstracts from more than 4,800 biomedical journals published in the United States and 70 other countries. The database contains over 12 million citations dating back to the mid-1960's. The Pubmed version is free. </li></ul>
  30. 30. Pubget <ul><li>Pubget is a search engine for PDFs in the life sciences. It indexes nearly 20 million life science research documents, including those in PubMed®. You search it like you would PubMed or Google Scholar. The difference is Pubget gets you the PDF right away . </li></ul>
  31. 31. Scopus <ul><li>Scopus is a multidisciplinary navigational tool that contains records going back to the mid 1960s, offering newly-linked citations across the widest body of scientific abstracts available in one place.  Biology is one of the many subjects covered in Scopus </li></ul>
  32. 32. Academic Search Premier <ul><li>This multi-disciplinary database provides full text for more than 8,500 journals, including full text for more than 4,600 peer-reviewed titles </li></ul><ul><li>Was discussed in the NJIT Research Roadmaps (given to freshmen) </li></ul><ul><li>Can be used to find articles on evolution or ecology </li></ul>
  33. 33. Scifinder Scholar <ul><li>Electronic Version of Chemical Abstracts (1907 to the present) </li></ul><ul><li>It contains many links to full-text articles </li></ul><ul><li>Searchable by chemical substance, reaction, research topic, author or affiliation </li></ul><ul><li>Its coverage of cell biology is limited to &quot;chemical aspects&quot; such as pharmacology.  It would not cover “pure biology.” </li></ul>
  34. 34. Scifinder Scholar <ul><li>Only one person at NJIT may search Scifinder Scholar at a time.  Please minimize time you are using it by: </li></ul><ul><ul><li>Evaluating your answer set while you are off line </li></ul></ul><ul><ul><li>Using the database during off-peak hours.  It is available almost 24 hours a day/7 days a week </li></ul></ul><ul><ul><li>Waiting at least 10 minutes before attempting to login again. </li></ul></ul><ul><li>How-to guides are available at : http:// </li></ul>
  35. 35. Databases related to Biology (At Rutgers but not at NJIT) <ul><li>Biological and Agricultural Index </li></ul><ul><li>Biosis Previews </li></ul><ul><li>Web of Science </li></ul>
  36. 36. Boolean Logic <ul><li>AND </li></ul><ul><li>The Boolean AND narrows your search by retrieving only documents that contain every one of the keywords that you enter.  The more terms you enter, the narrower your search becomes.      EXAMPLE: chromosome AND mutation </li></ul><ul><li>     EXAMPLE: chromosome AND mutation AND rats </li></ul><ul><li>OR </li></ul><ul><li>The Boolean OR expands your search by returning documents in which either or both keywords appear.  The more keywords you enter, the more documents you retrieve.    EXAMPLE: DNA OR RNA </li></ul><ul><li>   EXAMPLE: DNA OR RNA OR mitochondria </li></ul>
  37. 37. Boolean Logic <ul><li>NOT </li></ul><ul><li>The Boolean NOT limits your search by returning only the first keyword but not the second, even if the first word appears in that document, too    EXAMPLE DNA NOT RNA   </li></ul><ul><li>To do an effective search you must choose the most relevant database(s) and the appropriate Boolean Logic </li></ul>
  38. 38. Availability of Journals <ul><li>Once you do a search, you must locate the articles that you retrieved from the search that you think are relevant.  They may be available: Print only </li></ul><ul><li>Electronic Only </li></ul><ul><li>Print and Electronic </li></ul><ul><ul><li>Dates of electronic availability vary </li></ul></ul><ul><li>Not available at NJIT - order through interlibrary loan </li></ul>
  39. 39. Devising Optimal Search Strategies <ul><li>Choose the proper database(s) </li></ul><ul><ul><li>Be aware of the scope and limitations </li></ul></ul><ul><li>Use all relevant search terms and appropriate Boolean logic </li></ul><ul><ul><li>Think of concepts not words Devise a search strategy for: </li></ul></ul><ul><ul><li>Precise search </li></ul></ul><ul><ul><ul><li>Expand strategy if too few are found </li></ul></ul></ul><ul><ul><li>Exhaustive search </li></ul></ul><ul><ul><ul><li>Cut down if too many citations are retrieved </li></ul></ul></ul>
  40. 40. Evaluating References <ul><li>Look at the abstract to judge if the paper is relevant to your topic </li></ul><ul><li>If so, is the paper available from the NJIT Library? </li></ul><ul><li>Follow links in the database that you used to check for availability of the article. </li></ul>
  41. 41. Citing Your Sources and Managing References <ul><li>Please See: </li></ul><ul><ul><li>http:// </li></ul></ul>
  42. 42. For Further Help <ul><li>Contact Bruce Slutsky </li></ul><ul><ul><li>Robert Van Houten Library </li></ul></ul><ul><ul><li>[email_address] </li></ul></ul><ul><ul><li>973-642-4950 </li></ul></ul><ul><ul><li>Reference desk at 973-596-3210 </li></ul></ul>