Difference between revisions of "Hhinsch Week 11"

Revision as of 05:40, 14 November 2017

Bibliography Notes

• The complete bibliographic reference in the APA style (see http://libguides.lmu.edu/content.php?pid=25618&sid=184708. You will be using one of three formats, journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
  • The link to the abstract from PubMed.
  • The link to the full text of the article in PubMedCentral.
  • The link to the full text of the article (HTML format) from the publisher web site.
  • The link to the full PDF version of the article from the publisher web site.
  • Who owns the rights to the article and what is the availability?
    • Does the journal or the authors own the copyright?
    • Is the article available “Open Access” upon publication under a Creative Commons license?
    • If the article is not Open Access, is it available for free after a certain period of time has elapsed?
  • What organization is the publisher of the article?
    • What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization; see http://oaspa.org/membership/members/ for a list of members of the Open Access Scholarly Publishers Association)
  • Is this article available in print or online only?
    • Has LMU paid a subscription or other fee for your access to this article?
  • Are the data associated with this article available? If so, provide a link to the dataset.
• You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
• Use a keyword search for the first three databases/tools and answer the following:
  • PubMed
    • What original keyword(s) did you use? How many results did you get?
      • I originally used the keywords: "yeast cold shock microarray". The search keywords produced six results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I didn't need to narrow down the results because there were only six results from the original search.
  • Google Scholar
    • What original keyword(s) did you use? How many results did you get?
      • I originally used the keywords: "yeast cold shock microarray". I got 31,400 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I then used the keywords: "yeast cold shock microarray data over time". There were still over 20,000 results so I added a constraint that only showed articles published post 2017. The search narrowed down to 1,530 results.
  • Web of Science
    • What original keyword(s) did you use? How many results did you get?
      • I originally used the keywords: "yeast cold shock microarray". The search keywords produced ten results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I didn't need to narrow down the results because there were only ten results from the original search.
• Use the advanced search functions for each of these three databases/tools and answer the following:
  • PubMed
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • Again, I didn't feel like I needed to narrow down the search because there were only six results from the original search.
  • Google Scholar
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I used the allintitle: Saccharomyces cerevisiae microarray cold shock response data function in order to narrow down the search. I got one result. Most of the other keywords I tried didn't satisfy a narrow search and came up with zero results, or came up with too many.
  • Web of Science
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I used the (TS=(microarray AND data AND saccharomyces AND cerevisiae AND cold AND shock)) AND DOCUMENT TYPES: (Article) advanced search booleans for the Web of Science and came up with seven results. This narrowed down the topics of the articles.
  • Perform a prospective search on the following three review articles in Web of Science and answer the following:
    • Aguilera, J., Randez-Gil, F., & Prieto, J.A. (2007). Cold Response in Saccharomyces cerevisiae: New Functions for Old Mechanisms. FEMS Microbiological Reviews, 31, 327–341. doi: 10.1111/j.1574-6976.2007.00066.x
      • How many articles does this article cite?
        • This article cites 144 references.
      • How many articles cite this article?
        • 77 articles cite this article.
    • Al-Fageeh, M.B. & Smales, C.M. (2006). Control and Regulation of the Cellular Responses to Cold Shock: the Responses in Yeast and Mammalian Systems. Biochemical Journal, 397, 247–259. doi: 10.1042/BJ20060166
      • How many articles does this article cite?
        • This article cites 108 references.
      • How many articles cite this article?
        • 125 articles cite this article.
    • Thieringer, H.A., Jones, P.G.,& Inouye, M. (1998). Cold shock and adaptation. BioEssays, 20, 49–57. doi: 10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.0.CO;2-N
      • How many articles does this article cite?
        • This article cites 76 references.
      • How many articles cite this article?
        • 258 articles cite this article.

Bibliography

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., & Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6

• PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504
• PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/
• Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6
• Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf
• Copyright: The Author(s) 2015. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
• Publisher: Bulletin of Mathematical Biology
• Availability: Online
• Did LMU pay a fee for this article: No

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
• Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
• Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
• Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
• Publisher: American Society for Cell Biology (scientific society)
• Availability: in print and online
• Did LMU pay a fee for this article: no

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